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

Being a widely occurring protein post-translational modification, N-glycosylation features unique multi-dimensional structures including sequence and linkage isomers. There have been successful bioinformatics efforts in N-glycan structure identification using N-glycoproteomics data; however, symmetric "mirror" branch isomers and linkage isomers are largely unresolved. Here, we report deep structure-level N-glycan identification using feature-induced structure diagnosis (FISD) integrated with a deep learning model.

Benchmark N-glycoproteomics study of common differential tissue and serum N-glycoproteins of patients with hepatocellular carcinoma.

For hepatocellular carcinoma (HCC), N-glycosylation has been proved to be widely involved in various aspects of the disease, including development, metastasis, subtyping, diagnosis and prognosis. The common practice is to discover biomarkers in situ of cancer occurrence (i.e.

Mass spectrometry-based structure-specific glycoproteomics and biomedical applications.

linked glycosylation is a common posttranslational modification of proteins that results in macroheterogeneity of the modification site. However, unlike simpler modifications, glycosylation introduces an additional layer of complexity with tens of thousands of possible structures arising from various dimensions, including different monosaccharide compositions, sequence structures, linking structures, isomerism, and three-dimensional conformations. This results in additional microheterogeneity of the modification site of glycosylation, i.

Analysis of mutation-originated gain-of-glycosylation using mass spectrometry-based N-glycoproteomics.

Rationale: A general N-glycoproteomics analysis pipeline has been established for characterization of mutation-related gain-of-glycosylation (GoG) at intact N-glycopeptide molecular level, generating comprehensive site and structure information of N-glycosylation.

Methods: This study focused on mutation-originated GoG using a mass spectrometry-based N-glycoproteomics analysis workflow. In brief, GoG intact N-glycopeptide databases were built, consisting of 2701 proteins (potential GoG N-glycosites and amino acids derived from MUTAGEN, VARIANT and VAR_SEQ in UniProt) and 6709 human N-glycans (≤50 sequence isomers per monosaccharide composition).

Comprehensive characterization of differential glycation in hepatocellular carcinoma using tissue proteomics with stable isotopic labeling.

Glycation is a non-enzymatic posttranslational modification coming from the reaction between reducing sugars and free amino groups in proteins, where early glycation products (fructosyl-lysine, FL) and advanced glycation end products (AGEs) are formed. The occurrence of glycation and accumulation of AGEs have been closely associated with hepatocellular carcinoma (HCC). Here, we reported the characterization of differential glycation in HCC using tissue proteomics with stable isotopic labeling; early glycation-modified peptides were enriched with boronate affinity chromatography (BAC), and AGEs-modified peptides were fractionated with basic reversed-phase separation.

Hyaluronan degradation by HYAL2 is essential for odontoblastic differentiation and migration of mouse dental papilla cells.

The coordination between odontoblastic differentiation and directed cell migration of mesenchymal progenitors is necessary for regular dentin formation. The synthesis and degradation of hyaluronan (HA) in the extracellular matrix create a permissive niche that directly regulates cell behaviors. However, the role and mechanisms of HA degradation in dentin formation remain unknown.

High-throughput N-glycoproteomics with fast liquid chromatographic separation.

N-glycosylation is a common protein post translation modification, which has tremendous structure diversity and wide yet delicate regulation of protein structures and functions. Mass spectrometry-based N-glycoproteomics has become a state-of-the-art pipeline for both qualitative and quantitative characterization of N-glycosylation at the intact N-glycopeptide level, providing comprehensive information of peptide backbones, N-glycosites, monosaccharide compositions, sequence and linkage structures. For high-throughput analysis of large-cohort clinic samples, fast and high-performance separation is indispensable.

Investigation of the Catalytic Mechanism of a Soluble N-glycosyltransferase Allows Synthesis of N-glycans at Noncanonical Sequons.

The soluble N-glycosyltransferase from (ApNGT) can establish an N-glycosidic bond at the asparagine residue in the Asn-Xaa-Ser/Thr consensus sequon and is one of the most promising tools for N-glycoprotein production. Here, by integrating computational and experimental strategies, we revealed the molecular mechanism of the substrate recognition and following catalysis of ApNGT. These findings allowed us to pinpoint a key structural motif (DVYM) in ApNGT responsible for the peptide substrate recognition.

Gain-of-glycosylation in breast multi-drug-resistant MCF-7 adenocarcinoma cells and cancer stem cells characterized by site- and structure-specific N-glycoproteomics.

N-linked glycosylation (N-glycosylation) is a common protein post-translational modification, occurring on more than half of mammalian proteins; in striking contract with small molecule modifications (such as methylation, phosphorylation) with only single structures, N-glycosylation has multiple dimensional structural features (monosaccharide composition, sequence, linkage, anomer), which generates enormous N-glycan structures; and these structures widely regulate protein structure and functions. For the modification site, N-glycosylation occurs on the Asn residue among the consensus N-X-S/T/C (X≠P) motif; mutation-originated amino acid change may lead to loss of such an original motif and thus loss-of-glycosylation (LoG) or gain of such a new motif and thus gain-of-glycosylation (GoG). Both LoG and GoG generates new structures and functions of glycoproteins, which has been observed in the S protein of SARS-Cov-2 as well as malignant diseases.

Structural N-glycoproteomics characterization of cell-surface N-glycosylation of MCF-7/ADR cancer stem cells.

Breast cancer is responsible for the highest mortality all over the world. Cancer stem cells (CSCs) along with epithelial mesenchymal transition (EMT) are identified as a driver of cancer which are responsible for cancer metastasis and drug resistance. Several signaling pathways are associated with drug resistance.

The role of O-GlcNAcylation in innate immunity and inflammation.

O-linked β-N-acetylglucosaminylation (O-GlcNAcylation) is a highly dynamic and widespread post-translational modification (PTM) that regulates the activity, subcellular localization, and stability of target proteins. O-GlcNAcylation is a reversible PTM controlled by two cycling enzymes: O-linked N-acetylglucosamine transferase and O-GlcNAcase. Emerging evidence indicates that O-GlcNAcylation plays critical roles in innate immunity, inflammatory signaling, and cancer development.

Aberrant N-glycolylneuraminic acid in breast MCF-7 cancer cells and cancer stem cells.

N-Glycolylneuraminic acid (Neu5Gc) is not normally detected in humans because humans lack the hydroxylase enzyme that converts cytidine-5'-monophosphate-N-acetylneuraminic acid (CMP-Neu5Ac) to CMP-Neu5Gc; thus, any Neu5Gc appearing in the human body is aberrant. Neu5Gc has been observed in human cancer cells and tissues. Moreover, antibodies against Neu5Gc have been detected in healthy humans, which are obstacles to clinical xenotransplantation and stem cell therapies.

Sialic acid linkage-specific quantitative N-glycoproteomics using selective alkylamidation and multiplex TMT-labeling.

Protein sialylation participates many biological processes in a linkage-specific manner, and aberrant sialylation has been associated with many malignant diseases. Mass spectrometry-based quantitative N-glycoproteomics has been widely adopted for quantitative analysis of aberrant sialylation, yet multiplexing method at intact N-glycopeptides level is still lacking. Here we report our study of sialic acid linkage-specific quantitative N-glycoproteomics using selective alkylamidation and multiplex tandem mass tags (TMT)-labeling.

Proteoform Identification and Quantification Using Intact Protein Database Search Engine ProteinGoggle.

Proteomics studies the proteome of organisms, especially proteins that are differentially expressed under certain physiological or pathological conditions; qualitative identification of protein sequences and posttranslational modifications (PTMs) and their positions can help us systematically understand the structure and function of proteoforms. With the development and relative popularity of soft ionization technology (such as electrospray ionization technology) and high mass measurement accuracy and high-resolution mass spectrometers (such as orbitrap), the mass spectrometry (MS) characterization of complete proteins (the so-called top-down proteomics) has become possible and has gradually become popular. Corresponding database search engines and protein identification bioinformatics tools have also been greatly developed.

Exploration of quantitative site-specific serum O-glycoproteomics with isobaric labeling for the discovery of putative O-glycoprotein biomarkers.

Purpose: Exploration study of site-specific isobaric-TMT-labeling quantitative serum O-glycoproteomics for the discovery of putative O-glycoprotein cancer biomarkers.

Experimental Design: Sera of 10 breast cancer patients was used as the exploration cohort. More abundant N-glycosylation was first removed with PNGase F.

Comprehensive site- and structure-specific characterization of N-glycosylation in model plant Arabidopsis using mass-spectrometry-based N-glycoproteomics.

The N-glycosylation is an important bioprocess in plant. Monosaccharide composition-level characterization at the intact N-glycopeptides has been extensively reported, yet structure-specific study to resolve multiple sequence structures of a single composition is still lacking. Here, we present a comprehensive structure-specific identification of intact N-glycopeptides of Arabidopsis with both HILIC and RAX enrichment, as well as GPSeeker and pGlyco database search.

Structure-Specific Glycoproteomics Characterization of NIST Monoclonal Antibody Reference Material 8671.

The characteristics of monoclonal antibodies (mAbs) cohering various function effectors show great expectation in therapy. Glycosylation, one of the common post-translational modifications, deeply influences cohesion. It is necessary to grasp monosaccharide composition/sequence and glycan structures in mAbs.

Progress in quantification of nicotine content and form distribution in electronic cigarette liquids and aerosols.

Each electronic cigarette (e-cigarette) is a battery-powered system which converts electronic cigarette liquids (e-liquids) into the inhalable phase by heating the solution when it is in use. After four generations of development, e-cigarettes tend to be more customized and user-operable. The main components in the e-liquid and the aerosol are vegetable glycerin, propylene glycol, nicotine, organic acid and some flavor ingredients.

The glycosylation in SARS-CoV-2 and its receptor ACE2.

Coronavirus disease 2019 (COVID-19), a highly infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected more than 235 million individuals and led to more than 4.8 million deaths worldwide as of October 5 2021. Cryo-electron microscopy and topology show that the SARS-CoV-2 genome encodes lots of highly glycosylated proteins, such as spike (S), envelope (E), membrane (M), and ORF3a proteins, which are responsible for host recognition, penetration, binding, recycling and pathogenesis.

Genome‑wide association study and genomic prediction for growth traits in yellow-plumage chicken using genotyping-by-sequencing.

Background: Growth traits are of great importance for poultry breeding and production and have been the topic of extensive investigation, with many quantitative trait loci (QTL) detected. However, due to their complex genetic background, few causative genes have been confirmed and the underlying molecular mechanisms remain unclear, thus limiting our understanding of QTL and their potential use for the genetic improvement of poultry. Therefore, deciphering the genetic architecture is a promising avenue for optimising genomic prediction strategies and exploiting genomic information for commercial breeding.

-Glycoproteomics Study of Putative -Glycoprotein Biomarkers of Drug Resistance in MCF-7/ADR Cells.

Unlabelled: Currently, drug resistance of anti-cancer therapy has become the main cause of low survival rate and poor prognosis. Full understanding of drug resistance mechanisms is an urgent request for further development of anti-cancer therapy and improvement of prognosis. Here we present our -glycoproteomics study of putative -glycoprotein biomarkers of drug resistance in doxorubicin resistance breast cancer cell line michigan cancer foundation-7 (MCF-7/ADR) relative to parental michigan cancer foundation-7 (MCF-7) cells.

Methylation of PhoP by CheR Regulates Virulence.

The two-component system PhoP/PhoQ is essential for Salmonella enterica serovar Typhimurium virulence. Here, we report that PhoP is methylated extensively. Two consecutive glutamate (E) and aspartate (D)/E residues, i.

Promising Immunotherapies against COVID-19.

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a severe pandemic and deeply affected the livelihood of people worldwide. In response to the pandemic, researchers have been rapidly studying different aspects of COVID-19, such as virus detection, vaccinations, and epidemiological aspects of the disease. It has been reported that SARS-CoV-2 can induce uncontrolled inflammation and cause a lack of antiviral response, thereby aggravating the disease.

Putative N-glycoprotein markers of MCF-7/ADR cancer stem cells from N-glycoproteomics characterization of the whole cell lysate.

Breast cancer is one of the most malignant diseases among females. N-glycoproteomics studies have shown that N-glycosylation alteration of tumor cells is the key player of cancer progression, multidrug resistance (MDR) and high mortality. Cancer stem cells (CSCs) have the remarkable potential of self-renewing and differentiation which leads to drug resistance and metastasis.