Sequential Analysis of the N/O-Glycosylation of Heavily Glycosylated HIV-1 gp120 Using EThcD-sceHCD-MS/MS

Deciphering N-Glycosylation Dynamics of Serum Monoclonal Immunoglobulins in Multiple Myeloma via EThcD-sceHCD-MS/MS

Serum glycoprotein glycosylation changes can indicate disease onset and progression. However, the site-specific N-glycosylation of monoclonal immunoglobulins (M-proteins) in multiple myeloma (MM) and its clinical implications are unclear. In this study, we isolated pathogenic micromonoclonal IgA or IgG (approximately 2 μg) from IgA-MM patients (n = 22) and IgG-MM patients (n = 30), and normal polyclonal IgA and IgG from healthy controls (HCs) (n = 16). Using EThcD-sceHCD-MS/MS, the N-glycosylation dynamics of serum M-proteins in MM were determined. Compared with polyclonal IgA1 from HCs, monoclonal IgA1 from IgA-MM patients had higher fucosylation (58.1% vs 32.1%, p < 0.001), sialylation (68.0% vs 50.8%, p = 0.011), and mannosylation (1.5% vs 0.3%, p < 0.001). While, monoclonal IgG1 from IgG-MM patients had higher fucosylation (97.8% vs 95.3%, p < 0.001). In addition, specific N-glycan abundances correlated with MM clinical features: for IgA1, HexNAc5Hex5Fuc1NeuAc1 was associated with hypocomplementemia; for IgG1, HexNAc4Hex3Fuc1 was associated with the serum albumin level (r = -0.363, p = 0.049) and estimated glomerular filtration rate (r = -0.433, p = 0.017); and HexNAc4Hex5 was associated with therapeutic prognosis. In conclusion, monoclonal IgA1 and IgG1 in MM patients and their polyclonal isotypes in HCs have distinct N-glycosylation profiles, and specific N-glycans of M-proteins are associated with MM characteristics and therapeutic prognosis.

Glycation-mediated pea protein isolate-curcumin conjugates for uniform walnut oil dispersion: enhancing oxidative stability and shelf life

BACKGROUND

Traditional methods for fabricating protein-polyphenol conjugates have not preserved the structural and functional integrity essential for the food industry effectively. This research introduces an advanced encapsulation methodology designed to overcome these limitations, with the potential to enhance the stability of edible oil matrices significantly, leading to improved preservation techniques and extended shelf life.

RESULTS

Glycated pea protein isolate-curcumin conjugates (gPPI-CUR) were developed, demonstrating a marked improvement in the oxidative stability of walnut oil (WO), a proxy for edible oil matrices. Characterized by a Z-average diameter of 158.37 nm and an encapsulation efficiency of 80.94%, these conjugates demonstrated exceptional performance in reducing lipid oxidation and aldehyde formation. Molecular docking analysis confirmed the formation of robust bonds with curcumin, thereby amplifying antioxidant activity. The uniform distribution of gPPI-CUR throughout the walnut oil matrix, as validated by confocal microscopy, ensured sustained bioactivity and mitigated the risk of localized oxidation. Electron spin resonance spectroscopy corroborated the superior antioxidant properties of the conjugates, which translated into a substantial 19-day increase in the shelf-life of the oil.

CONCLUSION

The gPPI-CUR conjugates enhanced the oxidative stability of walnut oil significantly, as demonstrated by the increased shelf life and reduced lipid oxidation. This study introduced an effective encapsulation method that improved the stability and extended the shelf life of edible oils, aligning with consumer demands for high-nutrition food products. The results indicate that the gPPI-CUR conjugates could serve as a promising antioxidant strategy for food preservation, offering a practical approach to enhance food quality and safety. © 2025 Society of Chemical Industry.

Quantitative N-glycoproteomic analysis reveals glycosylation signatures of plasma immunoglobulin G in systemic sclerosis

Systemic sclerosis (SSc) is a perplexing autoimmune disorder, characterized by mysterious causes, high mortality rates, and a lack of effective treatments. The role of abnormal glycosylation in the onset of autoimmune diseases has been recognized for some time. Nonetheless, the intricate details of intact glycopeptides in SSc remain elusive owing to challenges in their detection. In this study, we characterized plasma immunoglobulin G (IgG) intact N-glycopeptides from 30 SSc patients and 30 healthy controls (HCs) via our recently developed intact glycopeptide analysis method GlycoQuant. Through this approach, twelve differentially expressed intact N-glycopeptides were identified. The correlation of specific intact N-glycopeptides with the clinical features of SSc patients was analyzed. The results revealed a notable increase in the levels of 6 intact N-glycopeptides (IgG2-N3H3F1, IgG2-N3H4F1, IgG2-N4H4F1, IgG2-N4H5F1, IgG2-N5H4F1, and IgG2-N5H5F1) and a decrease in the levels of another set of 6 intact N-glycopeptides (IgG1-N4H3F1, IgG2-N3H6F1A1, IgG2-N4H4F1A1, IgG2-N5H3F1, IgG3-N4H3F1, and IgG3-N4H4F1). These changes in the levels of intact N-glycopeptides are associated with various aspects of SSc, including diffuse SSc (dSSc), interstitial lung disease (ILD), disease progression, cardiovascular involvement and C-reactive protein in the peripheral blood. In summary, this study offers a detailed overview of the intact N-glycopeptide profile in the peripheral blood of patients with SSc, providing valuable insights that could propel further research into SSc.

GlycoPCT: Pressure Cycling Technology-Based Quantitative Glycoproteomics Reveals Distinctive N-Glycosylation in Human Liver Biopsy Samples of Nonalcoholic Fatty Liver Disease

Protein N-glycosylation is vital in the human liver and influences functions such as lipid metabolism, apoptosis, and inflammation. However, site-specific N-glycosylation patterns and variations in liver biopsy samples between healthy individuals and those with nonalcoholic fatty liver disease (NAFLD) remain incompletely characterized, primarily due to the limitations of current clinical glycoproteomic methods, including a large demand for clinical samples, low efficiency of tissue protein extraction, and a low recovery rate of intact N-glycopeptides (IGPs). To address this issue, we developed GlycoPCT, a quantitative glycoproteomic method based on pressure cycling technology. It enables efficient recovery of IGPs and accurate analysis of trace liver biopsy samples. Our research revealed a total of 4,459 unique IGPs and 361 glycans from 758 glycoproteins. High-mannose type, complex type, fucosylation type, and sialylation type N-glycans were significantly upregulated in the NAFLD group (p < 0.001, t test). Notably, we also identified 182 upregulated IGPs from 67 proteins (p < 0.05, FC > 1.50) and 108 downregulated IGPs from 44 proteins (p < 0.05, FC < 0.67) in the NAFLD group. Furthermore, we highlighted an essential acute phase glycoprotein, alpha-1-acid glycoprotein 1 (A1TA), which is synthesized in the liver and plays a significant role in NAFLD progression. These novel glyco-signatures provide crucial clues for the diagnosis and pathogenesis of NAFLD.

Quantitative site-specific N-glycosylation analysis reveals IgG glyco-signatures for pancreatic cancer diagnosis

BACKGROUND

Pancreatic cancer is a highly aggressive tumor with a poor prognosis due to a low early detection rate and a lack of biomarkers. Most of pancreatic cancer is pancreatic ductal adenocarcinoma (PDAC). Alterations in the N-glycosylation of plasma immunoglobulin G (IgG) have been shown to be closely associated with the onset and development of several cancers and could be used as biomarkers for diagnosis. The study aimed to explore intact N-glycosylation profile of IgG in patients with PDAC and find relation between intact N-glycosylation profile of IgG and clinical information such as diagnosis and prognosis.

METHODS

In this study, we employed a well-evaluated approach (termed GlycoQuant) to assess the site-specific N-glycosylation profile of human plasma IgG in both healthy individuals and patients with pancreatic ductal adenocarcinoma (PDAC). The datasets generated and analyzed during the current study are available in the ProteomeXchange Consortium ( http://www.proteomexchange.org/ ) via the iProX partner repository, with the dataset identifier PXD051436.

RESULTS

The analysis of rapidly purified IgG samples from 100 patients with different stages of PDAC, in addition to 30 healthy controls, revealed that the combination of carbohydrate antigen 19 - 9 (CA19-9), IgG1-GP05 (IgG1-TKPREEQYNSTYR-HexNAc [4]Hex [5]Fuc [1]NeuAc [1]), and IgG4-GP04 (IgG4-EEQFNSTYR- HexNAc [4]Hex [5]Fuc [1]NeuAc [1]) can be used to distinguish between PDAC patients and healthy individuals (AUC = 0.988). In addition, cross validation of the diagnosis model showed satisfactory result.

CONCLUSIONS

The study demonstrated that the integrated quantitative method can be utilized for large-scale clinical N-glycosylation research to identify novel N-glycosylated biomarkers. This could facilitate the development of clinical glycoproteomics.

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.

A Novel Integrated Pipeline for Site-Specific Quantification of N-glycosylation

The site-specific N-glycosylation changes of human plasma immunoglobulin gamma molecules (IgGs) have been shown to modulate the immune response and could serve as potential biomarkers for the accurate diagnosis of various diseases. However, quantifying intact N-glycopeptides accurately in large-scale clinical samples remains a challenge, and the quantitative N-glycosylation of plasma IgGs in patients with chronic kidney diseases (CKDs) has not yet been studied. In this study, we present a novel integrated intact N-glycopeptide quantitative pipeline (termed GlycoQuant), which combines our recently developed mass spectrometry fragmentation method (EThcD-sceHCD) and an intact N-glycopeptide batch quantification software tool (the upgraded PANDA v.1.2.5). We purified and digested human plasma IgGs from 58 healthy controls (HCs), 48 patients with membranous nephropathy (MN), and 35 patients with IgA nephropathy (IgAN) within an hour. Then, we analyzed the digested peptides without enrichment using EThcD-sceHCD-MS/MS, which provided higher spectral quality and greater identified depth. Using upgraded PANDA, we performed site-specific N-glycosylation quantification of IgGs. Several quantified intact N-glycopeptides not only distinguished CKDs from HCs, but also different types of CKD (MN and IgAN) and may serve as accurate diagnostic tools for renal tubular function. In addition, we proved the applicability of this pipeline to complex samples by reanalyzing the intact N-glycopeptides from cell, urine, plasma, and tissue samples that we had previously identified. We believe that this pipeline can be applied to large-scale clinical N-glycoproteomic studies, facilitating the discovery of novel glycosylated biomarkers.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s43657-023-00150-w.

O-glycosylation in viruses: A sweet tango

O-glycosylation is an ancient yet underappreciated protein posttranslational modification, on which many bacteria and viruses heavily rely to perform critical biological functions involved in numerous infectious diseases or even cancer. But due to the innate complexity of O-glycosylation, research techniques have been limited to study its exact role in viral attachment and entry, assembly and exit, spreading in the host cells, and the innate and adaptive immunity of the host. Recently, the advent of many newly developed methodologies (e.g., mass spectrometry, chemical biology tools, and molecular dynamics simulations) has renewed and rekindled the interest in viral-related O-glycosylation in both viral proteins and host cells, which is further fueled by the COVID-19 pandemic. In this review, we summarize recent advances in viral-related O-glycosylation, with a particular emphasis on the mucin-type O-linked α-N-acetylgalactosamine (O-GalNAc) on viral proteins and the intracellular O-linked β-N-acetylglucosamine (O-GlcNAc) modifications on host proteins. We hope to provide valuable insights into the development of antiviral reagents or vaccines for better prevention or treatment of infectious diseases.

GlycoTCFM: Glycoproteomics Based on Two Complementary Fragmentation Methods Reveals Distinctive O-Glycosylation in Human Sperm and Seminal Plasma

Human semen, consisting of spermatozoa (sperm) and seminal plasma, represents a special clinical sample type in human body fluid. Protein glycosylation in sperm and seminal plasma plays key roles in spermatogenesis, maturation, capacitation, sperm-egg recognition, motility of sperm, and fertilization. In this study, we profiled the most comprehensive O-glycoproteome map of human sperm and seminal plasma using our recently presented Glycoproteomics based on Two Complementary Fragmentation Methods (GlycoTCFM). We showed that sperm and seminal plasma contain many novel and distinctive O-glycoproteins, which are mostly located in the extracellular region (seminal plasma) and sperm membrane, enriched in the biological processes of cell adhesion and angiogenesis, and mainly involved in multiple biological functions including extracellular matrix structural constituents and binding. Based on GlycoTCFM, we created a comprehensive human sperm and seminal plasma O-glycoprotein database that contains 371 intact O-glycopeptides and 202 O-glycosites from 68 O-glycoproteins. Interestingly, 105 manually confirmed O-glycosites from 25 O-glycoproteins were reported for the first time, and they were mainly modified by core 1 O-glycans. We also found that three highly abundant, highly complex, and highly O-glycosylated proteins (semenogelin-1, semenogelin-2, and equatorin) may play important roles in sperm or seminal plasma composition and function. These data deepen our knowledge about O-glycosylation in sperm and seminal plasma and lay the foundation for the functional study of O-glycoproteins in male infertility.

Protein O-glycosylation regulates diverse developmental and defense processes in plants

Post-translational modifications affect protein functions and play key roles in controlling biological processes. Plants have unique types of O-glycosylation that are different from those of animals and prokaryotes, and they play roles in modulating the functions of secretory proteins and nucleocytoplasmic proteins by regulating transcription and mediating localization and degradation. O-glycosylation is complex because of the dozens of different O-glycan types, the widespread existence of hydroxyproline (Hyp), serine (Ser), and threonine (Thr) residues in proteins attached by O-glycans, and the variable modes of linkages connecting the sugars. O-glycosylation specifically affects development and environmental acclimatization by affecting diverse physiological processes. This review describes recent studies on the detection and functioning of protein O-glycosylation in plants, and provides a framework for the O-glycosylation network that underlies plant development and resistance.

Characterization of site-specific N-glycosylation signatures of isolated uromodulin from human urine

Uromodulin (Umod, Tamm-Horsfall protein) is the most abundant urinary N-glycoprotein produced exclusively by the kidney. It can form filaments to antagonize the adhesion of uropathogens. However, the site-specific N-glycosylation signatures of Umod in healthy individuals and patients with IgA nephropathy (IgAN) remain poorly understood due to the lack of suitable isolation and analytical methods. In this study, we first presented a simple and fast method based on diatomaceous earth adsorption to isolate Umod. These isolated glycoproteins were digested by trypsin and/or Glu-C. Intact N-glycopeptides with or without HILIC enrichment were analyzed using our developed EThcD-sceHCD-MS/MS. Based on the optimized workflow, we identified a total of 780 unique intact N-glycopeptides (7 N-glycosites and 152 N-glycan compositions) from healthy individuals. As anticipated, these glycosites exhibited glycoform heterogeneity. Almost all N-glycosites were modified completely by the complex type, except for one N-glycosite (N275), which was nearly entirely occupied by the high-mannose type for mediating Umod's antiadhesive activity. Then, we compared the N-glycosylation of Umod between healthy controls (n = 9) and IgAN patients (n = 9). The N-glycosylation of Umod in IgAN patients will drastically decrease and be lost. Finally, we profiled the most comprehensive site-specific N-glycosylation map of Umod and revealed its alterations in IgAN patients. Our method provides a high-throughput workflow for characterizing the N-glycosylation of Umod, which can aid in understanding its roles in physiology and pathology, as well as serving as a potential diagnostic tool for evolution of renal tubular function.

Variations in O-Glycosylation Patterns Influence Viral Pathogenicity, Infectivity, and Transmissibility in SARS-CoV-2 Variants

The highly glycosylated S protein plays a vital role in host cell invasion, making it the principal target for vaccine development. Differences in mutations observed on the spike (S) protein of SARS-CoV-2 variants may result in distinct glycosylation patterns, thus influencing immunological evasion, infectivity, and transmissibility. The glycans can mask key epitopes on the S1 protein and alter its structural conformation, allowing the virus to escape the immune system. Therefore, we comprehensively characterize O-glycosylation in eleven variants of SARS-CoV-2 S1 subunits to understand the differences observed in the biology of the variants. In-depth characterization was performed with a double digestion strategy and an efficient LC-MS/MS approach. We observed that O-glycosylation is highly conserved across all variants in the region between the NTD and RBD, whereas other domains and regions exhibit variation in O-glycosylation. Notably, omicron has the highest number of O-glycosylation sites on the S1 subunit. Also, omicron has the highest level of sialylation in the RBD and RBM functional motifs. Our findings may shed light on how differences in O-glycosylation impact viral pathogenicity in variants of SARS-CoV-2 and facilitate the development of a robust vaccine with high protective efficacy against the variants of concern.

Site-specific N-glycosylation characterization of micro monoclonal immunoglobulins based on EThcD-sceHCD-MS/MS

Monoclonal immunoglobulin produced by clonal plasma cells is the main cause in multiple myeloma and monoclonal gammopathy of renal significance. Because of the complicated purification method and the low stoichiometry of purified protein and glycans, site-specific N-glycosylation characterization for monoclonal immunoglobulin is still challenging. To profile the site-specific N-glycosylation of monoclonal immunoglobulins is of great interest. Therefore, in this study, we presented an integrated workflow for micro monoclonal IgA and IgG purification from patients with multiple myeloma in the HYDRASYS system, in-agarose-gel digestion, LC-MS/MS analysis without intact N-glycopeptide enrichment, and compared the identification performance of different mass spectrometry dissociation methods (EThcD-sceHCD, sceHCD, EThcD and sceHCD-pd-ETD). The results showed that EThcD-sceHCD was a better choice for site-specific N-glycosylation characterization of micro in-agarose-gel immunoglobulins (~2 μg) because it can cover more unique intact N-glycopeptides (37 and 50 intact N-glycopeptides from IgA1 and IgG2, respectively) and provide more high-quality spectra than sceHCD, EThcD and sceHCD-pd-ETD. We demonstrated the benefits of the alternative strategy in site-specific N-glycosylation characterizing micro monoclonal immunoglobulins obtained from bands separated by electrophoresis. This work could promote the development of clinical N-glycoproteomics and related immunology.

Comprehensive Plasma N-Glycoproteome Profiling Based on EThcD-sceHCD-MS/MS

Glycoproteins are involved in a variety of biological processes. More than one-third of the plasma protein biomarkers of tumors approved by the FDA are glycoproteins, and could improve the diagnostic specificity and/or sensitivity. Therefore, it is of great significance to perform the systematic characterization of plasma N-glycoproteome. In previous studies, we developed an integrated method based on the combinatorial peptide ligand library (CPLL) and stepped collision energy/higher energy collisional dissociation (sceHCD) for comprehensive plasma N-glycoproteome profiling. Recently, we presented a new fragmentation method, EThcD-sceHCD, which outperformed sceHCD in the accuracy of identification. Herein, we integrated the combinatorial peptide ligand library (CPLL) into EThcD-sceHCD and compared the performance of different mass spectrometry dissociation methods (EThcD-sceHCD, EThcD, and sceHCD) in the intact N-glycopeptide analysis of prostate cancer plasma. The results illustrated that EThcD-sceHCD was better than EThcD and sceHCD in the number of identified intact N-glycopeptides (two-folds). A combination of sceHCD and EThcD-sceHCD methods can cover almost all glycoproteins (96.4%) and intact N-glycopeptides (93.6%), indicating good complementarity between the two. Our study has great potential for medium- and low-abundance plasma glycoprotein biomarker discovery.

Comparative N-Glycoproteomics Analysis of Clinical Samples Via Different Mass Spectrometry Dissociation Methods

Site-specific N-glycosylation characterization requires intact N-glycopeptide analysis based on suitable tandem mass spectrometry (MS/MS) method. Electron-transfer/higher-energy collisional dissociation (EThcD), stepped collision energy/higher-energy collisional dissociation (sceHCD), higher-energy collisional dissociation-product-dependent electron-transfer dissociation (HCD-pd-ETD), and a hybrid mass spectrometry fragmentation method EThcD-sceHCD have emerged as valuable approaches for glycoprotein analysis. However, each of them incurs some compromise, necessitating the systematic performance comparisons when applied to the analysis of complex clinical samples (e.g., plasma, urine, cells, and tissues). Herein, we compared the performance of EThcD-sceHCD with those previous approaches (EThcD, sceHCD, HCD-pd-ETD, and sceHCD-pd-ETD) in the intact N-glycopeptide analysis, and determined its applicability for clinical N-glycoproteomic study. The intact N-glycopeptides of distinct samples, namely, plasma from prostate cancer (PCa) patients, urine from immunoglobulin A nephropathy (IgAN) patients, human hepatocarcinoma cell line (HepG2), and thyroid tissues from thyroid cancer (TC) patients were analyzed by these methods. We found that EThcD-sceHCD outperformed other methods in the balance of depth and accuracy of intact N-glycopeptide identification, and sceHCD and EThcD-sceHCD have good complementarity. EThcD-sceHCD holds great potential for biomarker discovery from clinical samples.