Advances in understanding N-glycosylation structure, function, and regulation in health and disease

Molecular and therapeutic insight into ER stress signalling in NSCLC

Endoplasmic Reticulum (ER) stress is intricately involved in cancer development, progression and response to chemotherapy. ER stress related genes might play an important role in predicting the prognosis in lung adenocarcinoma patients and may be manipulated to improve the treatment outcome and overall survival rate. In this review, we analysed the contribution of the three major ER stress pathways-IRE1, ATF6, and PERK-in lung cancer pathogenesis via modulation of tumour microenvironment (TME) and processes as metastasis, angiogenesis, apoptosis and N-glycosylation. Furthermore, we discuss the regulatory role of microRNAs in fine-tuning ER stress pathways in Non-Small Cell Lung Cancer (NSCLC). Our review also highlights various promising strategies to overcome chemoresistance by targeting ER stress pathways, offering new therapeutic opportunities.

Improvements in Glycoproteomics through Architecture Changes to the Orbitrap Tribrid MS Platform

Hardware changes introduced on the Orbitrap Ascend Tribrid MS include dual ion routing multipoles (IRMs) that enable parallelized accumulation, dissociation, and Orbitrap mass analysis of three separate ion populations. The balance between these instrument functions is especially important in glycoproteomics, where complexities of glycopeptide fragmentation necessitate large precursor ion populations and long ion accumulation times for quality MS/MS spectra. To compound matters further, dissociation methods like electron transfer dissociation (ETD) that benefit glycopeptide characterization come with overhead times that slow down scan acquisition. Here we explored how the Orbitrap Ascend's dual IRM architecture can improve glycopeptide analysis, with a focus on O-glycopeptide characterization using ETD with supplemental collisional activation (EThcD). We found that parallelization of ion accumulation and EThcD fragmentation increased scan acquisition speed without sacrificing spectral quality, subsequently increasing the number of O-glycopeptides identified relative to analyses on the Orbitrap Eclipse (i.e., the previous generation Tribrid MS). Additionally, we systematically evaluated ion-ion reaction times and supplemental activation energies used for EThcD to understand how best to utilize acquisition time. We observed that shorter-than-expected ion-ion reaction times minimized scan overhead time without sacrificing c/z•-fragment ion generation and that higher supplemental collision energies can generate combinations of glycan-retaining and glycan-neutral-loss peptide backbone fragments that benefit O-glycopeptide identification. We also saw improvements in N-glycopeptide analysis using collision-based dissociation, especially with methods using faster scan speeds. Overall, these data show how architectural changes to the Tribrid MS platform benefit glycoproteomic experiments by parallelizing scan functions to minimize overhead time and improve sensitivity.

Enhancing the persistence of engineered biotherapeutics in the gut: Adhesion, glycan metabolism, and environmental resistance

Engineered live biotherapeutic products (eLBPs) are receiving increasing attention as next-generation therapeutics to treat a variety of diseases with high specificity and effectiveness. Despite their potential, eLBPs face challenges, such as limited colonization, competition with native microbiota, nutrient depletion, and susceptibility to gastrointestinal stresses, which ultimately reduce their persistence in the gut and hinder their therapeutic efficacy. This review examines the key strategies to enhance the persistence and activity of eLBPs in the gut environment. First, methods to strengthen the adhesion capacity of eLBPs are discussed, including genetic engineering to express adhesins and chemical surface modifications to improve their binding to mucus and epithelial cells. Second, strategies to improve the ability of eLBPs to efficiently use mucin-derived sugars, which are continuously secreted by intestinal epithelial cells, were highlighted. These strategies involve the introduction and optimization of glycan-degrading enzymes and metabolic pathways for key mucin sugars, such as N-acetylglucosamine, galactose, and sialic acid, to support sustained energy production and enhance gut colonization. Third, strategies to improve the resistance of eLBPs against environmental stress are discussed, including genetic modifications to stabilize cell membranes, enhancement of ion pump activity, overexpression of stress-response proteins, and encapsulation techniques to provide protection. The implementation of these strategies can address challenges related to gut colonization by eLBPs, thereby enhancing their metabolic activity and enabling sustained and efficient secretion of therapeutic molecules. This review offers a comprehensive framework for developing and optimizing eLBPs, paving the way for their successful clinical application with enhanced effectiveness in treating gastrointestinal and systemic diseases.

Glucose metabolism through the hexosamine biosynthetic pathway drives hepatic de novo lipogenesis via promoting N-linked protein glycosylation

De novo lipogenesis (DNL) converts excess glucose into lipids, whereas the hexosamine biosynthetic pathway (HBP), a glycolytic branch, generates UDP-N-acetylglucosamine for protein glycosylation, including O-GlcNAcylation and N-linked glycosylation. Both pathways are active in hepatocytes and integral to glucose metabolism; however, their functional interplay remains unclear. Here, we investigated the role of HBP in hepatic DNL activation using both in vitro and in vivo models. AML12 hepatocytes were cultured in low- and high-glucose media with or without HBP blockade, both pharmacologically and genetically. For in vivo studies, male C57BL/6J mice were subjected to a fasting-refeeding regimen with or without intraperitoneal administration of azaserine, a competitive inhibitor of glutamine-fructose-6-phosphate transaminase 1 (GFPT1), the rate-limiting enzyme of the HBP. Our results demonstrated that, in AML12 cells, glucose exposure activated both DNL and HBP, leading to triacylglycerol (TAG) accumulation, whereas HBP inhibition ameliorated DNL and TAG accumulation. In mice, refeeding after a 24-h fasting induced hepatic DNL, which was abolished by HBP inhibition, indicating its mechanistic involvement in glucose-driven lipogenesis. Mechanistically, we identified ATF4 as a key regulator of GFPT1 upregulation under high-glucose conditions. As expected, both glucose-treated hepatocytes and livers from fasting-refed mice exhibited increased protein glycosylation. Notably, blocking N-linked glycosylation, but not O-GlcNAcylation, abolished glucose-induced DNL activation, indicating that HBP is essential for glucose-induced DNL pathway activation via promoting N-linked glycosylation, independent of O-GlcNAcylation. In conclusion, our findings establish that an intact HBP is required for glucose-induced hepatic DNL activation, primarily through promoting protein N-linked glycosylation.NEW & NOTEWORTHY High-glucose exposure activates both hepatic HBP and DNL pathways. The glucose metabolism into HBP is essential for the activation of the DNL pathway. ATF4 activation plays a mechanistic role in high glucose-induced HBP activation. HBP drives high glucose-induced hepatic DNL activation via promoting N-linked protein glycosylation.

Integrating N-glycan and CODEX imaging reveal cell-specific protein glycosylation in healthy human lung

Identifying cell-specific glycan structures in human lungs is critical for understanding the chemistry and mechanisms that guide cell-cell and cell-matrix interactions and determining nuanced functions of specific glycosylation. Our dual-modality omics platform, which uses matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) to profile glycan chemistry at 50 μm × 50 μm scale, combined with co-detection by indexing (CODEX) to provide cell identification from the exact same tissue section, is a significant step in this direction. It enabled us to detect, differentiate, and reveal chemical properties of N-glycans in the various cell types of a human lung, suggesting the cell-specific function of distinct carbohydrate moieties. This innovative technological combination bridges the gap between the specific protein glycosylation and their cellular origin, paving the way for targeted studies in the lungs and many other human tissues where glycans mediate cell-cell recognition events.

Selective bioorthogonal probe for N-glycan hybrid structures

Metabolic incorporation of chemically tagged monosaccharides is a facile means of tagging cellular glycoproteins and glycolipids. However, since the monosaccharide precursors are often shared by several pathways, selectivity has been difficult to attain. For example, N-linked glycosylation is a chemically complex and ubiquitous posttranslational modification, with three distinct classes of GlcNAc-containing N-glycan structures: oligomannose, hybrid and complex. Here we describe the synthesis of 1,3-Pr2-6-OTs GlcNAlk (MM-JH-1) as a next-generation metabolic chemical reporter for the selective labeling of hybrid N-glycan structures. We first developed a general strategy for defining the selectivity of labeling with chemically tagged monosaccharides. We then applied this approach to establish that MM-JH-1 is selectively incorporated into hybrid N-glycans. Using this metabolic chemical reporter as a detection tool, we performed imaging and fractionation to define features of the intracellular localization and trafficking of target proteins bearing hybrid N-glycan structures.

GPNMB disrupts SNARE complex assembly to maintain bacterial proliferation within macrophages

Xenophagy plays a crucial role in restraining the growth of intracellular bacteria in macrophages. However, the machinery governing autophagosome‒lysosome fusion during bacterial infection remains incompletely understood. Here, we utilize leprosy, an ideal model for exploring the interactions between host defense mechanisms and bacterial infection. We highlight the glycoprotein nonmetastatic melanoma protein B (GPNMB), which is highly expressed in macrophages from lepromatous leprosy (L-Lep) patients and interferes with xenophagy during bacterial infection. Upon infection, GPNMB interacts with autophagosomal-localized STX17, leading to a reduced N-glycosylation level at N296 of GPNMB. This modification promotes the degradation of SNAP29, thus preventing the assembly of the STX17-SNAP29-VAMP8 SNARE complex. Consequently, the fusion of autophagosomes with lysosomes is disrupted, resulting in inhibited cellular autophagic flux. In addition to Mycobacterium leprae, GPNMB deficiency impairs the proliferation of various intracellular bacteria in human macrophages, suggesting a universal role of GPNMB in intracellular bacterial infection. Furthermore, compared with their counterparts, Gpnmbfl/fl Lyz2-Cre mice presented decreased Mycobacterium marinum amplification. Overall, our study reveals a previously unrecognized role of GPNMB in host antibacterial defense and provides insights into its regulatory mechanism in SNARE complex assembly.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2021-2022

The use of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry for the analysis of carbohydrates and glycoconjugates is a well-established technique and this review is the 12th update of the original article published in 1999 and brings coverage of the literature to the end of 2022. As with previous review, this review also includes a few papers that describe methods appropriate to analysis by MALDI, such as sample preparation, even though the ionization method is not MALDI. The review follows the same format as previous reviews. It is divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of computer software for structural identification. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other general areas such as medicine, industrial processes, natural products and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. MALDI is still an ideal technique for carbohydrate analysis, particularly in its ability to produce single ions from each analyte and advancements in the technique and range of applications show little sign of diminishing.

Regulation of N-Glycosylation of CDNF on Its Protein Stability and Function in Hypoxia/Reoxygenation Model of H9C2 Cells

Myocardial ischemia-reperfusion (I/R) injury is a cause of high post-interventional mortality in patients with acute myocardial infarction (MI). Cerebral dopamine neurotrophic factor (CDNF) is an endoplasmic reticulum (ER) resident protein, and its expression and secretion are induced when tissues and cells are subjected to hypoxia, ischemia, or traumatic injury. As a novel cardiomyokine, CDNF plays a crucial role in the progression of myocardial I/R injury. In our previous study, we reported that the overexpression of CDNF inhibited tunicamycin-induced H9C2 cell apoptosis. Moreover, there is a unique N-glycosylation site at Asn57 in the CDNF protein, which likely affects its function in H9C2 cells. However, the detailed impact remains unexplored. In our current study, we observed elevated levels of CDNF in the serum of acute MI patients, myocardial tissue of I/R model mice, and H/R model H9C2 cells. To detect the effect of N-glycosylation on the CDNF protein, we constructed an Asn57 mutant (N57A) plasmid and found that the N57A protein presented similar intracellular localization to those of the wild-type CDNF protein. However, the N57A protein demonstrated reduced stability, and the mutant protein could not protect H/R-induced H9C2 cells from apoptosis. Moreover, this process may occur through the downregulation of the PI3K/Akt pathway. Therefore, N-glycosylation of CDNF may be essential for protein stability and its protective role in H/R injury in H9C2 cells.

Implications of Mucin-Type O-Glycosylation in Alzheimer's Disease

Alzheimer's disease (AD) is one of the most common neurodegenerative disorders linked to aging. Major hallmarks of AD pathogenesis include amyloid-β peptide (Aβ) plaques, which are extracellular deposits originating from the processing of the amyloid precursor protein (APP), and neurofibrillary tangles (NFTs), which are intracellular aggregates of tau protein. Recent evidence indicates that disruptions in metal homeostasis and impaired immune recognition of these aggregates trigger neuroinflammation, ultimately driving disease progression. Therefore, a more comprehensive approach is needed to understand the underlying causes of the disease. Patients with AD present abnormal glycan profiles, and most known AD-related molecules are either modified with glycans or involved in glycan regulation. A deeper understanding of how O-glycosylation influences the balance between amyloid-beta peptide production and clearance, as well as microglia's pro- and anti-inflammatory responses, is crucial for deciphering the early pathogenic events of AD. This review aims to provide a comprehensive summary of the extensive research conducted on the role of mucin-type O-glycosylation in the pathogenesis of AD, discussing its role in disease onset and immune recognition.

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.

Chemoenzymatic Synthesis of Core-Fucosylated Asymmetrical N-Glycans with Different-Length Oligo-N-Acetyllactosamine Motifs and Their Sialylated Extensions

An efficient chemoenzymatic approach for the diversity-oriented synthesis of core-fucosylated asymmetrical N-glycans bearing different lengths of oligo-N-acetyllactosamine (LacNAc) and their sialylated extensions is described. Two oligosaccharide precursors were chemically synthesized by length-controlled introduction of oligo-LacNAc motifs through stereoselectively iterative glycosylation of a common hexasaccharide intermediate. Both oligosaccharide precursors can be well recognized by α1,6-fucosyltransferase FUT8 to generate core-fucosylated N-glycans, which were subjected to divergent enzymatic extension using a galactosyltransferase module and two sialyltransferase modules to provide a wide array of core-fucosylated asymmetrical biantennary N-glycans having different-length oligo-LacNAc motifs capped by various sialic acid linkages.

Modulation of N-glycosylation in the PD-1: PD-L1 axis as a strategy to enhance cancer immunotherapies

The modulation of the N-glycosylation status in immune checkpoints, particularly the PD-1/PD-L1 axis, has emerged as a promising approach to enhance cancer immunotherapies. While immune checkpoint inhibitors (ICIs) targeting PD-1 and PD-L1 have achieved significant clinical success, recent studies highlight the critical role of N-glycosylation in regulating their expression, stability, and function. Alterations in N-glycosylation might affect the efficacy of ICIs by modulating the interactions between immune checkpoints and antibodies used in therapy. This review focuses on the glycosylation of PD-1 and its ligands PD-L1 and PD-L2, examining how N-glycans influence immune responses and contribute to immune evasion by tumors. It explores innovative strategies to modulate glycosylation in tumor and immune cells, including the use of N-glycosylation inhibitors and novel genetic manipulation techniques. Understanding the interplay between N-glycosylation and immune checkpoint functions is essential for optimizing immunotherapy outcomes and overcoming therapeutic resistance in cancer patients.

Variable domain glycosylation as a marker and modulator of immune responses: Insights into autoimmunity and B-cell malignancies

Glycosylation of antibodies is essential for shaping immune responses, as it contributes significantly to antibody function and diversity. While immunoglobulin G (IgG) Fc glycosylation is well-characterized, variable domain glycosylation (VDG) introduces an additional and less understood layer of complexity. Notably, VDG is associated with rheumatoid arthritis, where disease-specific IgG autoantibodies abundantly express this modification. Moreover, its presence on these antibodies correlates with disease progression in at-risk individuals and therapeutic outcomes. Emerging evidence links increased VDG levels to other autoimmune diseases and B-cell malignancies, highlighting its potential as both a marker and modulator in disease onset and progression. Importantly, VDG on IgG is now recognized to influence antigen binding, enhance antibody stability, and modulate interactions with the human neonatal Fc receptor. In addition, glycans in the antigen-binding domains of autoreactive B-cell receptors (BCRs) can significantly impact B cell activation. In follicular lymphoma and other B-cell malignancies, the presence of N-glycosylation sites in the immunoglobulin variable domains leads to the introduction of oligomannose glycans, which are postulated to bind to mannose-specific lectins. This interaction might promote antigen-independent activation of BCRs, thereby supporting malignant B cell survival and proliferation. Here, we explore the regulatory pathways of VDG and its functional roles across both physiological and pathological conditions, underscoring its prevalence and significance in various autoimmune diseases and B-cell malignancies. Ultimately, advancing our understanding of the regulatory factors influencing VDG and its functional implications could be highly rewarding for identifying potential therapeutic targets and strategies to prevent and treat autoimmune diseases and B-cell malignancies.

Inherited and de novo variants in young females potentially associated with pelvic organ prolapse

BACKGROUND

Pelvic organ prolapse is a common condition usually affecting postmenopausal women, but it is also seen in about 10% of women aged 20 to 39 years. In young females, genetic factors seem to be of particular interest.

OBJECTIVE

This study aimed to identify inherited and de novo variants relevant to pelvic organ prolapse in young females without a family history.

STUDY DESIGN

A total of 25 women aged ≤40 years with parity ≤2 and Pelvic Organ Prolapse Quantification stage ≥II were included in the study. Moreover, females had no history of pelvic organ prolapse and any previous history of urogynecological surgery. A trio-based exome analysis was performed on patients and both their parents. Bioinformatic analysis of raw whole exome sequencing data and genetic variant prioritization were performed using in-house bioinformatic pipeline. The ClinVar database, GeneCard, and the Human Protein Atlas were used to determine clinical significance, disease associations, and linked phenotypes of the genetic variants. The impact of causative genetic variants on protein structure and function was assessed using various prediction tools including Sorting Intolerant From Tolerant, PolyPhen2, MutPred2, Phyre2, and SNPeffect 4.0. To determine the molecular interaction network of the proteins, Search Tool for the Retrieval of Interacting Genes database was applied.

RESULTS

The mean age of women was 33.50 (±3.07) years, the mean body mass index value was 21.80 (±2.07), and the number of parity was 1.76 (±0.44). In the study group, 18 of 25 women required surgical treatment. Whole exome sequencing analysis identified 76 de novo variants, but only 19 were missense and 2 were nonsense variants. Three genetic variants in CSPG4, ITGA7, and MT-CO3 genes appear potentially relevant to pelvic organ prolapse. Interestingly, paternally inherited variants in SGCG, CYP24A1, and TK2 genes likely related to pelvic organ prolapse were found in carriers of new de novo variants.

CONCLUSION

In this study, no common genetic variants were found in the female group. Potentially causative patient-specific variants were found in genes related to extracellular matrix, mitochondria, or skeletal muscle conditions. The uncovered genetic variants presumably disrupt the functioning of muscles and mitochondria, which may consequently lead to pelvic floor dysfunction in young women.

Advancements in Electrochemical Biosensors for Comprehensive Glycosylation Assessment of Biotherapeutics

Proteins represent a significant portion of the global therapeutics market, surpassing hundreds of billions of dollars annually. Among the various post-translational modifications, glycosylation plays a crucial role in influencing protein structure, stability, and function. This modification is especially important in biotherapeutics, where the precise characterization of glycans is vital for ensuring product efficacy and safety. Although mass spectrometry-based techniques have become essential tools for glycomic analysis due to their high sensitivity and resolution, their complexity and lengthy processing times limit their practical application. In contrast, electrochemical methods provide a rapid, cost-effective, and sensitive alternative for glycosylation assessment, enabling the real-time analysis of glycan structures on biotherapeutic proteins. These electrochemical techniques, often used in conjunction with complementary methods, offer valuable insights into the glycosylation profiles of both isolated glycoproteins and intact cells. This review examines the latest advancements in electrochemical biosensors for glycosylation analysis, highlighting their potential in enhancing the characterization of biotherapeutics and advancing the field of precision medicine.

Glycosylation Regulation by TMEM230 in Aging and Autoimmunity

Aging is often a choice between developing cancer or autoimmune disorders, often due in part to loss of self-tolerance or loss of immunological recognition of rogue-acting tumor cells. Self-tolerance and cell recognition by the immune system are processes very much dependent on the specific signatures of glycans and glycosylated factors present on the cell plasma membrane or in the stromal components of tissue. Glycosylated factors are generated in nearly innumerable variations in nature, allowing for the immensely diverse role of these factors in aging and flexibility necessary for cellular interactions in tissue functionality. In previous studies, we showed that differential expression of TMEM230, an endoplasmic reticulum (ER) protein was associated with specific signatures of enzymes regulating glycan synthesis and processing and glycosylation in rheumatoid arthritis synovial tissue using single-cell transcript sequencing. In this current study, we characterize the genes and pathways co-modulated in all cell types of the synovial tissue with the enzymes regulating glycan synthesis and processing, as well as glycosylation. Genes and biological and molecular pathways associated with hallmarks of aging were in mitochondria-dependent oxidative phosphorylation and reactive oxygen species synthesis, ER-dependent stress and unfolded protein response, DNA repair (UV response and P53 signaling pathways), and senescence, glycolysis and apoptosis regulation through PI3K-AKT-mTOR signaling have been shown to play important roles in aging or neurodegeneration (such as Parkinson's and Alzheimer's disease). We propose that the downregulation of TMEM230 and RNASET2 may represent a paradigm for the study of age-dependent autoimmune disorders due to their role in regulating glycosylation, unfolded protein response, and PI3K-AKT-mTOR signaling.

Effect of N-glycosylation on secretion, degradation and lipoprotein distribution of human serum amyloid A4

Serum amyloid A (SAA) is a family of apolipoproteins predominantly synthesized and secreted by the liver. Human SAA4 is constitutively expressed and contains an N-glycosylation site that is not present in other SAA subtypes. SAA4 proteins are not fully glycosylated, resulting in the presence of both glycosylated and non-glycosylated forms in human plasma. The efficiency of N-glycosylation in SAA4 is known to be influenced by some reasons such as genetic polymorphism and metabolic disorders. However, the specific role of N-glycosylation in SAA4 remains largely unexplored. This study aimed to investigate how N-glycosylation affects the secretion, degradation, and lipoprotein distribution of SAA4. Initially, we designed and constructed an SAA4 plasmid vector to compare with the expression pattern of endogenous SAA4. The exogenous SAA4 was partially N-glycosylated, analogous to endogenous SAA4 in human hepatocellular carcinoma cells. Subsequently, we created a non-glycosylated mutant by replacing asparagine 76 with glutamine. Immunoblotting assays showed that the disruption of N-glycans did not affect the secretion and degradation of SAA4. Furthermore, we analyzed the lipoprotein profiles of SAA4 in the conditioned medium derived from transfected cells. The results revealed that non-glycosylated mutant SAA4 exhibited a distinct lipoprotein distribution compared to wild-type SAA4. Our findings suggest that N-glycosylation may be a key regulator of the distribution of SAA4 in lipoproteins, shedding light on the previously unknown physiological activities of human SAA4.

Identification of interferon-stimulated response elements (ISREs) in canines

Interferon (IFN) responses are vital for antiviral defense, with interferon-stimulated response elements (ISREs) crucial for regulating IFN signaling. While ISREs are well-studied in humans and mice, research on canine ISREs is limited. This study aimed to clarify the role of canine ISREs and create a new method for detecting IFN activity. Canine IFN α (CaIFNα) was produced using the Pichia pastoris (P. pastoris) system, and an ISRE-based flow cytometry method was developed to measure its activity. ISREs for CaIFNα were predicted via bioinformatics analysis. Subsequently, viral suppression assays were conducted using vesicular stomatitis virus, canine influenza virus, and H9N2 to evaluate the antiviral activity of recombinant CaIFNα. Fluorescence analysis confirmed that CaIFNα activates ISRE2, ISRE8, and ISRE10, thereby enhancing the transcription and expression of the enhanced green fluorescent protein (EGFP) fusion gene. A novel ISRE and EGFP based flow cytometry method enabled precise quantification of CaIFNα levels through fluorescence cell counts, with a detection sensitivity reaching 0.1 × 10- 7 mg/mL. Results demonstrate that CaIFNα possesses multiple antiviral activity and activates specific ISREs, augmenting gene expression. This approach advances the study of canine ISREs and supports the development and clinical application of CaIFNα for diagnosing viral infections and monitoring treatment efficacy.

Decoding the Nature of the Peritrich Stalk: A Distinctive Organelle in a Large Group of Ciliated Unicellular Eukaryotes

Ciliates represent a diverse assemblage of ancient single-celled eukaryotes characterized by diverse morphological features. Among certain sessilid peritrich ciliates, an exceptional morphological structure known as the stalk has been documented since the pioneering work of Antonie van Leeuwenhoek in the 17th century. This study conducts a comparative genomic analysis of three sessile peritrich species-Epistylis sp., Vorticella campanula, and Zoothamnium arbuscula-and two free-swimming species, Tetrahymena thermophila and Paramecium tetraurelia, within the class Oligohymenophorea. We find that carbohydrate-related components are consistently associated with diverse stalk substructures. Evidence suggests that the branched stalks of colonial E. hentscheli are supported by chitin-based ring-like structures. Through proteomic analysis of the Epistylis stalk, we found peritrich-specific genes, including coiled-coil domain-containing (CCDC) proteins and epidermal growth factor-like (EGF-like) proteins, as key stalk components. CCDC proteins are part of the stalk sheath, and their N-glycosylation may enhance adhesion between the cell body and stalk through lectin interactions. This study sheds light on the genetic innovations behind the stalk in peritrichs, which support their sessile and colonial lifestyles, and identifies peritrich-specific CCDC proteins as potential targets for disrupting the attachment of sessilids to aquaculture animals, addressing issues related to epibiotic burden.

Defective glycosylation and ELFN1 binding of mGluR6 congenital stationary night blindness mutants

Synaptic transmission from photoreceptors to ON-bipolar cells (BCs) requires the postsynaptic metabotropic glutamate receptor mGluR6, located at BC dendritic tips. Binding of the neurotransmitter glutamate initiates G protein signaling that regulates the TRPM1 transduction channel. mGluR6 also interacts with presynaptic ELFN adhesion proteins, and these interactions are important for mGluR6 synaptic localization. The mechanisms of mGluR6 trafficking and synaptic targeting remain poorly understood. In this study, we investigated mGluR6 missense mutations from patients with congenital stationary night blindness (CSNB), which is associated with loss of synaptic transmission to ON-BCs. We found that multiple CSNB mutations in the extracellular ligand-binding domain of mGluR6 impart a trafficking defect leading to lack of complex N-glycosylation but efficient plasma membrane insertion, suggesting a Golgi bypass mechanism. These mutants fail to bind ELFN1, consistent with lack of a necessary modification normally acquired in the Golgi. The same mutants were mislocalized in bipolar cells, explaining the loss of function in CSNB. The results reveal a key role of Golgi trafficking in mGluR6 function, and suggest a role of the extracellular domain in Golgi sorting.

Pig jejunal single-cell RNA landscapes revealing breed-specific immunology differentiation at various domestication stages

Background

Domestication of wild boars into local and intensive pig breeds has driven adaptive genomic changes, resulting in significant phenotypic differences in intestinal immune function. The intestine relies on diverse immune cells, but their evolutionary changes during domestication remain poorly understood at single-cell resolution.

Methods

We performed single-cell RNA sequencing (scRNA-seq) and marker gene analysis on jejunal tissues from wild boars, a Chinese local breed (Jinhua), and an intensive breed (Duroc). Then, we developed an immune cell evaluation system that includes immune scoring, gene identification, and cell communication analysis. Additionally, we mapped domestication-related clustering relationships, highlighting changes in gene expression and immune function.

Results

We generated a single-cell atlas of jejunal tissues, analyzing 26,246 cells and identifying 11 distinct cell lineages, including epithelial and plasma cells, and discovered shared and unique patterns in intestinal nutrition and immunity across breeds. Immune cell evaluation analysis confirmed the conservation and heterogeneity of immune cells, manifested by highly conserved functions of immune cell subgroups, but wild boars possess stronger immune capabilities than domesticated breeds. We also discovered four patterns of domestication-related breed-specific genes related to metabolism, immune surveillance, and cytotoxic functions. Lastly, we identified a unique population of plasma cells with distinctive antibody production in Jinhua pig population.

Conclusions

Our findings provide valuable single-cell insights into the cellular heterogeneity and immune function evolution in the jejunum during pig at various domestication stages. The single-cell atlas also serves as a resource for comparative studies and supports breeding programs aimed at enhancing immune traits in pigs.

Chemical Synthesis Reveals Pathogenic Role of N-Glycosylation in Microtubule-Associated Protein Tau

Alzheimer's disease (AD) is a neurodegenerative disorder characterized by the accumulation of tau protein aggregates. In this study, we investigated the effects of N-glycosylation on tau, focusing on its impact on aggregation and phase behavior. We chemically prepared homogeneous glycoproteins with high-mannose glycans or a single N-acetylglucosamine at the confirmed glycosylation sites in K18 and 2N4R tau. Our findings reveal that N-glycosylation significantly alters biophysical properties and potentially cellular functions of tau. Small glycans promote tau aggregation and liquid-liquid phase separation (LLPS), while larger glycans reduce these effects. High mannose glycans at N410 enhance phosphorylation by GSK3β, suggesting a pathological role in AD. Functional assays demonstrate that N-glycosylation does not impact microtubule polymerization dynamics but modulates aggregation kinetics and morphology. This research underscores the importance of glycosylation in tau pathology and opens new avenues for therapeutic interventions targeting glycan processing.

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.

A comprehensive view of N-glycosylation as clinical biomarker in prostate cancer

Alterations in the prostate cancer (PCa) N-glycome have gained attention as a potential biomarker. This comprehensive review explores the diversity of N-glycosylation patterns observed in PCa-related cell lines, tissue, serum and urine, focusing on prostate-specific antigen (PSA) and the total pool of glycoproteins. Within the context of PCa, altered N-glycosylation patterns are a mechanism of immune escape and a disruption in normal glycoprotein distribution and trafficking. Glycoproteins with PCa-induced N-glycosylation patterns tend to accumulate in prostate tissue and the bloodstream, thereby diminishing N-glycan proportions in urine. Based on literary observations, aberrations in N-glycan branching are probably a characteristic of metabolic reprogramming and (chronic) inflammation. Changes in (core) fucosylation, specific N-glycosylation structures (such as N,N'-diacetyllactosamine) and high-mannose glycans otherwise are more likely indicators of cancer development and progression. Further investigation into these PCa-specific alterations holds promise in the discovery of new diagnostic, prognostic and response prediction biomarkers in PCa.

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.

Molecular Mechanisms Underlying the Loop-Closing Dynamics of β-1,4 Galactosyltransferase 1

The β-1,4 galactosylation catalyzed by β-1,4 galactosyltransferases (β4Gal-Ts) is not only closely associated with diverse physiological and pathological processes in humans but also widely applied in the N-glycan modification of protein glycoengineering. The loop-closing process of β4Gal-Ts is an essential intermediate step intervening in the binding events of donor substrate (UDP-Gal/Mn2+) and acceptor substrate during its catalytic cycle, with a significant impact on the galactosylation activities. However, the molecular mechanisms in regulating loop-closing dynamics are not entirely clear. Here, we construct Markov state models (MSMs) based on approximately 20 μs of all-atom molecular dynamics simulations to explore the loop-closing dynamics for β-1,4 galactosyltransferase 1 (β4Gal-T1). Our MSM reveals five key metastable states of β4Gal-T1 upon substrate binding, indicating that the entire conformational transition occurs on a time scale of ∼10 μs. Moreover, a regulatory mechanism involving six conserved residues (R187, H190, F222, W310, I341, and D346) among β4Gal-Ts is validated to account for the loop-closing dynamics of the C-loop and W-loop by site-directed mutagenesis and enzymatic activity assays, exhibiting high consistency with our computational predictions. Overall, our research proposes detailed atomic-level insight into the loop-closing dynamics of the C-loop and W-loop on β4Gal-T1, contributing to a deeper understanding of catalytic mechanisms of β-1,4 galactosylation.

Role of surface glycans in enveloped RNA virus infections: A structural perspective

Enveloped RNA viruses have been causative agents of major pandemic outbreaks in the recent past. Glycans present on these virus surface proteins are critical for multiple processes during the viral infection cycle. Presence of glycans serves as a key determinant of immunogenicity, but intrinsic heterogeneity, dynamics, and evolutionary shifting of glycans in heavily glycosylated enveloped viruses confounds typical structure-function analysis. Glycosylation sites are also conserved across different viral families, which further emphasizes their functional significance. In this review, we summarize findings regarding structure-function correlation of glycans on enveloped RNA virus proteins.

ALG13-Related Epilepsy: Current Insights and Future Research Directions

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

Quantification and Site-Specific Analysis of Co-occupied N- and O-Glycopeptides

Protein glycosylation is a complex post-translational modification that is generally classified as N- or O-linked. Site-specific analysis of glycopeptides is accomplished with a variety of fragmentation methods, depending on the type of glycosylation being investigated and the instrumentation available. For instance, collisional dissociation methods are frequently used for N-glycoproteomic analysis with the assumption that one N-sequon exists per tryptic peptide. Alternatively, electron-based methods are preferable for O-glycosite localization. However, the presence of simultaneously N- and O-glycosylated peptides could suggest the necessity of electron-based fragmentation methods for N-glycoproteomics, which is not commonly performed. Thus, we quantified the prevalence of N- and O-glycopeptides in mucins and other glycoproteins. A much higher frequency of co-occupancy within mucins was detected whereas only a negligible occurrence occurred within nonmucin glycoproteins. This was demonstrated from analyses of recombinant and/or purified proteins, as well as more complex samples. Where co-occupancy occurred, O-glycosites were frequently localized to the Ser/Thr within the N-sequon. Additionally, we found that O-glycans in close proximity to the occupied Asn were predominantly unelaborated core 1 structures, while those further away were more extended. Overall, we demonstrate electron-based methods are required for robust site-specific analysis of mucins, wherein co-occupancy is more prevalent. Conversely, collisional methods are generally sufficient for analyses of other types of glycoproteins.

Mechanistic study of SCOOPs recognition by MIK2-BAK1 complex reveals the role of N-glycans in plant ligand-receptor-coreceptor complex formation

Ligand-induced receptor and co-receptor heterodimerization is a common mechanism in receptor kinase (RK) signalling activation. SERINE-RICH ENDOGENOUS PEPTIDEs (SCOOPs) mediate the complex formation of Arabidopsis RK MIK2 and co-receptor BAK1, triggering immune responses. Through structural, biochemical and genetic analyses, we demonstrate that SCOOPs use their SxS motif and adjacent residues to bind MIK2 and the carboxy-terminal GGR residues to link MIK2 to BAK1. While N-glycosylation of plant RKs is typically associated with protein maturation, plasma membrane targeting and conformation maintenance, a surprising revelation emerges from our crystal structural analysis of MIK2-SCOOP-BAK1 complexes. Specific N-glycans on MIK2 directly interact with BAK1 upon SCOOP sensing. The absence of N-glycosylation at the specific site in MIK2 neither affects its subcellular localization and protein accumulation in plant cells nor alters its structural conformation, but markedly reduces its affinity for BAK1, abolishing SCOOP-triggered immune responses. This N-glycan-mediated receptor and co-receptor heterodimerization occurs in both Arabidopsis and Brassica napus. Our findings elucidate the molecular basis of SCOOP perception by the MIK2-BAK1 immune complex and underscore the crucial role of N-glycans in plant receptor-coreceptor interactions and signalling activation, shaping immune responses.

Research Note: Comprehensive proteomic, phosphoproteomic, and N-glycoproteomic analysis of chicken egg yolk plasma

Chicken egg yolk plasma (EYP), the supernatant fraction of egg yolk obtained by water dilution and centrifugation, is a rich source of various bioactive substances and a significant bearer of yolk-emulsifying properties. This study utilized proteomics to conduct a comprehensive and in-depth analysis of both common and modified EYP proteins (phosphorylated proteins and N-glycosylated proteins). Total of 208 proteins were identified in EYP, including 42 phosphorylated proteins with 137 phosphorylation sites and 150 N-glycoproteins with 332 N-glycosylation sites. Among the phosphorylation sites, tyrosine accounted for 80.6%, while the N-glycosylation sites predominantly featured "N-X-T" motifs, accounting for 58.7%. Functional enrichment analysis revealed that most proteins were involved in regulating enzyme activity and inhibition with a particular focus on modulating peptidase activity. Notably, vitellogenins-2 (30 phosphorylation sites, 9 N-glycosylation sites) and apolipoprotein B (10 phosphorylation sites, 56 N-glycosylation sites) were the 2 proteins with the most modification sites. Additionally, EYP was found to contain the highly N-glycosylated complement proteins C3 and C4. These findings provide new insights into the protein composition of EYP and its roles in chicken embryo development and immune defense, offering a theoretical foundation for the application of EYP in various fields.

Predicting psychiatric risk: IgG N-glycosylation traits as biomarkers for mental health

Background

Growing evidence suggests that chronic inflammation, resulting from intricate immune system interactions, significantly contributes to the onset of psychiatric disorders. Observational studies have identified a link between immunoglobulin G (IgG) N-glycosylation and various psychiatric conditions, but the causality of these associations remains unclear.

Methods

Genetic variants for IgG N-glycosylation traits and psychiatric disorders were obtained from published genome-wide association studies. The inverse-variance-weighted (IVW) method, MR-Egger, and weighted median were used to estimate causal effects. The Cochran's Q test, MR-Egger intercept test, leave-one-out analyses, and MR-PRESSO global test were used for sensitivity analyses.

Results

In the Psychiatric Genomics Consortium (PGC) database, genetically predicted IGP7 showed a protective role in schizophrenia (SCZ), major depressive disorder (MDD), and bipolar disorder (BIP), while elevated IGP34, and IGP57 increased SCZ risk. High levels of IGP21 were associated with an increased risk of post-traumatic stress disorder (PTSD), while elevated levels of IGP22 exhibited a causal association with a decreased risk of attention-deficit/hyperactivity disorder (ADHD). No causal relationship between IgG N-glycan traits and autism spectrum disorder (ASD) and no evidence of reverse causal associations was found.

Conclusion

Here, we demonstrate that IgG N-glycan traits have a causal relationship with psychiatric disorders, especially IGP7's protective role, offering new insights into their pathogenesis. Our findings suggest potential strategies for predicting and intervening in psychiatric disorder risk through IgG N-glycan traits.

Towards Understanding the Role of the Glycosylation of Proteins Present in Extracellular Vesicles in Urinary Tract Diseases: Contributions to Cancer and Beyond

Extracellular vesicles (EVs) are a population of nanoscale particles surrounded by a phospholipid bilayer, enabling intercellular transfer of bioactive molecules. Once released from the parental cell, EVs can be found in most biological fluids in the human body and can be isolated from them. For this reason, EVs have significant diagnostic potential and can serve as an excellent source of circulating disease biomarkers. Protein glycosylation plays a key role in many biological processes, and aberrant glycosylation is a hallmark of various diseases. EVs have been shown to carry multiple glycoproteins, but little is known about the specific biological roles of these glycoproteins in the context of EVs. Moreover, specific changes in EV glycosylation have been described for several diseases, including cancers and metabolic, cardiovascular, neurological or kidney diseases. Urine is the richest source of EVs, providing almost unlimited (in terms of volume) opportunities for non-invasive EV isolation. Recent studies have also revealed a pathological link between urinary EV glycosylation and urological cancers, as well as other pathologies of the urinary tract. In this review, we discuss recent research advances in this field and the diagnostic/prognostic potential of urinary EV glycosylation. In addition, we summarize common methods for isolating EVs from urine and techniques used to study their glycosylation.

N-glycosylation Modification Reveals Insights into the Oxidative Reactions of Liver in Wuzhishan Pigs

Although porcine liver contributes to their growth and development by nutrition production and energy supply, oxidative stress-induced hepatocyte damage is inevitable during metabolism. N-glycosylation is a common modification in oxidation; nevertheless, the effects of N-glycosylation on pig liver oxidative reactions remain undefined. In this study, liver proteins with N-glycosylation were detected in Wuzhishan (WZS) pigs between 4 and 8 months old and Large White (LW) pigs at 4 months old based on LC-MS/MS. The results showed that the number of differentially expressed proteins (DEPs) was larger between different pig cultivars than that between WZS pigs at various growth periods. The enriched pathways of DEPs were mainly related to oxidative reactions, and 10 proteins were finally selected that primarily consisted of CYPs, GSTs and HSPs with expressions significantly correlating to liver size and weight. The oxidative genes shared N-glycosylation-modified models of N-x-S and N-G. Five out of 10 proteins were upregulated in WZS pigs compared to LW pigs at 4 months old, while five proteins increased in WZS pigs from 4 to 8 months old. In conclusion, this research provides valuable information on the N-glycosylation motifs in liver oxidation genes of WZS pigs.

The Research Progress of Metformin Regulation of Metabolic Reprogramming in Malignant Tumors

BACKGROUND

Metabolism reprogramming is a crucial hallmark of malignant tumors. Tumor cells demonstrate enhanced metabolic efficiency, converting nutrient inputs into glucose, amino acids, and lipids essential for their malignant proliferation and progression. Metformin, a commonly prescribed medication for type 2 diabetes mellitus, has garnered attention for its potential anticancer effects beyond its established hypoglycemic benefits.

METHODS

This review adopts a comprehensive approach to delineate the mechanisms underlying metabolite abnormalities within the primary metabolic processes of malignant tumors.

RESULTS

This review examines the abnormal activation of G protein-coupled receptors (GPCRs) in these metabolic pathways, encompassing aerobic glycolysis with increased lactate production in glucose metabolism, heightened lipid synthesis and cholesterol accumulation in lipid metabolism, and glutamine activation alongside abnormal protein post-translational modifications in amino acid and protein metabolism. Furthermore, the intricate metabolic pathways and molecular mechanisms through which metformin exerts its anticancer effects are synthesized and analyzed, particularly its impacts on AMP-activated protein kinase activation and the mTOR pathway. The analysis reveals a multifaceted understanding of how metformin can modulate tumor metabolism, targeting key nodes in metabolic reprogramming essential for tumor growth and progression. The review compiles evidence that supports metformin's potential as an adjuvant therapy for malignant tumors, highlighting its capacity to interfere with critical metabolic pathways.

CONCLUSION

In conclusion, this review offers a comprehensive overview of the plausible mechanisms mediating metformin's influence on tumor metabolism, fostering a deeper comprehension of its anticancer mechanisms. By expanding the clinical horizons of metformin and providing insight into metabolism-targeted tumor therapies, this review lays the groundwork for future research endeavors aimed at refining and advancing metabolic intervention strategies for cancer treatment.

Rational design of novel peptide-based vaccine against the emerging OZ virus

Oz virus (OZV) belongs to the Orthomyxoviridae family which includes viruses with a negative-sense, single-stranded, and segmented RNA genome. OZV is a zoonotic pathogen, particularly since the virus can cause deadly illness when injected intracerebrally into nursing mice. OZV is an emerging pathogen with the potential to spark a pandemic as there is no preventive and licensed treatment against this virus. The goal of this study was to develop a novel multi-epitope vaccination against OZV proteins utilizing immunoinformatics and immunological simulation analysis. This work evaluated immunological epitopes (B cells, MHC-I, and MHC-II) to identify highly antigenic OZV target proteins. Shortlisted epitopes were joined together by using appropriate linkers and adjuvants to design multi-epitope vaccine constructs (MEVC). The vaccine models were designed, improved, validated, and the globular regions and post-translational modifications (PTMs) were also evaluated in the vaccine's structure. Molecular docking analysis with the Toll-like receptor (TLR4) showed strong interactions and appropriate binding energies. Molecular dynamics (MD) simulation confirmed stable interactions between the vaccines and TLR4. Bioinformatics tools helped optimize codons, resulting in successful cloning into appropriate host vectors. This study showed that the developed vaccines are stable and non-allergenic in the human body and successfully stimulated immunological responses against OZV. Finally, a mechanism of action for the designed vaccine construct was also proposed. Further experimental validations of the designed vaccine construct will pave the way to create a potentially effective vaccine against this emerging pathogen.

Alteration of N-glycosylation of CDON promotes H2O2-induced DNA damage in H9c2 cardiomyocytes

Protein glycosylation is involved in DNA damage. Recently, DNA damage has been connected with the pathogenesis of heart failure. Cell adhesion associated, oncogene regulated (CDON), considered as an N-linked glycoprotein, is a transmembrane receptor for modulating cardiac function. But the role of CDON and its glycosylation in DNA damage remains unknown. In this study, we found that the knockdown of CDON caused DNA double-strand breaks as indicated by an increase in phosphorylated histone H2AX (γH2AX) protein level, immunofluorescent intensity of γH2AX and tail DNA moment in H9c2 cardiomyocytes. Conversely, overexpression of CDON led to decreasing DNA damage induced by hydrogen peroxide (H2O2) and upregulating the expression of genes related to DNA repair pathways-homologous recombination (HR) and non-homologous end joining (NHEJ). Moreover, we expressed nine predicted N-glycosylation site mutants in H9c2 cells prior to treatment with H2O2. The results showed that mutation of N-glycosylation sites (N99Q, N179Q, and N870Q) increased the accumulation of DNA damage and downregulated the expression of HR-related genes, demonstrating that CDON N-glycosylation on DNA damage is site-specific and these specific N-glycan sites may regulate HR repair-related transcript abundance of genes. Our data highlight that N-glycosylation of CDON is critical to cardiomyocyte DNA lesion. It may uncover the potential strategies targeting DNA damage pathway in heart disease.

KCTD1 regulation of Adenylyl cyclase type 5 adjusts striatal cAMP signaling

Dopamine transfers information to striatal neurons, and disrupted neurotransmission leads to motor deficits observed in movement disorders. Striatal dopamine converges downstream to Adenylyl Cyclase Type 5 (AC5)-mediated synthesis of cAMP, indicating the essential role of signal transduction in motor physiology. However, the relationship between dopamine decoding and AC5 regulation is unknown. Here, we utilized an unbiased global protein stability screen to identify Potassium Channel Tetramerization Domain 1 (KCTD1) as a key regulator of AC5 level that is mechanistically tied to N-linked glycosylation. We then implemented a CRISPR/SaCas9 approach to eliminate KCTD1 in striatal neurons expressing a Förster resonance energy transfer (FRET)-based cAMP biosensor. 2-photon imaging of striatal neurons in intact circuits uncovered that dopaminergic signaling was substantially compromised in the absence of KCTD1. Finally, knockdown of KCTD1 in genetically defined dorsal striatal neurons significantly altered motor behavior in mice. These results reveal that KCTD1 acts as an essential modifier of dopaminergic signaling by stabilizing striatal AC5.

Integrating N -glycan and CODEX imaging reveal cell-specific protein glycosylation in healthy human lung

N -linked glycosylation, the major post-translational modification of cellular proteins, is important for proper lung functioning, serving to fold, traffic, and stabilize protein structures and to mediate various cell-cell recognition events. Identifying cell-specific N -glycan structures in human lungs is critical for understanding the chemistry and mechanisms that guide cell-cell and cell-matrix interactions and determining nuanced functions of specific N -glycosylation. Our study, which used matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) combined with co-detection by indexing (CODEX) to reveal the cellular origin of N -glycans, is a significant step in this direction. This innovative technological combination enabled us to detect and differentiate N -glycans located in the vicinity of cells surrounding airways and blood vessels, parenchyma, submucosal glands, cartilage, and smooth muscles. The potential impact of our findings on future research is immense. For instance, our algorithm for grouping N -glycans based on their functional chemical features, combined with identifying group niches, paves the way for targeted studies. We found that fucosylated N -glycans are dominant around immune cells, tetra antennary N -glycans in the cartilage, high-mannose N -glycans surrounding the bronchus originate from associated collagenous structures, complex fucosylated-tetra antennary-polylactosamine N -glycans are spread over smooth muscle structures and in epithelial cells surrounding arteries, and N -glycans with Hex:6 HexNAc:6 compositions, which, according to our algorithm, can be ascribed to either tetra antennary or bisecting N -glycan, are highly abundant in the parenchyma. The findings suggest cell or region-specific functions for these localized glycan structures.

De novo lipid synthesis and polarized prenylation drive cell invasion through basement membrane

To breach the basement membrane, cells in development and cancer use large, transient, specialized lipid-rich membrane protrusions. Using live imaging, endogenous protein tagging, and cell-specific RNAi during Caenorhabditis elegans anchor cell (AC) invasion, we demonstrate that the lipogenic SREBP transcription factor SBP-1 drives the expression of the fatty acid synthesis enzymes POD-2 and FASN-1 prior to invasion. We show that phospholipid-producing LPIN-1 and sphingomyelin synthase SMS-1, which use fatty acids as substrates, produce lysosome stores that build the AC's invasive protrusion, and that SMS-1 also promotes protrusion localization of the lipid raft partitioning ZMP-1 matrix metalloproteinase. Finally, we discover that HMG-CoA reductase HMGR-1, which generates isoprenoids for prenylation, localizes to the ER and enriches in peroxisomes at the AC invasive front, and that the final transmembrane prenylation enzyme, ICMT-1, localizes to endoplasmic reticulum exit sites that dynamically polarize to deliver prenylated GTPases for protrusion formation. Together, these results reveal a collaboration between lipogenesis and a polarized lipid prenylation system that drives invasive protrusion formation.

Valtrate Suppresses TNFSF14-Mediated Arrhythmia After Myocardial Ischemia-Reperfusion by Inducing N-linked Glycosylation of LTβR to Regulate MGA/MAX/c-Myc/Cx43

Myocardial ischemia-reperfusion (MIR)-induced arrhythmia remains a major cause of death in patients with cardiovascular diseases. The reduction of Cx43 has been known as a major inducer of arrhythmias after MIR, but the reason for the reduction of Cx43 remains largely unknown. The aim of this study was to find the key mechanism underlying the reduction of Cx43 after MIR and to screen out an herbal extract to attenuate arrhythmia after MIR. The differentially expressed genes in the peripheral blood mononuclear cell (PBMCs) after MIR were analyzed using the data from several gene expression omnibus data sets, followed by the identification in PBMCs and the serum of patients with myocardial infarction. Tumor necrosis factor superfamily protein 14 (TNFSF14) was increased in PBMCs and the serum of patients, which might be associated with the injury after MIR. The toxic effects of TNFSF14 on cardiomyocytes were investigated in vitro . Valtrate was screened out from several herbal extracts. Its protection against TNFSF14-induced injury was evaluated in cardiomyocytes and animal models with MIR. Recombinant TNFSF14 protein not only suppressed the viability of cardiomyocytes but also decreased Cx43 by stimulating the receptor LTβR. LTβR induces the competitive binding of MAX to MGA rather than the transcriptional factor c-Myc, thereby suppressing c-Myc-mediated transcription of Cx43. Valtrate promoted the N-linked glycosylation modification of LTβR, which reversed TNFSF14-induced reduction of Cx43 and attenuated arrhythmia after MIR. In all, valtrate suppresses TNFSF14-induced reduction of Cx43, thereby attenuating arrhythmia after MIR.

Clinical glycoproteomics: methods and diseases

Glycoproteins, representing a significant proportion of posttranslational products, play pivotal roles in various biological processes, such as signal transduction and immune response. Abnormal glycosylation may lead to structural and functional changes of glycoprotein, which is closely related to the occurrence and development of various diseases. Consequently, exploring protein glycosylation can shed light on the mechanisms behind disease manifestation and pave the way for innovative diagnostic and therapeutic strategies. Nonetheless, the study of clinical glycoproteomics is fraught with challenges due to the low abundance and intricate structures of glycosylation. Recent advancements in mass spectrometry-based clinical glycoproteomics have improved our ability to identify abnormal glycoproteins in clinical samples. In this review, we aim to provide a comprehensive overview of the foundational principles and recent advancements in clinical glycoproteomic methodologies and applications. Furthermore, we discussed the typical characteristics, underlying functions, and mechanisms of glycoproteins in various diseases, such as brain diseases, cardiovascular diseases, cancers, kidney diseases, and metabolic diseases. Additionally, we highlighted potential avenues for future development in clinical glycoproteomics. These insights provided in this review will enhance the comprehension of clinical glycoproteomic methods and diseases and promote the elucidation of pathogenesis and the discovery of novel diagnostic biomarkers and therapeutic targets.

The NADPH oxidases DUOX1 and DUOX2 are sorted to the apical plasma membrane in epithelial cells via their respective maturation factors DUOXA1 and DUOXA2

The membrane-integrated NADPH oxidases DUOX1 and DUOX2 are recruited to the apical plasma membrane in epithelial cells to release hydrogen peroxide, thereby playing crucial roles in various functions such as thyroid hormone synthesis and host defense. However, it has remained unknown about the molecular mechanism for apical sorting of DUOX1 and DUOX2. Here we show that DUOX1 and DUOX2 are correctly sorted to the apical membrane via the membrane-spanning DUOX maturation proteins DUOXA1 and DUOXA2, respectively, when co-expressed in MDCK epithelial cells. Impairment of N-glycosylation of DUOXA1 results in mistargeting of DUOX1 to the basolateral membrane. Similar to DUOX1 complexed with the glycosylation-defective DUOXA1, the naturally non-glycosylated oxidase NOX5, which forms a homo-oligomer, is targeted basolaterally. On the other hand, a mutant DUOXA2 deficient in N-glycosylation is less stable than the wild-type protein but still capable of recruiting DUOX2 to the apical membrane, whereas DUOX2 is missorted to the basolateral membrane when paired with DUOXA1. These findings indicate that DUOXA2 is crucial but its N-glycosylation is dispensable for DUOX2 apical recruitment; instead, its C-terminal region seems to be involved. Thus, apical sorting of DUOX1 and DUOX2 is likely regulated in a distinct manner by their respective partners DUOXA1 and DUOXA2.

Endometrial regeneration cell-derived exosomes loaded with siSLAMF6 inhibit cardiac allograft rejection through the suppression of desialylation modification

BACKGROUNDS

Acute transplant rejection is a major component of poor prognoses for organ transplantation. Owing to the multiple complex mechanisms involved, new treatments are still under exploration. Endometrial regenerative cells (ERCs) have been widely used in various refractory immune-related diseases, but the role of ERC-derived exosomes (ERC-Exos) in alleviating transplant rejection has not been extensively studied. Signaling lymphocyte activation molecule family 6 (SLAMF6) plays an important role in regulating immune responses. In this study, we explored the main mechanism by which ERC-Exos loaded with siSLAMF6 can alleviate allogeneic transplant rejection.

METHODS

C57BL/6 mouse recipients of BALB/c mouse kidney transplants were randomly divided into four groups and treated with exosomes. The graft pathology was evaluated by H&E staining. Splenic and transplanted heart immune cell populations were analyzed by flow cytometry. Recipient serum cytokine profiles were determined by enzyme-linked immunosorbent assay (ELISA). The proliferation and differentiation capacity of CD4+ T cell populations were evaluated in vitro. The α-2,6-sialylation levels in the CD4+ T cells were determined by SNA blotting.

RESULTS

In vivo, mice treated with ERC-siSLAMF6 Exo achieved significantly prolonged allograft survival. The serum cytokine profiles of the recipients were significantly altered in the ERC-siSLAMF6 Exo-treated recipients. In vitro, we found that ERC-siSLAMF6-Exo considerably downregulated α-2,6-sialyltransferase (ST6GAL1) expression in CD4+ T cells, and significantly reduced α-2,6-sialylation levels. Through desialylation, ERC-siSLAMF6 Exo therapy significantly decreased CD4+ T cell proliferation and inhibited CD4+ T cell differentiation into Th1 and Th17 cells while promoting regulatory T cell (Treg) differentiation.

CONCLUSIONS

Our study indicated that ERC-Exos loaded with siSLAMF6 reduce the amount of sialic acid connected to α-2,6 at the end of the N-glycan chain on the CD4+ T cell surface, increase the number of therapeutic exosomes endocytosed into CD4+ T cells, and inhibit the activation of T cell receptor signaling pathways, which prolongs allograft survival. This study confirms the feasibility of using ERC-Exos as natural carriers combined with gene therapy, which could be used as a potential therapeutic strategy to alleviate allograft rejection.

Insights into the role of glycosyltransferase in the targeted treatment of gastric cancer

Gastric cancer is a remarkably heterogeneous tumor. Despite some advances in the diagnosis and treatment of gastric cancer in recent years, the precise treatment and curative outcomes remain unsatisfactory. Poor prognosis continues to pose a major challenge in gastric cancer. Therefore, it is imperative to identify effective targets to improve the treatment and prognosis of gastric cancer patients. It should be noted that glycosylation, a novel form of posttranslational modification, is a process capable of regulating protein function and influencing cellular activities. Currently, numerous studies have shown that glycosylation plays vital roles in the occurrence and progression of gastric cancer. As crucial enzymes that regulate glycan synthesis in glycosylation processes, glycosyltransferases are potential targets for treating GC. Hence, investigating the regulation of glycosyltransferases and the expression of associated proteins in gastric cancer cells is highly important. In this review, the related glycosyltransferases and their related signaling pathways in gastric cancer, as well as the existing inhibitors of glycosyltransferases, provide more possibilities for targeted therapies for gastric cancer.

Glycosylation in aging and neurodegenerative diseases

Aging, a complex biological process, involves the progressive decline of physiological functions across various systems, leading to increased susceptibility to neurodegenerative diseases. In society, demographic aging imposes significant economic and social burdens due to these conditions. This review specifically examines the association of protein glycosylation with aging and neurodegenerative diseases. Glycosylation, a critical post-translational modification, influences numerous aspects of protein function that are pivotal in aging and the pathophysiology of diseases such as Alzheimer's disease, Parkinson's disease, and other neurodegenerative conditions. We highlight the alterations in glycosylation patterns observed during aging, their implications in the onset and progression of neurodegenerative diseases, and the potential of glycosylation profiles as biomarkers for early detection, prognosis, and monitoring of these age-associated conditions, and delve into the mechanisms of glycosylation. Furthermore, this review explores their role in regulating protein function and mediating critical biological interactions in these diseases. By examining the changes in glycosylation profiles associated with each part, this review underscores the potential of glycosylation research as a tool to enhance our understanding of aging and its related diseases.

Glycolytic PFKFB3 and Glycogenic UGP2 Axis Regulates Perfusion Recovery in Experimental Hind Limb Ischemia

BACKGROUND

Despite being in an oxygen-rich environment, endothelial cells (ECs) use anaerobic glycolysis (Warburg effect) as the primary metabolic pathway for cellular energy needs. PFKFB (6-phosphofructo-2-kinase/fructose-2,6-biphosphatase)-3 regulates a critical enzymatic checkpoint in glycolysis and has been shown to induce angiogenesis. This study builds on our efforts to determine the metabolic regulation of ischemic angiogenesis and perfusion recovery in the ischemic muscle.

METHODS

Hypoxia serum starvation (HSS) was used as an in vitro peripheral artery disease (PAD) model, and hind limb ischemia by femoral artery ligation and resection was used as a preclinical PAD model.

RESULTS

Despite increasing PFKFB3-dependent glycolysis, HSS significantly decreased the angiogenic capacity of ischemic ECs. Interestingly, inhibiting PFKFB3 significantly induced the angiogenic capacity of HSS-ECs. Since ischemia induced a significant in PFKFB3 levels in hind limb ischemia muscle versus nonischemic, we wanted to determine whether glucose bioavailability (rather than PFKFB3 expression) in the ischemic muscle is a limiting factor behind impaired angiogenesis. However, treating the ischemic muscle with intramuscular delivery of D-glucose or L-glucose (osmolar control) showed no significant differences in the perfusion recovery, indicating that glucose bioavailability is not a limiting factor to induce ischemic angiogenesis in experimental PAD. Unexpectedly, we found that shRNA-mediated PFKFB3 inhibition in the ischemic muscle resulted in an increased perfusion recovery and higher vascular density compared with control shRNA (consistent with the increased angiogenic capacity of PFKFB3 silenced HSS-ECs). Based on these data, we hypothesized that inhibiting HSS-induced PFKFB3 expression/levels in ischemic ECs activates alternative metabolic pathways that revascularize the ischemic muscle in experimental PAD. A comprehensive glucose metabolic gene qPCR arrays in PFKFB3 silenced HSS-ECs, and PFKFB3-knock-down ischemic muscle versus respective controls identified UGP2 (uridine diphosphate-glucose pyrophosphorylase 2), a regulator of protein glycosylation and glycogen synthesis, is induced upon PFKFB3 inhibition in vitro and in vivo. Antibody-mediated inhibition of UGP2 in the ischemic muscle significantly impaired perfusion recovery versus IgG control. Mechanistically, supplementing uridine diphosphate-glucose, a metabolite of UGP2 activity, significantly induced HSS-EC angiogenic capacity in vitro and enhanced perfusion recovery in vivo by increasing protein glycosylation (but not glycogen synthesis).

CONCLUSIONS

Our data present that inhibition of maladaptive PFKFB3-driven glycolysis in HSS-ECs is necessary to promote the UGP2-uridine diphosphate-glucose axis that enhances ischemic angiogenesis and perfusion recovery in experimental PAD.

Serum Calcification Propensity Is Increased in Myocardial Infarction and Hints at a Pathophysiological Role Independent of Classical Cardiovascular Risk Factors

BACKGROUND

Vascular calcification is associated with increased mortality in patients with cardiovascular disease. Secondary calciprotein particles are believed to play a causal role in the pathophysiology of vascular calcification. The maturation time (T50) of calciprotein particles provides a measure of serum calcification propensity. We compared T50 between patients with ST-segment-elevated myocardial infarction and control subjects and studied the association of T50 with cardiovascular risk factors and outcome.

METHODS

T50 was measured by nephelometry in 347 patients from the GIPS-III trial (Metabolic Modulation With Metformin to Reduce Heart Failure After Acute Myocardial Infarction: Glycometabolic Intervention as Adjunct to Primary Coronary Intervention in ST Elevation Myocardial Infarction: a Randomized Controlled Trial) and in 254 matched general population controls from PREVEND (Prevention of Renal and Vascular End-Stage Disease). We also assessed the association between T50 and left ventricular ejection fraction, as well as infarct size, the incidence of ischemia-driven reintervention during 5 years of follow-up, and serum nitrite as a marker of endothelial dysfunction.

RESULTS

Patients with ST-segment-elevated myocardial infarction had a significantly lower T50 (ie, higher serum calcification propensity) compared with controls (T50: 289±63 versus 338±56 minutes; P<0.001). In patients with ST-segment-elevated myocardial infarction, lower T50 was associated with female sex, lower systolic blood pressure, lower total cholesterol, lower LDL (low-density lipoprotein) cholesterol, lower triglycerides, and higher HDL (high-density lipoprotein) cholesterol but not with circulating nitrite or nitrate. Ischemia-driven reintervention was associated with higher LDL (P=0.03) and had a significant interaction term for T50 and sex (P=0.005), indicating a correlation between ischemia-driven reintervention and T50 above the median in men and below the median in women, between 150 days and 5 years of follow-up.

CONCLUSIONS

Serum calcification propensity is increased in patients with ST-segment-elevated myocardial infarction compared with the general population, and its contribution is more pronounced in women than in men. Its lack of/inverse association with nitrite and blood pressure confirms T50 to be orthogonal to traditional cardiovascular disease risk factors. Lower T50 was associated with a more favorable serum lipid profile, suggesting the involvement of divergent pathways of calcification stress and lipid stress in the pathophysiology of myocardial infarction.

TMEM9 activates Rab9-dependent alternative autophagy through interaction with Beclin1

Transmembrane protein 9 (TMEM9) is a transmembrane protein that regulates lysosomal acidification by interacting with the v-type ATPase complex. However, the role of TMEM9 in the lysosome-dependent autophagy machinery has yet to be identified. In this study, we demonstrate that the lysosomal protein TMEM9, which is involved in vesicle acidification, regulates Rab9-dependent alternative autophagy through its interaction with Beclin1. The cytosolic domain of TMEM9 interacts with Beclin1 via its Bcl-2-binding domain. This interaction between TMEM9 and Beclin1 dissociates Bcl-2, an autophagy-inhibiting partner, from Beclin1, thereby activating LC3-independent and Rab9-dependent alternative autophagy. Late endosomal and lysosomal TMEM9 apparently colocalizes with Rab9 but not with LC3. Furthermore, we show that multiple glycosylation of TMEM9, essential for lysosomal localization, is essential for its interaction with Beclin1 and the activation of Rab9-dependent alternative autophagy. These findings reveal that TMEM9 recruits and activates the Beclin1 complex at the site of Rab9-dependent autophagosome to induce alternative autophagy.