Recommendations for reproducibility of cerebrospinal fluid extracellular vesicle studies

Journal of Extracellular Vesicles, Год журнала: 2023, Номер 13(1)

Опубликована: Дек. 29, 2023

Cerebrospinal fluid (CSF) is a clear, transparent derived from blood plasma that protects the brain and spinal cord against mechanical shock, provides buoyancy, clears metabolic waste transports extracellular components to remote sites in brain. Given its contact with cord, CSF most informative biofluid for studies of central nervous system (CNS). In addition other components, contains vesicles (EVs) carry bioactive cargoes (e.g., lipids, nucleic acids, proteins), can have biological functions within beyond CNS. Thus, EVs likely serve as both mediators contributors communication Accordingly, their potential biomarkers CNS diseases has stimulated much excitement attention EV research. However, on present unique challenges relative biofluids, including invasive nature collection, limited volumes low numbers compared plasma. Here, objectives International Society Extracellular Vesicles Task Force are promote reproducibility by providing current reporting best practices, recommendations guidelines, studies. To accomplish this, we created distributed world-wide survey ISEV members assess methods considered 'best practices' EVs, then performed detailed literature review publications was used curate resources. Based responses curated information publications, herein guidelines seven domains: (i) Collection, Processing, Storage; (ii) Separation/Concentration; (iii) Size Number Measurements; (iv) Protein Studies; (v) RNA (vi) Omics Studies (vii) Functional Studies.

Язык: Английский

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Comprehensive Glycoprofiling of Oral Tumors Associates N-Glycosylation With Lymph Node Metastasis and Patient Survival

Molecular & Cellular Proteomics, Год журнала: 2023, Номер 22(7), С. 100586 - 100586

Опубликована: Июнь 1, 2023

While altered protein glycosylation is regarded a trait of oral squamous cell carcinoma (OSCC), the heterogeneous and dynamic glycoproteome tumor tissues from OSCC patients remain unmapped. To this end, we here employ an integrated multi-omics approach comprising unbiased quantitative glycomics glycoproteomics applied to cohort resected primary with (n = 19) without 12) lymph node metastasis. all displayed relatively uniform N-glycome profiles suggesting overall stable global N-glycosylation during disease progression, expression six sialylated N-glycans was found correlate Notably, advanced statistical analyses uncovered site-specific revealing previously unknown associations several clinicopathological features. Importantly, data unveiled that comparatively high abundance two core-fucosylated (Glycan 40a Glycan 46a) one N-glycopeptide fibronectin were associated low patient survival, while N-glycopeptides both afamin CD59 also poor survival. This study provides insight into complex tissue N-glycoproteome, thereby forming important resource further explore underpinning mechanisms uncover new prognostic glycomarkers for OSCC.

Язык: Английский

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Advancing mass spectrometry–based glycoproteomic software tools for comprehensive site-specific glycoproteome analysis

Current Opinion in Chemical Biology, Год журнала: 2024, Номер 80, С. 102442 - 102442

Опубликована: Март 8, 2024

Язык: Английский

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Can We Boost N-Glycopeptide Identification Confidence? Smart Collision Energy Choice Taking into Account Structure and Search Engine

Journal of the American Society for Mass Spectrometry, Год журнала: 2024, Номер 35(2), С. 333 - 343

Опубликована: Янв. 29, 2024

High confidence and reproducibility are still challenges in bottom-up mass spectrometric N-glycopeptide identification. The collision energy used the MS/MS measurements database search engine to identify species perhaps two most decisive factors. We investigated how structural features of N-glycopeptides choice influence optimal energy, delivering highest identification confidence. carried out LC-MS/MS using a series energies on large set with both glycan peptide part varied studied behavior Byonic, pGlyco, GlycoQuest scores. found that engines show range between peptide-centric glycan-centric, which manifests itself already dependence m/z. Using classical statistical machine learning methods, we revealed hydrophobicity, masses, number mobile protons also have significant search-engine-dependent influence, as opposed other parameters probed. envisioned an workflow making smart based online available such hydrophobicity (described by retention time) (potentially from scout MS/MS). Our assessment suggests this can lead gain (up 100%) confidence, particularly for low-scoring hits close filtering limit, has potential enhance analyses. Data via MassIVE (MSV000093110).

Язык: Английский

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Protein glycosylation and glycoinformatics for novel biomarker discovery in neurodegenerative diseases

Ageing Research Reviews, Год журнала: 2023, Номер 89, С. 101991 - 101991

Опубликована: Июнь 21, 2023

Glycosylation is a common post-translational modification of brain proteins including cell surface adhesion molecules, synaptic proteins, receptors and channels, as well intracellular with implications in development functions. Using advanced state-of-the-art glycomics glycoproteomics technologies conjunction glycoinformatics resources, characteristic glycosylation profiles tissues are increasingly reported the literature growing evidence shows deregulation central nervous system disorders, aging associated neurodegenerative diseases. Glycan signatures tissue also frequently described cerebrospinal fluid due to its enrichment brain-derived molecules. A detailed structural analysis glycans collected publications healthy conditions was undertaken data compiled create browsable dedicated set GlyConnect database glycoproteins (https://glyconnect.expasy.org/brain). The shared molecular composition enhances likelihood novel glycobiomarker discovery for neurodegeneration, which may aid unveiling disease mechanisms, therefore, providing therapeutic targets diagnostic progression monitoring tools.

Язык: Английский

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Integrative Quantitative Analysis of Platelet Proteome and Site-Specific Glycoproteome Reveals Diagnostic Potential of Platelet Glycoproteins for Liver Cancer

Analytical Chemistry, Год журнала: 2025, Номер unknown

Опубликована: Янв. 15, 2025

The role of peripheral blood platelets as indicators cancer progression is increasingly recognized, and the significance abnormal glycosylation in platelet function related disorders gaining attention. However, potential a source protein site-specific for diagnosis remains underexplored. In this study, we proposed general pipeline that integrates quantitative proteomics with glycoproteomics, allowing an in-depth investigation glycoproteome. With pipeline, generated data set comprising 3,466 proteins qualitative information, 3,199 3,419 glycans information 3,377 from hepatocellular carcinoma (HCC) patients, metastatic liver (mLC) healthy controls. integrated analysis revealed significant changes N-glycosylation patients. Further systems biology lectin pull-down-coupled ELISA assays independent clinical samples confirmed two N-glycoproteins specific glycan types, complement C3 (C3) oligomannose modification integrin β-3 (ITGB3) sialylation, biomarkers distinguishing patients individuals, without differentiating between HCC mLC patient group. These findings highlight biomarkers.

Язык: Английский

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Uncovering missing glycans and unexpected fragments with pGlycoNovo for site-specific glycosylation analysis across species

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Сен. 14, 2024

Язык: Английский

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HEXB drives raised paucimannosylation in colorectal cancer and stratifies patient risk

Molecular & Cellular Proteomics, Год журнала: 2025, Номер unknown, С. 100927 - 100927

Опубликована: Фев. 1, 2025

Highlights•Multi-omics investigation of colorectal cancer specimens (tissues, PBMCs, plasma).•Paucimannosidic proteins immune and origins dominate in CRC tumors.•HEXB, a truncating glycoenzyme, drives paucimannosidic protein formation CRC.•Plasma hexosaminidase activity associates with five-year survival patients.AbstractNon-invasive prognostic markers are needed to improve the (CRC) patients. Towards this goal, we applied untargeted systems glycobiology approaches snap frozen formalin-fixed paraffin-embedded tumor tissues peripheral blood mononuclear cells (PBMCs) from patients spanning different disease stages matching controls faithfully uncover molecular changes associated CRC. Quantitative glycomics immunohistochemistry (IHC) revealed that non-canonical N-glycans elevated tumors relative normal adjacent tissues. Cell origin-focused glycoproteomics enabled using well-curated Human Protein Atlas combined IHC recapitulated these findings indicated were part tumor-infiltrating monocytes (e.g. MPO, AZU1) cell origin LGALS3BP, PSAP). Biosynthetically explaining observations, N-acetyl-β-D-hexosaminidase (Hex) subunit β (HEXB) was found be over-expressed colocalization enzyme inhibition studies confirmed HEXB facilitates biosynthesis cells. Employing sensitive, quick robust assay, then showed Hex plasma PBMCs advanced those early-stage disease. Surveying large cohort, raised correlated indicating is potential risk marker for patient outcome. Our glycoproteomics-driven open avenues better prognostication stratification CRC.Graphical abstract

Язык: Английский

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Ultradeep N-glycoproteome Atlas of Mouse Reveals Spatiotemporal Signatures of Brain Aging and Neurodegenerative Diseases

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Фев. 19, 2025

Abstract The current depth of site-specific N-glycoproteomics is insufficient to fully characterize glycosylation events in biological samples. Herein, we achieved an ultradeep and precision analysis the N-glycoproteome mouse tissues by integrating multiple workflows. largest N-glycoproteomic dataset date was established on mice, which contained 91,972 precursor glycopeptides, 62,216 glycoforms, 8,939 glycosites 4,563 glycoproteins. database consisted 6.8 million glyco-spectra (containing oxonium ions), among 160,928 were high-quality spectra with confident N-glycopeptide identifications. large-scale enhanced performance artificial intelligence models for glycopeptide tandem spectrum prediction. Using this dataset, observed tissue specific microheterogeneity functional implications protein mice. Furthermore, region-resolved brain N-glycoproteomes Alzheimer’s Diseases, Parkinson Disease aging mice revealed spatiotemporal signatures distinct pathological functions N-glycoproteins. A comprehensive resource experimental data from study previous literatures further established. This atlas serves as a promising tool revealing role systems.

Язык: Английский

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Current issues of tandem mass spectrum (MS2)-based glycoproteomics and efforts to complement them.

BBA Advances, Год журнала: 2025, Номер 7, С. 100158 - 100158

Опубликована: Янв. 1, 2025

With the development of liquid chromatography/mass spectrometers that support proteomics and associated analytical methods data analysis software, number proteins can be identified quantified in a single is approaching level transcriptomics. However, many problems remain to solved protein glycosylation analysis. This mini-review discusses technical issues MS2-based glycoprotein identification efforts complement them by Human Glycome Atlas (HGA) Project Japan.

Язык: Английский

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