LC-MS/MS Analysis of the glycosylation of human SIDT1 and SIDT2
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo Sapiens
SUBMITTER: 
Fuquan Yang
PROVIDER: PXD043824 | iProX | Mon Jul 17 00:00:00 BST 2023
REPOSITORIES: iProX
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Project description:Microglia are the immune cells in the central nervous system (CNS) and become pro-inflammatory/activated in Alzheimer’s disease (AD). Cell surface glycosylation plays an important role in immune cells, however, the N-glycosylation and glycosphingolipid (GSL) signatures of activated microglia are poorly understood. Here, we study comprehensive combined transcriptomic and glycomic profiles using human induced pluripotent stem cells-derived microglia (hiMG). Distinct changes in N-glycosylation patterns in Aβ oligomer (AβO) and LPS -treated hiMG were observed. In AβO treated cells, the relative abundance of bisecting N-acetylglucosamine (GlcNAc) N-glycans decreased, corresponding with a downregulation of MGAT3, the gene responsible for bisecting GlcNAc N-glycan formation. The sialylation of N-glycans increased in response to AβO, accompanied by an upregulation of genes involved in N-glycan sialylation (ST3GAL2, 4, and 6). Moreover, we found that the N-glycosylation signature of LPS-induced hiMG differed from that of AβO-induced hiMG. LPS-induced hiMG exhibited a decreased abundance of complex-type N-glycans, aligned with downregulation of mannosidase genes (MAN1A1, MAN2A2, MAN1C1). Fucosylation increased in LPS-induced hiMG, aligned with upregulated fucosyltransferase 4 (FUT4) and downregulated alpha-L-fucosidase 1 (FUCA1) gene expression. However, the GSL profile did not exhibit significant changes in response to AβO or LPS activation. AβO- and LPS- specific glycosylation changes could contribute to impaired microglia function, highlighting glycosylation pathways as potential therapeutic targets for AD.
2025-04-17 | GSE277259 | GEO
Project description: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. Studies reporting the N-glycosylation profiles for this monoclonal immunoglobulin have been rare until now. Therefore, in this study, we presented an integrated workflow for micro serum 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 immunoglobulin proteins (~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 disease-related proteins obtained from bands separated by electrophoresis. This work could promote the development of clinical N-glycoproteomics and related immunology.
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Project description:Alpha-1-acid glycoprotein (AGP) is an acute phase glycoprotein in blood, which is primarily synthetized in the liver and whose biological role is not completely understood. It consists 45% of carbohydrates attached in the form of five N-linked complex glycans. AGP N-glycosylation was shown to be changed in many different diseases and some changes appear to be disease-specific, thus it has a great diagnostic and prognostic potential. However, AGP glycosylation was mainly analyzed in small cohorts and without detailed site-specific glycan information. Here, we developed a cost-effective method for a high-throughput and site-specific N-glycosylation LC-MS analysis of AGP which can be applied on large cohorts, aid in search for novel disease biomarkers and enable better understanding of AGP’s role and function in health and disease.
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Project description:Glycosylation is central to the localization and function of biomolecules1. We recently discovered that small RNAs undergo N-glycosylation2 at the modified RNA base 3-(3-amino-3-carboxypropyl) uridine (acp3U)3. However, the functional significance of N-glycosylation of RNAs is unknown. Here we show that the N-glycans on glycoRNAs prevent innate immune sensing of endogenous small RNAs. We found that de-N-glycosylation of cell culture-derived and circulating human and mouse glycoRNA elicited potent inflammatory responses including the production of type I interferons in a TLR3- and TLR7-dependent manner. Further, we show that N-glycans of cell surface RNAs prevent apoptotic cells from triggering endosomal RNA sensors in efferocytes, thus facilitating the non-inflammatory clearance of dead cells. Mechanistically, N-glycans conceal the hypermodified uracil base acp3U, which we identified as immunostimulatory when exposed in RNA. Consistent with this, genetic deletion of an enzyme (DTWD2) that synthesizes acp3U abrogated innate immune activation by de-N-glycosylated of small RNAs and apoptotic cells. Additionally, synthetic acp3U-containing RNAs are sufficient to trigger innate immune responses. Thus, our study has uncovered a natural mechanism by which N-glycans block RNAs from inducing acp3U-driven innate immune activation, demonstrating how glycoRNAs exist on the cell surface and in the endosomal network without inducing autoinflammatory responses.
2025-08-11 | GSE291767 | GEO
Project description:Protein glycosylation plays essential roles in regulating innate and adaptive immune response. Previous studies have typically focused on individual protein-glycan interaction or specific glycoform changes associated with T cell activation, yet a systematic characterization of protein glycosylation alterations remains insufficiently elucidated. To address these limitations, we conducted temporally-resolved quantitative multi-proteomic analysis on activated Jurkat T cells. Through an integrative analysis of glycoforms, site-specific glycans, glycoproteins, and glycosylation enzymes, we portrayed the dynamic landscape of protein glycosylation during Jurkat T cell activation. We found the heterogeneity and number of significantly up-regulated intact glycopeptides increased along with stimulation time. For most glycopeptides, their alteration patterns did not correlate well with the abundance of their glycoprotein substrates. Comparative analysis of global peptides, glycopeptides, and phosphopeptides revealed their distinctive changing patterns along Jurkat T cell activation, and only glycosylation demonstrated a steady increase trend with a large proportion of up-regulated glycopeptides. Collectively, this integrated multi-proteomics characterization of activated Jurkat T cells provided insights for the crucial role of glycosylation in modulating immune response, and would aid the development of novel therapeutic strategy targeting glycosylation.
2025-11-30 | PXD058431 | JPOST Repository
Project description:Our lab has previously used the Glyco v3 gene-chip to analyze RNA from human macrophages and T-cells, as part of a project examining the effect of cellular origin on the viral infectivity of HIV/SIV. Our experiments have led us to hypothesize that the different glycosylation pathways present in macrophages and T-cells result in the production of virions with differently glycosylated viral proteins and different glycans present on the virion surface. Furthermore, studies with glycosidases using the Glyco v3 gene-chip have indicated that these differences in the glycosylation profiles of virions derived from different cell types may influence viral infectivity. Here we used glyco v3 chips for identifying the enzymes active in the glycosylation pathways of 174xCEM and 293 cells, which are cell types commonly used in HIV and SIV research. These analyses will allow us a better understanding of the role of glycans and glycosylation in cell-type specific effects on viral infectivity because there is a much larger amount of data on virus derived from these cell types and we will be able to relate our studies more directly to previous work in our lab and other labs. RNA from 174xCEM and HEK293 cells, cell types commonly used in HIV and SIV research, was isolated and sent to Microarray Core (E). RNA was prepared in duplicate, totaling 4 samples. Samples were labeled and hybridized to the GLYCOv3 array and gene expression patterns were used to identify enzymes active in glycosylation pathways.
2011-06-14 | E-GEOD-29924 | biostudies-arrayexpress
Project description:The characterization of therapeutic glycoproteins is challenging due to the structural micro- and macro-heterogeneity of the protein glycosylation. This study presents an in-depth strategy for glycosylation analysis using first-generation erythropoietin (epoetin beta), including a developed top-down mass spectrometric workflow for N-glycan analysis, bottom-up mass spectrometric methods for site-specific N-glycosylation and a LC-MS approach for O-glycan identi-fication. Permethylated N-glycans, peptides and enriched glycopeptides of erythropoietin were analyzed by nanoLC-MS/MS and de-N-glycosylated erythropoietin was measured by LC-MS, enabling the qualitative and quantitative analysis of glycosylation and different glycan modifications (e.g., phosphorylation and O-acetylation). Extending the coverage of our newly developed Python script to phosphorylated N-glycans enabled the identification of 140 N-glycan compositions (237 N-glycan structures) from erythropoietin. The site-specificity of N-glycans was revealed at glycopeptide level by pGlyco software using different proteases. In total, 215 N-glycan compositions were identified from N-glycan and glycopeptide analysis. Moreover, LC-MS analysis of de-N-glycosylated erythropoietin species identified two different O-glycan compositions, based on the mass shifts between non-O-glycosylated and O-glycosylated species. This integrated strategy allows the in-depth glycosylation analysis of a therapeutic glycoprotein to understand its pharmacological properties and improving the manufacturing processes.
2021-06-14 | PXD024835 | Pride
Project description:<h4><strong>BACKGROUND:</strong> Multiple myeloma is characterized by clonal proliferation of malignant plasma cells in the bone marrow that produce monoclonal immunoglobulins. N-glycosylation changes of these monoclonal immunoglobulins have been reported in multiple myeloma, but previous studies only detected limited serum N-glycan features.</h4><h4><strong>METHODS:</strong> Here, a more detailed study of the human serum N-glycome of 91 multiple myeloma patients and 51 controls was performed. We additionally analyzed sequential samples from patients (n = 7) which were obtained at different time points during disease development as well as 16 paired blood serum and bone marrow plasma samples. N-glycans were enzymatically released and measured by mass spectrometry after linkage specific derivatization of sialic acids.</h4><h4><strong>RESULTS:</strong> A decrease in both α2,3- and α2,6-sialylation, galactosylation and an increase in fucosylation within complex-type N-glycans were found in multiple myeloma patients compared to controls, as well as a decrease in difucosylation of diantennary glycans. The observed glycosylation changes were present in all ISS stages, including the 'low-risk' ISS I. In individual patients, difucosylation of diantennary glycans decreased with development of the disease. Protein N-glycosylation features from blood and bone marrow showed strong correlation. Moreover, associations of monoclonal immunoglobulin (M-protein) and albumin levels with glycan traits were discovered in multiple myeloma patients.</h4><h4><strong>CONCLUSIONS & GENERAL SIGNIFICANCE: </strong>In conclusion, serum protein N-glycosylation analysis could successfully distinguish multiple myeloma from healthy controls. Further studies are needed to assess the potential roles of glycan trait changes and the associations of glycans with clinical parameters in multiple myeloma early detection and prognosis.</h4>
2022-04-27 | MTBLS676 | MetaboLights
Project description:Vascular endothelial growth factor receptor-2 (VEGFR2) is a highly N-glycosylated receptor tyrosine kinase involved in pro-angiogenic signaling in physiological and pathological contexts, including cancer. VEGFR2 post-translational modifications (PTMs) and their roles in receptor function and signaling have been extensively studied. However, until recently, co- and post-translational N-glycosylation of RTKs has been regarded as decorative rather than functional. N-glycosylation is a non-template based process that generates heterogeneously modified proteins. Emerging evidence suggests that the tumor microenvironment modulates expression of glycosyltransferases involved in the trimming and remodeling of nascent N-linked glycans into their heterogeneous mature forms, and that these changes alter the functions of modified proteins and thereby impact cellular signaling and adhesion. We sought to understand the consequences of altered glycosylation on VEGFR2 signaling. We used multiple strategies, including: enzymatic removal of N-linked glycans from the receptor, site-directed mutagenesis of specific N-glycosylation sites near the VEGF ligand binding site of VEGFR2, mass spectrometry of VEGFR2 glycopeptides, and concurrent measurement of receptor activation, signaling, and dimerization to interrogate how N-glycosylation modulates VEGFR2 ligand-dependent pro-angiogenic signaling. We demonstrate that VEGFR2 glycosylation at site N247 regulates ligand-dependent receptor activation and signaling. Complex N-glycans with α2-6 linked sialic acid residues at site N247 hinder receptor activation, while asialo-glycans favor VEGFR2 ligand-mediated activation and signaling.
2021-09-08 | PXD012629 | Pride
Project description:Activation of murine CD4+ and CD8+ T lymphocytes leads to dramatic remodeling of N-linked glycans. Naïve and activated CD4 T cells, CD8 T cells and B cells were compared for their N-linked glycan structures by MALDI-TOF MS profiling and for expression of glycan transferase genes to assess the biosynthetic basis for any change observed. The major change observed in activated CD4 and CD8 T cells was dramatic reduction of sialylated bi-antennary N-glycans carrying the terminal NeuGc?2-6Gal sequence, and corresponding increase in glycans carrying the Gal?1-3Gal sequence. This change was accounted for by a decrease in the expression of the sialyltransferase ST6Gal, and increase in the expression of the galactosyltransferase ?1-3GalT. Conversely, in B cells no change in terminal sialylation of N-linked glycans was evident, and the expression of the same two glycosyltransferases were increased and decreased, respectively. Keywords = N-linked glycosylation, T cell, B cell, activation, glycosyltransferase, carbohydrate, glycomics, glycan, galactosyltransferase, sialyltransferase Keywords: other
2005-05-03 | GSE2554 | GEO