Glycosylation in health and disease

Fusion of enzymatic proteins: Enhancing biological activities and facilitating biological modifications

The fusion of enzymatic proteins represents a dynamic frontier in biotechnology and enzymatic engineering. This in-depth review looks at the many different ways that fusion proteins can be used, showing their importance in biosensing, gene therapy, targeted drug delivery, and biocatalysis. Fusion proteins have shown an astounding ability to improve and fine-tune biological functions by combining the most beneficial parts of different enzymes. Our first step is to explain how protein fusion increases biological functions. This will provide a broad picture of how this phenomenon has changed many fields. We dissect the intricate mechanisms through which fusion proteins orchestrate cellular processes, underscoring their potential to revolutionize the landscape of molecular biology. We also explore the complicated world of structural analysis and design strategies, stressing the importance of molecular insights for making the fusion protein approach work better. These insights broaden understanding of the underlying principles and illuminate the path toward unlocking untapped potential. The review also introduces cutting-edge techniques for constructing fusion protein libraries, such as DNA shuffling and phage display. These new methods allow scientists to build a molecular orchestra with an unprecedented level of accuracy, and thus use fusion proteins to their full potential in various situations. In conclusion, we provide a glimpse into the current challenges and prospects in fusion protein research, shedding light on recent advancements that promise to reshape the future of biotechnology. As we make this interesting journey through the field of enzymatic protein combination, it becomes clear that the fusion paradigm is about to start a new era of innovation that will push the limits of what is possible in biology and molecular engineering.

FUT2-dependent fucosylation of LAMP1 promotes the apoptosis of colorectal cancer cells by regulating the autophagy-lysosomal pathway

Fucosyltransferase 2 (FUT2) is an enzyme that adds fucose to proteins or lipids via α-1,2-fucosylation in the intestinal mucosa. While FUT2 deficiency is linked to increased susceptibility to inflammatory bowel disease (IBD), its role in colorectal cancer (CRC) is unclear, and the molecular mechanisms involved remain largely unknown. We established an azoxymethane (AOM) and dextran sulfate sodium (DSS) model to induce CRC. FUT2 expression was assessed in human CRC tissues, AOM/DSS-induced mouse models, and CRC cell lines using qRT-PCR, western blotting, and UEA-I staining. FUT2 knockout (FUT2△IEC) mice were treated with AOM/DSS, and FUT2-overexpressing CRC cells were created to evaluate the effects of FUT2 on apoptosis in both in vitro and in vivo settings through Western blot analyses and functional assays. N-glycoproteomics, UEA-I chromatography, and co-immunoprecipitation were utilized to identify regulatory mechanisms and target fucosylated proteins. FUT2 expression and α-1,2-fucosylation were significantly decreased in CRC. FUT2 deficiency worsened AOM/DSS-induced CRC and reduced tumor apoptosis, while FUT2 overexpression induced apoptosis and inhibited proliferation in CRC cells and xenografts. Mechanistically, FUT2 appears to suppress autophagy by impairing lysosomal function and directly targeting and fucosylating LAMP1, contributing to lysosomal dysfunction. Our study reveals a fucosylation-dependent antitumor mechanism of FUT2 in CRC, suggesting potential therapeutic strategies for CRC treatment.

Targeting PD-1 post-translational modifications for improving cancer immunotherapy

Programmed cell death protein 1 (PD-1) is a critical immune checkpoint receptor that suppresses immune responses largely through its interaction with PD-L1. Tumors exploit this mechanism to evade immune surveillance, positioning immune checkpoint inhibitors targeting the PD-1/PD-L1 axis as groundbreaking advancements in cancer therapy. However, the overall effectiveness of these therapies is often constrained by an incomplete understanding of the underlying mechanisms. Recent research has uncovered the pivotal role of various post-translational modifications (PTMs) of PD-1, including ubiquitination, UFMylation, phosphorylation, palmitoylation, and glycosylation, in regulating its protein stability, localization, and protein-protein interactions. As much, dysregulation of these PTMs can drive PD-1-mediated immune evasion and contribute to therapeutic resistance. Notably, targeting PD-1 PTMs with small-molecule inhibitors or monoclonal antibodies (MAbs) has shown potential to bolster anti-tumor immunity in both pre-clinical mouse models and clinical trials. This review highlights recent findings on PD-1's PTMs and explores emerging therapeutic strategies aimed at modulating these modifications. By integrating these mechanistic insights, the development of combination cancer immunotherapies can be further rationally advanced, offering new avenues for more effective and durable treatments.

Fast NMR-Based Assessment of Cancer-Associated Protein Glycosylations from Serum Samples

Nuclear magnetic resonance (NMR) spectra of blood serum and plasma show signals arising from metabolites, lipoproteins, and N-acetyl methyl groups of N-glycans covalently linked to acute-phase proteins. These glycan signals often called glycoprotein A (GlycA) and glycoprotein B (GlycB) arise from N-acetyl methyl groups and have been proposed as biomarkers, initially for cardiovascular diseases, but also for other inflammatory conditions. For the detection of glycan resonances, J-edited, diffusion, and relaxation filtered NMR spectroscopy (JEDI) has been proposed to suppress the lipoprotein signals. JEDI is however limited to measure those acetyl signals, whereas all other glycan resonance cannot be observed. For improved glycoprotein profiling, the signals arising from the pyranose ring protons are essential. Here, we show how selective frequency excitation combined with scalar coupling filtering can be used to dramatically increase the number of N-glycan signals observable in NMR spectra of serum and plasma samples, facilitating glycosylation profiling in less than 30 min. This approach grants selective detection of sialylation, galactosylation, N-acetylglucosaminylation, and fucosylation of dominant N-glycans and, to some extent, N-glycan branching complexity. Notably, sialylated and nonsialylated Lewisx and Lewisa antigens can also be observed. Lewisa antigen is well established as a cancer biomarker, known as CA19-9. NMR glycosylation profiles from nine isolated serum glycoproteins show excellent agreement with well-established UHPLC-MS analysis. The proposed NMR method facilitates the detection of glycoprotein biomarkers without the need for enzymatic treatment of serum or plasma and provides a robust read-out as exemplified by samples from 33 patients with hepatocellular carcinoma.

Proton-Detected Solid-State NMR for Deciphering Structural Polymorphism and Dynamic Heterogeneity of Cellular Carbohydrates in Pathogenic Fungi

Carbohydrate polymers in their cellular context display highly polymorphic structures and dynamics essential to their diverse functions, yet they are challenging to analyze biochemically. Proton-detection solid-state NMR spectroscopy offers high isotopic abundance and sensitivity, enabling the rapid and high-resolution structural characterization of biomolecules. Here, an array of 2D/3D 1H-detection solid-state NMR techniques are tailored to investigate polysaccharides in fully protonated or partially deuterated cells of three prevalent pathogenic fungi: Rhizopus delemar, Aspergillus fumigatus, and Candida albicans, representing filamentous species and yeast forms. Selective detection of acetylated carbohydrates reveals 15 forms of N-acetylglucosamine units in R. delemar chitin, which coexists with chitosan, and associates with proteins only at limited sites. This is supported by distinct order parameters and effective correlation times of their motions, analyzed through relaxation measurements and model-free analysis. Five forms of α-1,3-glucan with distinct structural origins and dynamics were identified in A. fumigatus, important for this buffering polysaccharide to perform diverse roles of supporting wall mechanics and regenerating a soft matrix under antifungal stress. Eight α-1,2-mannan side chain variants in C. albicans were resolved, highlighting the crucial role of mannan side chains in maintaining interactions with other cell wall polymers to preserve structural integrity. These methodologies provide novel insights into the functional structures of key fungal polysaccharides and create new opportunities for exploring carbohydrate biosynthesis and modifications across diverse organisms.

Glycosylation as an intricate post-translational modification process takes part in glycoproteins related immunity

Protein glycosylation, the most ubiquitous and diverse type of post-translational modification in eukaryotic cells, proteins are input into endoplasmic reticulum and Golgi apparatus for sorting and modification with intricate quality control, are then output for diverse functional glycoproteins that are utilized by cells to precisely regulate various biological processes. In order to maintain the precise spatial structure of glycoprotein, misfolded and unfolded glycoproteins are recognized, segregated and degraded to ensure the fidelity of protein folding and maturation. This review enumerates the role of five immune-related glycoproteins and reveals the relevance of glycosylation to their antigen presentation, immune effector function, immune recognition, receptor binding and activation, and cell adhesion and migration. With the knowledgement of glycoproteins in immune responses and etiologies, we propose several relevant therapeutic strategies on targeting glycosylation process for immunotherapy.

Further elucidation of GMPPB as a risk gene for depression through integrative multi-omics analyses

Depression, a prevalent and recurrent mental disorder, significantly impairs the quality of life and social functioning. Traditional genome-wide association studies GWAS is difficult to accurately locate causative genes due to linkage disequilibrium and tissue-specific expression quantitative trait loci (eQTL) effects, while single-tissue transcriptome-wide association study (TWAS) may overlook cross-tissue regulatory heterogeneity or produce spurious associations. To address these limitations, the combined sparse canonical correlation analysis (sCCA) with the Aggregated Cauchy Association Test (ACAT) analysis was employed for capturing shared expression patterns across multiple tissues, reducing spurious associations and enhancing its power to detect genes with heterogeneous regulatory effects. The present investigation employed sCCA-ACAT, integrating two GWAS datasets with eQTL data from 49 tissues of the Genotype-Tissue Expression (GTEx) project, constructing a cross-tissue gene expression signature for depression. Four susceptibility genes were identified through FUSION and the Multi-marker Analysis of GenoMic Annotation (MAGMA) analysis. GMPPB was further validated as a robust risk gene via Mendelian randomization and colocalization analysis in the amygdala and anterior cingulate cortex. Functional annotation suggested that GMPPB might regulate inflammatory responses through glycosylation pathways to increase the risk of depression, though this hypothesis requires experimental validation. This study found that GMPPB in the amygdala and anterior cingulate cortex is associated with depression and might regulate inflammatory responses through glycosylation modifications, increasing the risk of depression. This finding provides new insights for further mechanistic studies, prevention, and treatment of depression.

Cell surface RNA biology: new roles for RNA binding proteins

Much of our understanding of RNA-protein interactions, and how these interactions shape gene expression and cell state, have come from studies looking at these interactions in vitro or inside the cell. However, recent data demonstrates the presence of extracellular and cell surface-associated RNA such as glycosylated RNA (glycoRNA), suggesting an entirely new environment and cellular topology in which to study RNA-RNA binding protein (RBP) interactions. Here, we explore emerging ideas regarding the landscape of cell surface RNA and RBPs. We also discuss open questions concerning the trafficking and anchoring of RBPs to the cell surface, whether cell surface RBPs (csRBPs) directly interact with cell surface RNA, and how changes in the presentation of csRBPs may drive autoimmune responses.

Protein glycopatterns for natural regulation of microbiota in lung adenocarcinoma

Despite medical advancements, lung cancer remains a leading cause of mortality, necessitating a deeper understanding. Recent studies show that protein glycopatterns and lung microbiome are crucial in lung cancer development, but their relationship in adenocarcinoma remains unexplored. Therefore, this study evaluated protein glycopatterns and microbial changes between lung adenocarcinoma (n = 70) and paracancerous tissues (n = 70) through lectin microarrays and 16S rDNA sequencing. Further, we explored the impact of protein glycopatterns against a decreased abundant microbiota using extracted glycoproteins reflecting high expression protein glycopatterns observed in lung adenocarcinoma tissues. The results demonstrated a significant up-regulation of protein glycopatterns in tumor tissues, including WGA binding to multivalent Sia/(GlcNAc)n (P = 0.0078) and Jacalin binding to T/Tn antigens (P = 0.0313). Meanwhile, two bacterial species of the genus Sphingomonas showed a significant decrease (P < 0.01) in adenocarcinoma as compared to paracancerous tissue. Interestingly, adhesion assay results showed glycoproteins (25-100 μg/ml) with multivalent Sia and (GlcNAc)n structures extracted by WGA-magnetic particle conjugates significantly reduce (P < 0.0001) Sphingomonas mucosissima adhesion and toxicity to lung cancer cells (A-549). The findings indicated that protein glycopatterns could inhibit cancer-instigating oncomicrobes to intercept cancer progression, offering insights into molecular mechanisms driving disease progression and aiding to develop new treatment strategies.

Bi-allelic UGGT1 variants cause a congenital disorder of glycosylation

Congenital disorders of glycosylation (CDGs) comprise a large heterogeneous group of metabolic conditions caused by defects in glycoprotein and glycolipid glycan assembly and remodeling, a fundamental molecular process with wide-ranging biological roles. Herein, we describe bi-allelic UGGT1 variants in fifteen individuals from ten unrelated families of various ethnic backgrounds as a cause of a distinctive CDG of variable severity. The cardinal clinical features of UGGT1-CDG involve developmental delay, intellectual disability, seizures, characteristic facial features, and microcephaly in the majority (9/11 affected individuals for whom measurements were available). The more severely affected individuals display congenital heart malformations, variable skeletal abnormalities including scoliosis, and hepatic and renal involvement, including polycystic kidneys mimicking autosomal recessive polycystic kidney disease. Clinical studies defined genotype-phenotype correlations, showing bi-allelic UGGT1 loss-of-function variants associated with increased disease severity, including death in infancy. UGGT1 encodes UDP-glucose:glycoprotein glucosyltransferase 1, an enzyme critical for maintaining quality control of N-linked glycosylation. Molecular studies showed that pathogenic UGGT1 variants impair UGGT1 glucosylation and catalytic activity, disrupt mRNA splicing, or inhibit endoplasmic reticulum (ER) retention. Collectively, our data provide a comprehensive genetic, clinical, and molecular characterization of UGGT1-CDG, broadening the spectrum of N-linked glycosylation disorders.

Sugar symphony: glycosylation in cancer metabolism and stemness

Glycosylation is a complex co-translational and post-translational modification (PTM) in eukaryotes that utilizes glycosyltransferases to generate a vast array of glycoconjugate structures. Recent studies have highlighted the role of glycans in regulating essential molecular, cellular, tissue, organ, and systemic biological processes with significant implications for human diseases, particularly cancer. The metabolic reliance of cancer, spanning tumor initiation, disease progression, and resistance to therapy, necessitates a range of uniquely altered cellular metabolic pathways. In addition, the intricate interplay between cell-intrinsic and -extrinsic mechanisms is exemplified by the communication between cancer cells, cancer stem cells (CSCs), cancer-associated fibroblasts (CAFs), and immune cells within the tumor microenvironment (TME). In this review article, we explore how differential glycosylation in cancer influences the metabolism and stemness features alongside new avenues in glycobiology.

Glycolytic activity instructs germ layer proportions through regulation of Nodal and Wnt signaling

Metabolic pathways can influence cell fate decisions, yet their regulative role during embryonic development remains poorly understood. Here, we demonstrate an instructive role of glycolytic activity in regulating signaling pathways involved in mesoderm and endoderm specification. Using a mouse embryonic stem cell (mESC)-based in vitro model for gastrulation, we found that glycolysis inhibition increases ectodermal cell fates at the expense of mesodermal and endodermal lineages. We demonstrate that this relationship is dose dependent, enabling metabolic control of germ layer proportions through exogenous glucose levels. We further show that glycolysis acts as an upstream regulator of Nodal and Wnt signaling and that its influence on cell fate specification can be decoupled from its effects on growth. Finally, we confirm the generality of our findings using a human gastrulation model. Our work underscores the dependence of signaling pathways on metabolic conditions and provides mechanistic insight into the nutritional regulation of cell fate decision-making.

Computational profiling of molecular biomarkers in congenital disorders of glycosylation Type-I and binding analysis of Ginkgolide A with P4HB

AIMS

Congenital disorders of glycosylation (CDG) comprise a diverse group of genetic diseases characterized by aberrant glycosylation that leads to severe multi-systematic effects. Despite advancements in understanding the underlying molecular mechanisms, curative options remain limited. This study employed computational methods to identify key molecular biomarkers for CDG-I and examine the pharmacological effects of Ginkgolide A (GA), a potent bioactive natural compound.

METHODS

We analyzed the GSE8440 microarray dataset to discover differentially expressed genes (DEGs) in patients compared to healthy individuals with CDG-I utilizing GEO2R. Functional enrichments, including gene ontologies (GO) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses, were conducted to contextualize the biological mechanisms and molecular signatures involved in CDG-I (Congenital Disorders of Glycosylation Type-1). The protein-protein interaction (PPI) network for DEGs was constructed using the STRING database, and the central hub genes within the PPI network were identified using Cytohubba. Furthermore, the 3D structure of the top hub gene (P4HB) was predicted by using the Robetta server. The CASTp was employed to evaluate the active sites. Molecular docking of P4HB with GA was carried out to investigate the binding affinity using the PyRx tool, and the stability of the docked complex was validated through MD simulation. The pharmacokinetics, toxicity, and bioactivity score of GA were comprehensively assessed using SwissADME, ProTox-II, and Molinspiration.

RESULTS

Our findings indicated 247 significant DEGs, including 146 up-regulated and 101 down-regulated genes. GO and KEGG pathway analyses confirmed that the up-regulated and hub genes were strongly associated with protein folding, glycoprotein processing in the endoplasmic reticulum, and endoplasmic reticulum stress (ER) pathways. P4HB emerged as the top hub gene in CDG-I, playing a significant role in protein folding and ER stress. The 3D structure of P4HB was refined and validated, achieving 95.8 % residues in the most favored region of the Ramachandran plot, with an overall quality of 92.97 %. The CASTp server predicted the largest active site with an area of 2243.660 Å2 and a volume of 3236.584 Å3. Molecular docking revealed that GA has a strong binding affinity with P4HB (-8.9 kcal/mol). The ADME (Absorption, Distribution, Metabolism, Excretion) and toxicity assessments confirmed promising drug-like characteristics, excellent bioavailability, and minimal toxicity risk.

CONCLUSION

This study emphasizes GA as a potential treatment possibility option to alleviated CDG-I pathology by targeting protein misfolding and ER stress, which are fundamental aspects of the disease. Additionally, our findings indicate that P4HB is a critical molecular target in CDG-I. These results pave the way for future preclinical and clinical investigations aimed at advancing the targeted and tailored treatments for CDG.

A comprehensive update of genotype-phenotype correlations in PMM2-CDG: insights from molecular and structural analyses

PMM2-CDG (phosphomannomutase 2-deficiency) is the most prevalent N-glycosylation disorder and results from impairments of PMM2 activity. This disease presents a large variety of pathogenic variants, which cause a wide phenotypical spectrum. This diversity, together with the low number of affected patients, raises the challenge of determining genotype-phenotype correlations in PMM2-CDG. This type of correlation could be highly significant in determining disease progression, prognosis, severity and in developing genome-personalized therapies. Structural analyses offer a valuable approach for assessing the pathogenic mechanisms within the PMM2 protein structure at a molecular level. Such an approach can reveal novel insights into the consequences of missense variants and their relationship with patients'phenotype. In this comprehensive review, we evaluate at a structural level 41 missense mutations in PMM2-CDG, examining their phenotypical characteristics and clinical severity, protein properties and interference at the enzymatic level. This work broadens the understanding of the intricate relationships between genotype and clinical manifestations of PMM2-CDG.

Combined effect of areca nut, cigarettes, alcohol and SNPs in glycosyltransferase family genes on lung cancer development in Hainan, China

BACKGROUND

Abnormal glycosylation modification is closely related to the development and metastasis of cancers. As a carcinogen by the International Agency for Research on Cancer (IARC) of the WHO, areca nut lacked of combined effect' study with genetic factors related to lung cancer. The aim of this study was to investigate the combined effect of polymorphisms of glycosyltransferase family genes and behavioral factors on the susceptibility of lung cancer.

METHODS

A case‒control study was conducted in Hainan, which included 428 patients with lung cancer and 428 cancer-free controls. Six single-nucleotide polymorphisms (SNPs) (FUT2 rs1047781, rs601338, FUT3 rs28362459, rs3745635, ST6Gal-I rs2239611 and MGAT5 rs34944508) were detected by the MassARRAY System. The association between these SNPs and the risk of lung cancer, clinicopathological characteristics, and combined effect of behavioral factors (areca nuts, cigarettes, alcohol) and genotypes on lung cancer were estimated using by logistic regression analysis.

RESULTS

In this study, individuals with AA genotype in ST6Gal-I rs2239611 significantly increased lung cancer risk (ORadj = 2.077; 95%CI:1.191-3.624; Padj = 0.010), particularly in smokers (Padj = 0.038) and alcohol consumers (Padj = 0.049). FUT2 rs1047781 was associated with clinical stage (Padj = 0.047) and lymph node metastasis (Padj = 0.014). Significant gene-environment interactions were observed between behavioral factors (cigarette smoking, alcohol drinking, and betel quid chewing) and both FUT2 rs1047781 (Padj = 0.013) and ST6Gal-I rs2239611 (Padj = 0.047), collectively elevating lung cancer risk.

CONCLUSION

ST6Gal-I rs2239611 was a potential genetic biomarker for lung cancer. Areca nut chewing, cigarette smoking, alcohol drinking interacts with glycosyltransferase gene polymorphisms (FUT2 rs1047781 and ST6Gal-I rs2239611), increasing lung cancer risk-a novel finding given the lack of prior studies on this combination.

N-deglycosylation targeting chimera (DGlyTAC): a strategy for immune checkpoint proteins inactivation by specifically removing N-glycan

Among the leading methods for triggering therapeutic anti-cancer immunity is the inhibition of immune checkpoint pathways. N-glycosylation is found to be essential for the function of various immune checkpoint proteins, playing a critical role in their stability and interaction with immune cells. Removing the N-glycans of these proteins seems to be an alternative therapy, but there is a lack of a de-N-glycosylation technique for target protein specificity, which limits its clinical application. Here, we developed a novel technique for specifically removing N-glycans from a target protein on the cell surface, named deglycosylation targeting chimera (DGlyTAC), which employs a fusing protein consisting of Peptide-N-glycosidase F (PNGF) and target-specific nanobody/affibody (Nb/Af). The DGlyTAC technique was developed to target a range of glycosylated surface proteins, especially these immune checkpoints-CD24, CD47, and PD-L1, which minimally affected the overall N-glycosylation landscape and the N-glycosylation of other representative membrane proteins, ensuring high specificity and minimal off-target effects. Importantly, DGlyTAC technique was successfully applied to lead inactivation of these immune checkpoints, especially PD-L1, and showed more potential in cancer immunotherapy than inhibitors. Finally, PD-L1 targeted DGlyTAC showed therapeutic effects on several tumors in vivo, even better than PD-L1 antibody. Overall, we created a novel target-specific N-glysocylation erasing technique that establishes a modular strategy for directing membrane proteins inactivation, with broad implications on tumor immune therapeutics.

Perfluorooctanoic acid disrupts thyroid hormone biosynthesis by altering glycosylation of Na+/I- symporter in larval zebrafish

Perfluorooctanoic acid (PFOA) is a well-known thyroid disruptor that has been found to induce hypothyroidism. However, the exact molecular mechanism by which PFOA reduces thyroid hormone levels remains unclear. In this study, we have discovered that PFOA disrupts the glycosylation process of the sodium/iodide symporter (NIS), which inhibits the translocation of NIS onto the plasma membrane of thyroid follicular cells. Our results also demonstrate that PFOA disrupts thyroid stimulating hormone (TSH)-dependent signaling pathways involved in cellular glycosylation, impairing NIS glycosylation and reducing the ability of iodine uptake. This leads to an insufficiency of iodine for thyroid hormone production inside the follicular cells of the thyroid, resulting in lower-than-normal thyroxine levels detected in zebrafish larvae. These findings are consistent with our previously published data, which showed that PFOA induces neural behavior changes during the early stages of neuronal development in zebrafish. This new discovery provides valuable insights into the molecular characteristics of endocrine-disrupting chemicals (EDCs) that are known to affect the thyroid. It may also contribute to a better understanding of how altered glycosylation could be a potential risk factor for the association between exposure to specific per- and polyfluoroalkyl substances (PFAS) and various health effects in humans.

Deciphering the Metabolic Impact and Clinical Relevance of N-Glycosylation in Colorectal Cancer through Comprehensive Glycoproteomic Profiling

Colorectal cancer (CRC) progression is driven by complex metabolic alterations, including aberrant N-glycosylation patterns that critically influence tumor development. However, the metabolic and functional roles of N-glycosylation in CRC remain poorly understood. Herein, comprehensive proteomic and N-linked intact glycoproteomics analyses are performed on 45 CRC tumors, and normal adjacent tissues (NATs) are matched, identifying 7125 intact N-glycopeptides from 704 glycoproteins. Through analysis of glycoform expression profiles and structural characteristics, a glycosylation site-protein function association network is constructed to uncover metabolic dysregulation driven by N-glycosylation in CRC. Moreover, an arithmetic model is developed that integrates N-glycan expression patterns, which effectively distinguishes tumors from NATs, reflecting metabolic reprogramming in cancer. These findings identify Chloride Channel Accessory 1 (CLCA1) and Olfactomedin 4 (OLFM4) as potential metabolic biomarkers for CRC diagnosis. Immunohistochemistry and Cox regression analyses validated the prognostic power of these markers. Notably, the critical role of specific N-glycosylation at N196 of Adipocyte plasma membrane-associated protein (APMAP) is highlighted, a key player in tumor metabolism and CRC progression, providing a potential target for therapeutic intervention. These findings offer valuable insights into the metabolic roles of N-glycosylation in CRC, advancing biomarker discovery, enhancing metabolic-based diagnostic precision, and improving personalized treatment strategies targeting cancer metabolism.

Portable SERS for salivary-based detection of oral pre-malignant lesions and carcinomas: a step toward clinical implementation

The rising incidence of oral cancer has emerged as a serious menace to our civilization. Modern dietary habits, lack of awareness, and delays in early detection are major contributing factors to the global spread of this issue. This work reports the promising findings for diagnostic accuracy of oral cancer in pre-malignant stages by analyzing surface enhanced Raman spectroscopy (SERS) profiles of different stages of oral cancer combined with multivariate analysis. Using 99 clinical samples from which 39 samples were from malignant stage, 28 from pre-malignant and 32 from healthy controls, SERS analysis was carried out by employing label-free silver nanorods as SERS substrates. The SERS spectra of malignant and pre-malignant samples manifest distinct peaks associated with varying concentrations of inorganic metabolites and proteins. Primarily, the elevated level of thiocyanate dominates the SERS spectra in malignant samples while antioxidants like uric acid, xanthine and hypoxanthine's are the key elements in the pre-malignant samples. A ratio-metric analysis of 2130 and 1435 cm-1 peak revealed that the pre-malignant lesions consistently lie between 2 and 3, whereas malignant samples have ratio greater than 3 due to higher intensity of thiocyanate peak. The multivariate analysis successfully separates between oral cancer positive and negative samples with a sensitivity and specificity of 93.5 and 92.7 % respectively. This study presents promising results for the early detection of oral cancer, which could assist clinicians in saving lives.

Immunoglobulin G N-Glycosylation and Inflammatory Factors: Analysis of Biomarkers for the Diagnosis of Moyamoya Disease

Purpose

N-glycosylation-modified immunoglobulin G (IgG) is crucial for managing the inflammatory response balance and significantly influences the progression of many inflammatory disorders. IgG N-glycosylation has been demonstrated to correlate with many risk factors for moyamoya disease (MMD), such as hypertension, diabetes, and dyslipidemia. This research aimed to evaluate the diagnostic efficacy of IgG N-glycosylation for MMD.

Methods

Ultra-high-performance liquid chromatography (UPLC) was employed to examine the properties of IgG N-glycans in blood samples from 116 patients with MMD and 126 controls, resulting in the quantitative determination of 24 initial glycan peaks (GP). Through the Lasso algorithm and multivariate logistic regression analysis, we constructed a diagnostic model based on initial glycans and related inflammatory factors to distinguish MMD patients from healthy individuals.

Results

After adjusting for potential confounding variables, including age, fasting blood glucose (FBG), total cholesterol (TC), high-density lipoprotein (HDL), low-density lipoprotein (LDL), neutrophil count (NEUT), and lymphocyte count (LYM), our study demonstrated significant differences in the characteristics of 6 initial glycans and 16 derived glycans between the MMD cohort and the healthy control group. Based on the above findings, we developed an MMD diagnostic model that combines initial glycans with related inflammatory factors. The curve of receiver operating characteristic (ROC) was utilized to evaluate the model's ability to distinguish MMD patients from healthy subjects. The findings indicated a robust area under the curve (AUC) of 0.963 (95% CI: 0.940, 0.987).

Conclusion

This study found that the occurrence and progression of MMD may be associated with decreased levels of sialylation, galactosylation, and fucosylation and increased bisecting GlcNAc. This may be involved in the occurrence of MMD by regulating the balance of inflammation. Therefore, the IgG N-glycosylation is expected to become a potential biomarker for the screening of MMD.

Engineered Proteins and Chemical Tools to Probe the Cell Surface Proteome

The cell surface proteome, or surfaceome, is the hub for cells to interact and communicate with the outside world. Many disease-associated changes are hard-wired within the surfaceome, yet approved drugs target less than 50 cell surface proteins. In the past decade, the proteomics community has made significant strides in developing new technologies tailored for studying the surfaceome in all its complexity. In this review, we first dive into the unique characteristics and functions of the surfaceome, emphasizing the necessity for specialized labeling, enrichment, and proteomic approaches. An overview of surfaceomics methods is provided, detailing techniques to measure changes in protein expression and how this leads to novel target discovery. Next, we highlight advances in proximity labeling proteomics (PLP), showcasing how various enzymatic and photoaffinity proximity labeling techniques can map protein-protein interactions and membrane protein complexes on the cell surface. We then review the role of extracellular post-translational modifications, focusing on cell surface glycosylation, proteolytic remodeling, and the secretome. Finally, we discuss methods for identifying tumor-specific peptide MHC complexes and how they have shaped therapeutic development. This emerging field of neo-protein epitopes is constantly evolving, where targets are identified at the proteome level and encompass defined disease-associated PTMs, complexes, and dysregulated cellular and tissue locations. Given the functional importance of the surfaceome for biology and therapy, we view surfaceomics as a critical piece of this quest for neo-epitope target discovery.

Fine-Tuning the Active-Site Microenvironment of β-Galactosidase to Enhance the Synthesis Ability of Galactooligosaccharides while Minimizing the Impairment to Transglycosylation Activity

Most reported mutations at -1 subsites of β-galactosidases that improved galactooligosaccharides (GOS) synthesis ability significantly reduced total activity (e.g., <10%), likely due to the introduction of significant disturbances within the active-site microenvironment. In this study, a fine-tuning strategy encompassing aromatic residue interchange as well as substitution among T, S, and A was proposed and subsequently evaluated in Bgal1-3 and three commercial β-galactosidases. For each of them, 2-4 positive mutants were acquired with residual activities of 30-357%. When 40% (w/v) lactose was employed as a substrate, their GOS yields were 1.2-18% higher than those of wild types. Moreover, the best mutants produced greater amounts of GOS in skim milk (2.9-11.8 g/L higher) at a lactose conversion rate of 90%. Ultimately, a mutation set (∼14 mutations) was designed for the convenience of using this approach in other glycoside hydrolases. This fine-tuning strategy may hold great potential for promoting the enzymatic synthesis of valuable carbohydrate-containing compounds.

Targeting epigenetic and post-translational modifications of NRF2: key regulatory factors in disease treatment

Nuclear factor erythroid 2-related factor 2 (NRF2) is a key transcription factor involved in regulating cellular antioxidant defense and detoxification mechanisms. It mitigates oxidative stress and xenobiotic-induced damage by inducing the expression of cytoprotective enzymes, including HO-1 and NQO1. NRF2 also modulates inflammatory responses by inhibiting pro-inflammatory genes and mediates cell death pathways, including apoptosis and ferroptosis. Targeting NRF2 offers potential therapeutic avenues for treating various diseases. NRF2 is regulated through two principal mechanisms: post-translational modifications (PTMs) and epigenetic alterations. PTMs, including phosphorylation, ubiquitination, and acetylation, play a pivotal role in modulating NRF2's stability, activity, and subcellular localization, thereby precisely controlling its function in the antioxidant response. For instance, ubiquitination can lead to NRF2 degradation and reduced antioxidant activity, while deubiquitination enhances its stability and function. Epigenetic modifications, such as DNA methylation, histone modifications, and interactions with non-coding RNAs (e.g., MALAT1, PVT1, MIR4435-2HG, and TUG1), are essential for regulating NRF2 expression by modulating chromatin architecture and gene accessibility. This paper systematically summarizes the molecular mechanisms by which PTMs and epigenetic alterations regulate NRF2, and elucidates its critical role in cellular defense and disease. By analyzing the impact of PTMs, such as phosphorylation, ubiquitination, and acetylation, as well as DNA methylation, histone modifications, and non-coding RNA interactions on NRF2 stability, activity, and expression, the study reveals the complex cellular protection network mediated by NRF2. Furthermore, the paper explores how these regulatory mechanisms affect NRF2's roles in oxidative stress, inflammation, and cell death, identifying novel therapeutic targets and strategies. This provides new insights into the treatment of NRF2-related diseases, such as cancer, neurodegenerative disorders, and metabolic syndrome. This research deepens our understanding of NRF2's role in cellular homeostasis and lays the foundation for the development of NRF2-targeted therapies.

Expedient Assembly of Multiantennary N-Glycans from Common N-Glycan Cores with Orthogonal Protection for the Profiling of Glycan-Binding Proteins

Complex-type N-glycans are structurally diverse molecules, responsible for many biological processes, yet the specific sequences of N-glycans involved in biological recognition remain largely unknown. Despite the recent development of many efficient chemoenzymatic approaches, it is still lacking a general approach to produce structurally diverse complex-type N-glycans. Here, we designed two common precursors equipped with orthogonal protecting groups for antennary differentiation and selective glycan elongation. The N-acetyllactosamine (LacNAc) repeat modules were synthesized separately based on iterative Au(I) promoted glycosylation and programmable one-pot strategy and were incorporated into the N-glycan core structure in a site-specific manner. The final removal of benzyl groups was cleanly achieved using pressurized flow chemistry. A total of 51 N-glycans were assembled and presented as an array to study the binding specificity toward a panel of influenza hemagglutinins and other lectins. The established method allows a rapid and previously infeasible synthesis of asymmetric bi- and triantennary N-glycans, especially with the LacNAc repeats residing at a specific arm, bringing in new opportunities to study carbohydrate-receptor interactions.

Visible Light-Mediated Diastereoselective Synthesis of Novel Glycopeptide Mimetics

Herein, we introduce a mild and operationally simple visible-light photochemistry protocol for the synthesis of novel glycopeptide mimetics. This method capitalizes on the reaction between 1,4-dihydropyridine (DHP) containing amino acids and peptides with glycosyl nitrones, showing exceptional stereoselectivity and robust performance across a diverse array of substrates, encompassing both modified glycosides and intricate peptide structures. Furthermore, we underscore the versatility of the resultant compounds through their seamless integration and utility in bioconjugation strategies.

Spatial Glycomics and Kidney Disease

Glycans are critical for the kidney's physiological and pathological cellular functions, and our ability to see their spatial distributions within tissues has helped us reveal how these carbohydrate moieties are involved in many of these processes. This review discusses the role of different types of glycans in kidney biology and disease, common approaches used for glycan imaging, and how glycan imaging has helped us better understand kidney pathology. We mainly focus on emerging methods using mass spectrometry imaging (MSI) because this technology is untargeted and provides complete information on glycan composition compared to the other methods, such as lectin and metabolite labeling, which are targeted and often inform only on the specific part of a glycan structure. We especially focus on protein N-glycosylation, as this is one of the most common post-translational modifications, and these moieties play a vital role in renal structure and function. The recent advancements in MSI of N-glycans we reviewed have provided new insights into the pathophysiology of the kidney and paved the way for clinical application. Semin Nephrol 36:x-xx © 20xx Elsevier Inc. All rights reserved.

Neuronal CDK5RAP3 deficiency leads to encephalo-dysplasia via upregulation of N-glycosylases and glycogen deposition

CDK5RAP3 is a binding protein of CDK5 activating proteins and also one of the key co-factors of the E3 enzyme in the UFMylation system. Several reports have implicated the involvement of CDK5 and other components of the UFMylation system in neuronal development and multiple psychiatric disorders. However, the precise role of CDK5RAP3 in neurons remains elusive. In this study, we generated CDK5RAP3 neuron-specific knockout mice (CDK5RAPF/F: Nestin-Cre). CDK5RAP3 conditional knockout (CDK5RAP3 CKO) mice exhibited severe encephalo-dysplasia and a slower developmental trajectory compared to wild-type (WT) mice and succumbed to postnatal demise by day 14. Transcriptome sequencing unveiled that CDK5RAP3 deficiency affects synapse formation, transmembrane trafficking and physiological programs in the brain. Morphological analysis demonstrated that neuronal CDK5RAP3 deficiency leads to increased SLC17A6 and N-glycosylase (RPN1 and ALG2) protein expression, and while causing endoplasmic reticulum (ER) stress. In vitro experiments utilizing CDK5RAP3F/F: ROSA26-ERT2Cre MEFs were conducted to elucidate similar mechanism following CDK5RAP3 deletion. Both in vivo and in vitro, CDK5RAP3 deficiency significantly increased the expression of N-glycosylases (RPN1 and ALG2), as well as the total amount of glycoproteins. CDK5RAP3 may potentially maintain a balance by enhancing the degradation of RPN1 and ALG2 through proteolytic degradation pathways and autophagy. This study underscores the indispensable role of CDK5RAP3 in neuronal development and sheds new light on drug discovery endeavors targeting early brain abnormalities.

ST6GAL1-Mediated Sialylation of PECAM-1 Promotes a Transcellular Diapedesis-Like Process That Directs Lung Tropism of Metastatic Breast Cancer

Metastasis is the leading cause of mortality in breast cancer, with lung metastasis being particularly detrimental. Identification of the processes determining metastatic organotropism could enable the development of approaches to prevent and treat breast cancer metastasis. In this study, we found that lung-tropic and non-lung-tropic breast cancer cells differ in their response to sialic acids, affecting the sialylation of surface proteins. Lung-tropic cells showed higher levels of ST6GAL1, whereas non-lung-tropic cells had more ST3GAL1. ST6GAL1-mediated α-2,6-sialylation, unlike ST3GAL1-mediated α-2,3-sialylation, increased lung metastasis by promoting cancer cell migration through pulmonary endothelial layers and reducing junction protein levels. α-2,6-Sialylated platelet/endothelial cell adhesion molecule 1 (PECAM-1) on breast cancer cells facilitated extravasation through the pulmonary endothelium, a critical step in lung metastasis. Knockdown of ST6GAL1 or PECAM-1 significantly reduced lung metastasis. The human pulmonary endothelium displayed high PECAM-1 levels. Through transhomophilic interaction with pulmonary PECAM-1, α-2,6-sialylated PECAM-1 on ST6GAL1-positive cancer cells increased pulmonary extravasation in a diapedesis-like, cell-autonomous manner. Additionally, lung-tropic cells and their exosomes increased the permeability of pulmonary endothelial cells, promoting metastasis in a non-cell-autonomous manner. Analysis of human breast cancer samples showed a correlation between elevated ST6GAL1/PECAM-1 expression and lung metastasis. These results suggest that targeting ST6GAL1-mediated α-2,6-sialylation could be a potential therapeutic strategy to prevent lung metastasis in patients with breast cancer. Significance: ST6GAL1-mediated α-2,6-sialylation of PECAM-1 dictates lung-tropic metastasis of breast cancer, revealing that the pattern of sialylation of breast cancer cells is a determinant of metastatic organ tropism and a potential therapeutic target.

The glycosyltransferase ALG3 is an AKT substrate that regulates protein N-glycosylation

The PI3K/AKT signaling pathway is frequently dysregulated in cancer and controls key cellular processes such as survival, proliferation, metabolism and growth. Protein glycosylation is essential for proper protein folding and is also often deregulated in cancer. Cancer cells depend on increased protein folding to sustain oncogene-driven proliferation rates. The N-glycosyltransferase asparagine-linked glycosylation 3 homolog (ALG3), a rate-limiting enzyme during glycan biosynthesis, catalyzes the addition of the first mannose to glycans in an alpha-1,3 linkage. Here we show that ALG3 is phosphorylated downstream of the PI3K/AKT pathway in both growth factor-stimulated cells and PI3K/AKT hyperactive cancer cells. AKT directly phosphorylates ALG3 in the amino terminal region at Ser11/Ser13. CRISPR/Cas9-mediated depletion of ALG3 leads to improper glycan formation and induction of endoplasmic reticulum stress, the unfolded protein response, and impaired cell proliferation. Phosphorylation of ALG3 at Ser11/Ser13 is required for glycosylation of cell surface receptors EGFR, HER3 and E-cadherin. These findings provide a direct link between PI3K/AKT signaling and protein glycosylation in cancer cells.

Targeting the tumour cell surface in advanced prostate cancer

Prostate cancer remains a substantial health challenge, with >375,000 annual deaths amongst men worldwide. Most prostate cancer-related deaths are attributable to the development of resistance to standard-of-care treatments. Characterization of the diverse and complex surfaceome of treatment-resistant prostate cancer, combined with advances in drug development that leverage cell-surface proteins to enhance drug delivery or activate the immune system, have provided novel therapeutic opportunities to target advanced prostate cancer. The prostate cancer surfaceome, including proteins such as prostate-specific membrane antigen (PSMA), B7-H3, six transmembrane epithelial antigen of the prostate 1 (STEAP1), delta-like ligand 3 (DLL3), trophoblastic cell-surface antigen 2 (TROP2), prostate stem cell antigen (PSCA), HER3, CD46 and CD36, can be exploited as therapeutic targets, as regulatory mechanisms might contribute to the heterogeneity of expression of these proteins and subsequently affect treatment response and resistance. Specific treatment strategies targeting the surfaceome are in clinical development, including radionuclides, antibody-drug conjugates, T cell engagers and chimeric antigen receptor (CAR) T cells. Ultimately, biomarker development and clinical implementation of these agents will be informed and refined by further understanding of the biology of various targets; the target specificity and sensitivity of different agents; and off-target and toxic effects associated with these agents. Understanding the dynamic nature of cell-surface targets and non-overlapping expression patterns might also lead to future combinational strategies.

A tale of two sugars: O-GlcNAc and O-fucose orchestrate growth, development, and acclimation in plants

Post-translational modifications of nucleocytoplasmic proteins by O-linked beta-N-acetylglucosamine (O-GlcNAc) and O-linked fucose (O-fucose) are emerging as key signaling mechanisms in plants. O-fucosylation and O-GlcNAcylation are catalyzed by SPINDLY (SPY) and SECRET AGENT (SEC), respectively, which are redundantly essential for viability and growth yet function antagonistically or independently in specific developmental contexts. Proteomic studies have identified hundreds of O-GlcNAcylated and O-fucosylated nucleocytoplasmic proteins, revealing their regulatory roles and intersections with phosphorylation pathways that mediate nutrient and hormone signaling. Functional studies on O-glycosylated proteins demonstrate diverse impacts on protein activity and biological processes. Together, O-fucosylation, O-GlcNAcylation, and phosphorylation form a regulatory network that controls plant growth, development, and acclimation. This review highlights recent progress and outlines future directions in studying O-fucosylation and O-GlcNAcylation in plants.

Elevated A2F bisect N-glycans of serum IgA reflect progression of liver fibrosis in patients with MASLD

BACKGROUND

Advanced liver fibrosis in cases of metabolic dysfunction-associated steatotic liver disease (MASLD) leads to cirrhosis and hepatocellular carcinoma. The current gold standard for liver fibrosis is invasive liver biopsy. Therefore, a less invasive biomarker that accurately reflects the stage of liver fibrosis is highly desirable.

METHODS

This study enrolled 269 patients with liver biopsy-proven MASLD. Patients were divided into three groups (F0/1 (n = 41/85), F2 (n = 47), and F3/4 (n = 72/24)) according to fibrosis stage. We performed serum N-glycomics and identified glycan biomarker for fibrosis stage. Moreover, we explored the carrier proteins and developed a sandwich ELISA to measure N-glycosylation changes of carrier protein.

RESULTS

Comprehensive N-glycomic analysis revealed significant changes in the expression of A2F bisect and its precursors as fibrosis progressed. The sum of neutral N-glycans carrying bisecting GlcNAc and core Fuc (neutral sum) had a better diagnostic performance to evaluate advanced liver fibrosis (AUC = 0.804) than conventional parameters (FIB4 index, aspartate aminotransferase-to-alanine aminotransferase ratio (AAR), and serum level of Mac-2-binding protein glycol isomer (M2BPGi). The combination of the neutral sum and FIB4 index enhanced diagnostic performance (AUC = 0.840). IgM, IgA, and complement C3 were identified as carrier proteins with A2F bisect N-glycan. A sandwich ELISA based on N-glycans carrying bisecting GlcNAc and IgA showed similar diagnostic performance than the neutral sum.

CONCLUSIONS

A2F bisect N-glycan and its precursors are promising candidate biomarkers for advanced fibrosis in MASLD patients. Analysis of these glycan alterations on IgA may have the potential to serve as a novel ELISA diagnostic tool for MASLD in routine clinical practice.

CLINICAL TRIAL NUMBER

UMIN000030720.

Recent advances in analytical methods and bioinformatic tools for quantitative glycomics

The significance of glycans in various biological processes has been widely acknowledged. Quantitative glycomics is emerging as an important addition to clinical biomarker discovery, as it helps uncover disease-associated glycosylation patterns that are valuable for diagnosis, prognosis, and treatment evaluation. Compared to glycoproteomics and other established omics approaches, quantitative glycomics exhibits greater methodological diversity and it encounters various challenges in automation and standardization. Nonetheless, numerous advancements have been made in this field over the past 5 years. Here, we have reviewed recent progress in analytical methods and software to improve mass spectrometry-based quantitative glycomics primarily on N- and O-glycosylation. The discussion is organized into four sections: stable isotopic labeling, isobaric labeling, label-free, and fluorescence labeling strategies, with a particular emphasis on quantitative data interpretation. Novel derivatization methods and advanced techniques have been developed for high-throughput and highly sensitive glycan quantification with high accuracy. However, due to variations in glycan derivatization and difficulties in structural identification, most glycomic quantification methods are tailored to specific applications, and manual inspection is frequently necessary for precise data interpretation. Therefore, further advancements in glycan sample preparation, structural characterization, and automated data interpretation are essential to facilitate comprehensive and accurate quantification across a wide array of glycans.

The emerging role of glycans and the importance of sialylation in cardiovascular disease

Glycosylation is the process by which glycans (i.e. 'sugars') are enzymatically attached to proteins or lipids to form glycoconjugates. Growing evidence points to glycosylation playing a central role in atherosclerosis. Glycosylation occurs in all human cells and post-translationally modifies many signalling molecules that regulate cardiovascular disease, affecting their binding and function. Glycoconjugates are present in abundance on the vascular endothelium and on circulating lipoproteins, both of which have well-established roles in atherosclerotic plaque development. Sialic acid is a major regulator of glycan function and therefore the process of sialylation, in which sialic acid is added to glycans, is likely to be entwined in any regulation of atherosclerosis. Glycans and sialylation regulators have the potential to present as new biomarkers that predict atherosclerotic disease or as targets for pharmacological intervention, as well as providing insights into novel cardiovascular mechanisms. Moreover, the asialoglycoprotein receptor 1 (ASGR1), a glycan receptor, is emerging as an exciting new regulator of lipid metabolism and coronary artery disease. This review summarises the latest advances in the growing body of evidence that supports an important role for glycosylation and sialylation in the regulation of atherosclerosis.

GlycoDash: automated, visually assisted curation of glycoproteomics datasets for large sample numbers

The challenge of robust and automated glycopeptide quantitation from liquid chromatography-mass spectrometry (LC-MS) data has yet to be adequately addressed by commercial software. Recently, open-source tools like Skyline and LaCyTools have advanced the field of label-free MS1 level quantitation. Yet, important steps late in the data processing workflow remain manual. Because manual data curation is time-consuming and error-prone, it presents a bottleneck, especially in an era of emerging high-throughput methodologies and increasingly complex analyses such as antigen-specific antibody glycosylation. We addressed this gap by developing GlycoDash, an R Shiny-based interactive web application designed to democratize label-free high-throughput glycoproteomics data analysis. The software comes in at a stage where analytes have been identified and quantified, but whole measurement and individual analyte signals of insufficient quality for quantitation remain and reduce the quality of the overall dataset. GlycoDash focuses on these challenges by incorporating several options for measurement and metadata linking, spectral and analyte curation, normalization, and repeatability assessment, and additionally includes glycosylation trait calculation, data visualization, and reporting capabilities that adhere to FAIR principles. The performance and versatility of GlycoDash were demonstrated across antibody glycoproteomics data of increasing complexity, ranging from relatively simple monoclonal antibody glycosylation analysis to a clinical cohort with over a thousand measurements. In a matter of hours, these large, diverse, and complex datasets were curated and explored. High-quality datasets with integrated metadata ready for final analysis and visualization were obtained. Critical aspects of the curation strategy underlying GlycoDash are discussed. GlycoDash effectively automates and streamlines the curation of glycopeptide quantitation data, addressing a critical need for high-throughput glycoproteomics data analysis. Its robust performance across diverse datasets and its comprehensive feature toolbox significantly enhance both research and clinical applications in glycoproteomics.

Functional Polarization of Liver Macrophages by Glyco Gold Nanoparticles

Macrophages are crucial drivers of innate immunity. Reprogramming macrophages to a restorative phenotype in cancer or autoimmune diseases can stop their cancer-promoting activity or trigger anti-inflammatory immunity. Glycans have emerged as key components for immunity as they are involved in many pathophysiological disorders. Previous studies have demonstrated that supraphysiological amounts of mannose (Man) or sialic acid (Sia) can inhibit tumor growth and stimulate differentiation of regulatory T cells. Man is known to affect glucose metabolism in glycolysis by competing for the same intracellular transporters and affecting macrophage polarization, whereas Sia alters macrophage differentiation via signaling through Siglec-1. Herein, this work describes a macrophage targeting platform using gold nanoparticles (GNPs) functionalized with Man and Sia monosaccharides which exhibit high liver tropism. A single dose of glyco-GNPs can convert macrophages to a restorative phenotype in two completely different immune environments. Man promotes tumor-associated macrophages toward an antitumorigenic activity in a MC38 liver colorectal cancer model by secretion of TNF-α, IL -1β, and IL -6 in the tumor microenvironment. However, in a proinflammatory environment, as observed in a mouse model of autoimmune disease, primary biliary cholangitis, Man impairs the production of TNF-α, IL-1β, Arg1, and IL-6 cytokines. The results probe the dual role of Man in macrophage repolarization in response to the immune system. This study is a proof-of-concept that demonstrates that nanomedicine using specific glycans designed to target other immune cells such as myeloid cells, are a promising strategy not only against cancer but also against other pathologies such as autoimmune diseases.

TNF-α-Driven Changes in Polarized EGF Receptor Trafficking Facilitate Phosphatidylinositol 3-Kinase/Protein Kinase B Signaling From the Apical Surface of MDCK Epithelial Cells

This manuscript describes a novel unconventional secretory pathway that facilitates EGF receptor (EGFR) signaling from apical membranes in polarized epithelial cells responding to immune cell mediators. Epithelial tissues provide a physical barrier between our bodies and the external environment and share an intimate relationship with circulating and local immune cells. Our studies describe an unexpected connection between the proinflammatory cytokine tumor necrosis factor-alpha (TNF-α) and EGFR typically localized to basolateral membranes in polarized epithelial cells. These two molecules sit atop complex biological networks with a long history of shared investigative interest from the vantage point of signaling pathway interactions. We have discovered that TNF-α alters the functional landscape of fully polarized epithelial cells by changing the speed and direction of EGFR secretion. Our results show apical EGFR delivery occurs within minutes of de novo synthesis likely via a direct route from the endoplasmic reticulum without passage through the Golgi complex. Additionally, our studies have revealed that apical cellular compartmentalization constitutes an important mechanism to specify EGFR signaling via phosphatidylinositol-4,5-bisphosphate 3-kinase/protein-kinase-B pathways. Our study paves the way for a better understanding of how inflammatory cytokines fine-tune local homeostatic and inflammatory responses by altering the spatial organization of epithelial cell signaling systems.

SUGAR-seq reveals the transcriptome and N-linked glycosylation landscape of mononuclear phagocytes at single-cell resolution in a mouse model of autosomal dominant osteopetrosis type 2

BACKGROUND

Heterozygous mutation of CLCN7 (R286W) is commonly found in patients with benign autosomal dominant osteopetrosis. However, there is no evidence from animal models to confirm that it is a disease mutation. And the characteristics of the bone marrow cell (BMC) landscape in osteopetrosis at the single-cell level are completely unknown till now.

RESULTS

In this study, we generated the first autosomal dominant osteopetrosis type 2 (ADO2) mouse model with typical phenotypes carried a mutation Clcn7 (r284w) corresponding to CLCN7 (R286W) observed in human patients using gene editing technology. And then, we conducted the first-ever single-cell analysis of the RNA expression and N-linked glycosylation profiles for the mouse BMCs by SUrface-protein Glycan And RNA-sequencing (SUGAR-seq). We identified 14 distinct cell types and similar proportion of neutrophils in both ADO2 and wild type mice, confirmed by flow cytometry analysis. The N-linked glycosylation modifications of BMCs were significantly downregulated detecting by SUGAR-seq, which was similar to the situation of N-Glycan profiling by the 4D Label-Free N-Glycosylation Proteomics Analysis. Particularly noteworthy is the heterogeneity of classic monocytes. We identified six cell subtypes, but only two cell subtypes were found with different proportion of cell, whose different expressed genes were associated with NF-κB-inducing kinase / Nuclear Factor-kappa B (NIK/NF-κB) signaling and other pathway associated with osteoclast differentiation.

CONCLUSIONS

Our murine model confirms that the human CLCN7 (R286W) is a pathogenic mutation for ADO2. Additionally, our single-cell analyses reveal the heterogeneity of monocytes in ADO2, and the abnormal glycosylation modifications across various subtypes may represent important events in the pathogenesis of osteopetrosis.

Leveraging glycosylation for early detection and therapeutic target discovery in pancreatic cancer

Pancreatic cancer (PC) remains one of the most lethal malignancies, primarily due to late-stage diagnosis, limited biomarker specificity, and aggressive metastatic potential. Recent glycoproteomic studies have illuminated the crucial role of glycosylation in PC progression, revealing altered glycosylation patterns that impact cell adhesion, immune evasion, and tumor invasiveness. Biomarkers such as CA19-9 remain the clinical standard, yet limitations in sensitivity and specificity, especially in early disease stages, necessitate the exploration of alternative markers. Emerging glycoproteins-such as mesothelin, thrombospondin-2, and glycan modifications like sialyl-Lewis x-offer diagnostic promise when combined with CA19-9 or used in profiling panels. Furthermore, therapeutic strategies targeting glycosylation processes, including sialylation, and fucosylation, have shown potential in curbing PC metastasis and enhancing immune response. Translational platforms, such as patient-derived xenografts and advanced in vitro models, are pivotal in validating these findings and assessing glycosylation potential therapeutic impact. Continued exploration of glycosylation-driven mechanisms and biomarker discovery in PC can significantly advance early detection and treatment efficacy, offering new hope in the management of this challenging disease.

Atomistic Insights into gp82 Binding: A Microsecond, Million-Atom Exploration of Trypanosoma cruzi Host-Cell Invasion

Chagas disease, caused by the protozoan Trypanosoma cruzi, affects millions globally, leading to severe cardiac and gastrointestinal complications in its chronic phase. The invasion of host cells by T. cruzi is mediated by the interaction between the parasite's glycoprotein gp82 and the human receptor lysosome-associated membrane protein 2 (LAMP2). While experimental studies have identified a few residues involved in this interaction, a comprehensive molecular-level understanding has been lacking. In this study, we present a 1.44-million-atom computational model of the gp82 complex, including over 3300 lipids, glycosylation sites, and full molecular representations of gp82 and LAMP2, making it the most complete model of a parasite-host interaction to date. Using microsecond-long molecular dynamics simulations and dynamic network analysis, we identified critical residue interactions, including novel regions of contact that were previously uncharacterized. Our findings also highlight the significance of the transmembrane domain of LAMP2 in stabilizing the complex. These insights extend beyond traditional hydrogen bond interactions, revealing a complex network of cooperative motions that facilitate T. cruzi invasion. This study not only confirms key experimental observations but also uncovers new molecular targets for therapeutic intervention, offering a potential pathway to disrupt T. cruzi infection and combat Chagas disease.

Integrated technologies for molecular profiling of genetic and modified biomarkers in extracellular vesicles

Extracellular vesicles (EVs) are nanoscale membrane vesicles actively released by cells into a variety of biofluids. EVs carry myriad molecular cargoes; these include classical genetic biomarkers inherited from the parent cells as well as EV modifications by other entities (e.g., small molecule drugs). Aided by these diverse cargoes, EVs enable long-distance intercellular communication and have been directly implicated in various disease pathologies. As such, EVs are being increasingly recognized as a source of valuable biomarkers for minimally-invasive disease diagnostics and prognostics. Despite the clinical potential, EV molecular profiling remains challenging, especially in clinical settings. Due to the nanoscale dimension of EVs as well as the abundance of contaminants in biofluids, conventional EV detection methods have limited resolution, require extensive sample processing and can lose rare biomarkers. To address these challenges, new micro- and nanotechnologies have been developed to discover EV biomarkers and empower clinical applications. In this review, we introduce EV biogenesis for different cargo incorporation, and discuss the use of various EV biomarkers for clinical applications. We also assess different chip-based integrated technologies developed to measure genetic and modified biomarkers in EVs. Finally, we highlight future opportunities in technology development to facilitate the clinical translation of various EV biomarkers.

N-glycosylation enzyme Mpi is essential for mucin O-glycosylation, host-microbe homeostasis, Paneth cell defense, and metabolism

Intestinal homeostasis relies on a protective mucus layer that separates bacteria from the host, with Muc2 as its primary component. This secreted, gel-forming mucin is heavily O-glycosylated, allowing it to retain water and support beneficial bacteria. For the first time, we demonstrate that Muc2 N-glycosylation plays a critical in mucin maturation, O-glycosylation, barrier integrity, and the prevention of dysbiosis. Using mouse models with global and intestine-specific N-glycan deficiency- caused by the loss of the mannose producing enzyme, Mpi- we uncover an unexpected link between N-glycosylation and intestinal homeostasis. Our findings reveal that Mpi hypomorphic mice are highly sensitive to DSS-induced colitis, while Mpi flox; Villin Cre mice spontaneously develop disease, exhibiting increased ER stress and dysbiosis. Additionally, electron microscopy, proteomics, and gene expression analyses of goblet and Paneth cells indicate immaturity, mitochondrial loss, and disruptions in lipid metabolism. These results highlight the fundamental role of N-glycosylation in maintaining intestinal homeostasis.

Glycoproteomics of IgA1: uncovering key N-glycan composition in ankylosing spondylitis

OBJECTIVE

This study aimed to identify distinct IgA1 N-glycan composition in patients with ankylosing spondylitis (AS) compared with healthy controls and to explore their associations with inflammatory markers and disease activity indices.

METHODS

Serum samples were collected from 36 patients with AS and 35 healthy controls. The diagnosis of AS was based on the New York criteria. Clinical assessments included inflammatory markers (ESR, CRP, and IgA) and disease activity indices (BASDAI, ASDAS-ESR, and ASDAS-CRP). IgA1 was isolated using affinity purification and gel filtration chromatography, followed by mass spectrometry to identify N-glycans.

RESULTS

Among the 23 detected N-glycan patterns, significant differences were observed in 13 of the 18 N-glycans at the N144 site and in all five N-glycans at the N340 site between patients with AS and controls. Notably, the glycans HexNAc3Hex4NeuAc1, HexNAc4Hex4NeuAc1 and HexNAc5Hex5NeuAc1 at N144 demonstrated strong associations with all three inflammatory markers, including ESR, CRP, and IgA (P < 0.001). Levels of HexNAc4Hex4NeuAc1 were significantly elevated in patients with AS compared with those in the healthy controls. Increased sialylation and galactosylation, along with decreased fucosylation, were noted at N144 of IgA1 in patients with AS. Conversely, no glycans at N340 showed a correlation with all inflammatory markers simultaneously or with any disease activity indicators.

CONCLUSION

IgA1 from patients with AS exhibited distinct glycosylation traits compared with controls, with elevated levels of HexNAc₄Hex₄NeuAc₁ at N144 associated with inflammatory markers. These findings suggested that differential glycosylation patterns of IgA1 may play a role in the pathogenesis of AS.

Extracting informative glycan-specific ions from glycopeptide MS/MS spectra with GlyCounter

Glycopeptide tandem mass spectra typically contain numerous glycan-specific fragments that can inform several features of glycan modifications, including glycan class, composition, and structure. While these fragment ions are often straightforward to observe by eye, few tools exist to systemically explore these common glycopeptide spectral features or explore their relationships to each other. Instead, most studies rely on manual inspection to understand glycan-informative ion content in their data, or they are restricted to evaluating the presence of these ions only in the small fraction of spectra that are identified by glycopeptide search algorithms. Here we introduce GlyCounter as a freely available, open-source tool to rapidly extract oxonium, Y-type, and custom ion information from raw data files. We highlight GlyCounter's utility by evaluating glycan-specific fragments in a diverse selection of publicly available datasets to demonstrate how others in the field can make immediate use of this software. In several cases, we show how conclusions drawn in these publications are evident simply through GlyCounter's extracted ion information without requiring database searches or experiment-specific programs. Although one of our goals is to decouple spectral evaluation from glycopeptide identification, we also show that evaluating oxonium ion content with GlyCounter can supplement a database search as valuable spectral evidence to validate conclusions. In all, we present GlyCounter as a user-friendly platform that can be easily incorporated into most glycoproteomic workflows to refine sample preparation, data acquisition, and post-acquisition identification methods through straightforward evaluation of the glycan content of glycoproteomic data. Software and instructions are available at https://github.com/riley-research/GlyCounter.

Expediting Glycospace Exploration: Therapeutic Glycans via Automated Synthesis

Glycans regulate a vast spectrum of disease-related processes, yet effectively leveraging these important mediators in a therapeutic context remains a frontier in contemporary medicine. Unlike many other classes of clinically important biopolymers, carbohydrates derive from discrete biosynthetic pathways and are not produced directly from genes. The conspicuous absence of a biological blueprint to achieve amplification creates a persistent challenge in obtaining well-defined glycostructures for therapeutic translation. Isolating purified sugars from biological sources is not without challenge, rendering synthetic organic chemistry the nexus of this advancing field. Chemical synthesis has proven to be an unfaltering pillar in the production of complex glycans, but laborious syntheses coupled with purification challenges frequently introduce reproducibility issues. In an effort to reconcile these preparative challenges with the societal importance of glycans, automated glycan synthesis was conceptualised at the start of the 21st century. This rapidly expanding, multifaceted field of scientific endeavor has effectively merged synthetic chemistry with technology and engineering to expedite the precision synthesis of target glycans. This minireview describes the structural diversity and function of glycans generated by automated glycan synthesis platforms over the last five years. The translational impact of these advances is discussed together with current limitations and future directions.

Highly variable aggregation and glycosylation profiles and their roles in immunogenicity to protein-based therapeutics

Production of antibodies against protein-based therapeutics (e.g., monoclonal antibodies (mAbs)) by a recipient's immune system can vary from benign symptoms to chronic neutralization of the compound, and in rare cases, a lethal cytokine storm. One critical factor that can induce or contribute to an anti-drug antibody (ADA) response is believed to be the presence of aggregated proteins in protein-based therapeutics. There is a high level of variability in the aggregation of different proteins, which adds to the complexity in understanding the immune response to these drugs. Furthermore, the level of glycosylation of proteins, which increases drug stability, functionality, and serum half-life, is highly variable and may influence their immunogenicity. Considering the abundance of literature on the effect of aggregation and glycosylation on the immunogenicity of protein-based therapeutics, this review aims to summarize the current knowledge and clarify the immunogenic effects of different protein-based therapeutics such as mAbs. This review focuses on the properties of aggregated proteins and elucidates their relationship with immunogenicity. The contribution of different immune cell subsets and the mechanisms in aggregation-induced immunogenicity are also reviewed. Finally, the potential effects of each glycan, such as sialic acid, mannose, and fucose, on protein-based therapeutics' immunogenicity and stability is discussed.

Plasma N-Glycoproteomics in monozygotic twin pairs discordant for body mass index reveals an obesity signature related to inflammation and iron metabolism

BACKGROUND

N-glycosylation is a complex, post-translational modification which influences protein function and is sensitive to physiological changes. Obesity is associated with alterations in protein function; however, little is known about the glycoproteome in obesity beyond observations of association with types and structures of selected glycopeptides. Most often, due to technical challenges, glycan composition and structure information are missing. Here, we combined label-free data-independent proteomics and targeted quantitative glycoproteomics to study N-glycosylation of plasma proteins in obesity. Using a monozygotic twin study design, we controlled for genetic variation and focused only on the acquired effects of obesity.

METHODS

Using plasma samples of 48 monozygotic twin pairs discordant for BMI (intrapair difference > 2.5 kg/m2), we identified using mass spectrometry, differential protein and glycopeptide levels between heavier and leaner co-twins. We used a within-twin paired analysis model and considered p < 0.05 as significant.

RESULTS

We identified 48 protein and 33 N-glycosylation expression differences (p < 0.05) between co-twins. These differences occurred either both in the protein expression and glycoprotein (sometimes in opposing directions) or independently from each other. Haptoglobin protein was upregulated (Fold Change = 1.10, p = 0.001) in heavier co-twins along with seven upregulated glycan compositions at N-glycosylation site Asn241. The complement protein C3 was upregulated (Fold Change = 1.08, p = 0.014) along with one upregulated glycopeptide at Asn85. Additionally, many glycopeptides were upregulated despite non-significant differences in protein-backbone plasma levels.

CONCLUSION

Differential protein expression related to cholesterol biosynthesis and acute phase signalling as well as N-glycosylation of proteins related to iron metabolism and inflammation can be linked to acquired obesity.

STT3B promotes porcine epidemic diarrhea virus replication by regulating N-glycosylation of PEDV S protein

Porcine epidemic diarrhea virus (PEDV), a highly pathogenic enteric coronavirus, has caused significant economic losses worldwide in recent years. The PEDV spike (S) protein has been reported to undergo extensive N-glycosylation, suggesting that glycosylation plays a crucial role in PEDV replication. In this study, we demonstrated that the N-glycosylation pathway promotes PEDV replication by facilitating the glycosylation of the S protein. First, we observed that pharmacological inhibition of host N-glycosylation using specific inhibitors significantly reduces viral replication. Furthermore, genetic ablation of STT3A or STT3B, the catalytically active subunits of the oligosaccharyltransferase (OST) complex, revealed that the STT3B-OST complex, but not STT3A, is preferentially required for PEDV replication. Notably, we showed that the N-glycosylation of the PEDV S protein depends on the oligosaccharyltransferase activity of STT3B. Together, the study demonstrated the critical role of the N-glycosylation pathway in PEDV replication by elucidating the relationship between the N-glycosylation of the PEDV S protein and STT3B, thereby presenting a potential new target for the prevention and control of PEDV.IMPORTANCEThe highly N-glycosylated spike protein of porcine epidemic diarrhea virus (PEDV) is a multifunctional protein that plays a crucial role in the viral replication cycle. In this study, using pharmacological inhibitors, we demonstrated the importance of the N-glycosylation pathway in PEDV replication. Genetic analysis revealed that STT3B, one of the catalytically active subunits of the oligosaccharyltransferase complex, promotes viral proliferation by regulating the N-glycosylation of the PEDV spike protein. Our findings enhance the understanding of the role of the N-glycosylation pathway in viral infection and identify STT3B as a potential therapeutic target for controlling PEDV infection.

AAV-based gene replacement therapy prevents and halts manifestation of abnormal neurological phenotypes in a novel mouse model of PMM2-CDG

Inherited Phosphomannomutase 2 (PMM2) deficiency, also known as PMM2-CDG, is the most prevalent N-linked congenital disorder of glycosylation (CDG), occurring in approximately 1 in 20,000 individuals in certain populations. Patients exhibit a spectrum of symptoms, with neurological involvement being a prominent feature, often manifesting as the initial clinical sign, and can range from isolated neurological deficits to severe multi-organ dysfunction. Given the absence of curative treatments and a high mortality rate before the age of two, alongside considerable lifelong morbidity, there is an urgent need for innovative therapeutic approaches. To address this unmet need, we developed a tamoxifen-inducible Pmm2 knockout (KO) mouse model with widespread tissue deficiency of Pmm2 expression. Characterization of the mouse model to-date revealed distinct neurological phenotypes relevant to PMM2-CDG, as assessed by the Composite Phenotype Scoring System and Open Field Test. Notably, PMM2 augmentation through AAV9-PMM2 gene replacement therapy prevented and halted the disease-relevant neurological phenotypes induced by Pmm2 KO in the animals. These findings underscored the promise of AAV9-PMM2 gene replacement in managing PMM2-CDG.

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.