PXD062160

PXD062160 is an original dataset announced via ProteomeXchange.

Title	Comparative evaluation of methods for isolating extracellular vesicles from ICC cell culture supernatants: Insights into proteomic and glycomic analysis
Description	Extracellular vesicles (EVs) are specialized nanoscale vesicular structures that act as mediators of intercellular communication, playing crucial roles in the pathological processes of cancers. Aberrant glycosylation is a hallmark of cancer, the analysis of EVs and protein glycosylation provides valuable insights into cancer research. Intrahepatic cholangiocarcinoma (ICC) is a highly aggressive and insidious malignancy, characterized by significant abnormalities in sialylation glycosylation. This study focused on the comprehensive analysis of the biophysical properties and cargo of EVs secreted by ICC cells. First, we evaluated five EVs isolation methods and identified ultracentrifugation (UC) as the optimal technique. Subsequently, we applied TMT-based quantitative proteome and light/heavy methylamine labeling for the quantification of sialylated N-glycan linkage isomers to investigate alterations in proteins and N-glycans within EVs secreted by HuCCT1 and HCCC-9810 cells overexpressing ST6GAL1. This integrated analytical strategy enhanced our ability to quantify EVs proteome and N-glycome in conditioned media, allowing us to quantify over 2,292 proteins and 65 N-glycans in ICC-derived EVs. The results revealed that ST6GAL1 overexpression induced variations in proteins associated with cancer cell adhesion and glycosylation pathways, as well as alterations in specific N-glycan structures. In addition, our comprehensive evaluation also considered the bioactivity of the extracted EVs, making them suitable for subsequent bioanalytical studies. In the future, we will focus on mechanistic investigations to elucidate the impact of ST6GAL1-induced EVs protein glycosylation changes on the pathogenesis of ICC.
HostingRepository	iProX
AnnounceDate	2025-03-24
AnnouncementXML	Submission_2025-07-30_19:43:14.367.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Linlin Wu
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480; matrix-assisted laser desorption ionization

Revision	Datetime	Status	ChangeLog Entry
0	2025-03-23 22:36:47	ID requested
⏵ 1	2025-07-30 19:43:14	announced

Dataset with its publication pending

submitter keyword: Extracellular vesicles, Cell culture supernatants, Proteome, N-glycome

Chunfang Gao
contact affiliation	Shanghai University of Traditional Chinese Medicine, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine
contact email	gaocf1115@163.com
lab head
Linlin Wu
contact affiliation	Shanghai University of Traditional Chinese Medicine, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine
contact email	15216753293@163.com
dataset submitter

iProX dataset URI