Evidence map›Paper›PMID 40301937›Full record

ArticleCell communication and signaling : CCS2025

Comparative evaluation of methods for isolating extracellular vesicles from ICC cell culture supernatants: Insights into proteomic and glycomic analysis.

Linlin Wu, Jiao Wei, Yueping Zhan, Xiao Xiao, Xuewen Xu, Chenjun Huang, Tian Long, Yueyue Li, Bin Fu, Mengmeng Wang and 1 more

Abstract readComparative Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell communication and signaling : CCS, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Review
  2. Review
  3. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors.

Linlin Wu *Clinical Laboratory Medicine Center, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China.
Jiao Wei *Clinical Laboratory Medicine Center, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China.
Yueping ZhanClinical Laboratory Medicine Center, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China.
Xiao XiaoClinical Laboratory Medicine Center, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China.
Xuewen XuClinical Laboratory Medicine Center, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China.
Chenjun HuangClinical Laboratory Medicine Center, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China.
Tian LongClinical Laboratory Medicine Center, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China.
Yueyue LiShanghai Cancer Center and Institutes of Biomedical Sciences and Department of Chemistry and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, 200030, China.
Bin FuShanghai Cancer Center and Institutes of Biomedical Sciences and Department of Chemistry and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, 200030, China.
Mengmeng WangClinical Laboratory Medicine Center, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China.
Chunfang GaoClinical Laboratory Medicine Center, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China. gaocf1115@163.com.

Funding

National Natural Science Foundation of China 22404113National Natural Science Foundation of China 82372321
6 · The paper itself

Abstract

backgroundExtracellular vesicles (EVs) are nanoscale structures involved in intercellular communication and play a key role in cancer pathology. Intrahepatic cholangiocarcinoma (ICC) is a highly invasive malignancy marked by abnormal sialylated glycosylation. Analyzing proteins and glycans in EVs provides insights into ICC molecular subtyping and mechanisms. Optimizing EV isolation methods for ICC-derived EVs enables comprehensive proteomic and glycomic analysis.

methodsWe systematically evaluated five EV isolation methods-Ultracentrifugation (UC), exoEasy, Total Exosome Isolation (TEI), EVtrap, and ÄKTA-by analyzing the biophysical properties, proteomic profiles, and glycomic structures of EVs. 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 with overexpressing ST6 β‑galactoside α2,6‑sialyltransferase 1 (ST6GAL1).

resultsBy evaluating the biophysical properties, proteome, and N-glycome of EVs extracted using five different methods, UC was identified as the optimal approach for this study, as it offered a balance between operational complexity, cost-effectiveness, and the preservation of EVs activity. In this study, a total of 1,928 high-confidence proteins and over 84 high-confidence glycans were quantified. EVs secreted by HuCCT1 and HCCC-9810 cells overexpressing ST6GAL1 exhibited consistent upregulation of 16 proteins, consistent downregulation of 10 proteins, as well as consistent upregulation of 3 glycans and consistent downregulation of 3 glycans.

conclusionsQuantitative proteomic and glycomic analysis of ICC-derived EVs revealed that ST6GAL1 overexpression led to significant alterations in proteins involved in cancer cell adhesion and glycosylation pathways, along with specific changes in N-glycan structures. Notably, these modifications extended beyond α2,6-sialylation, suggesting that interactions between glycosyltransferases and glycans may drive these alterations.

Indexed as

CholangiocarcinomaExtracellular VesiclesGlycomicsProteomicsCell Line, TumorGlycosylationHumansPolysaccharidesProteomeSialyltransferasesPolysaccharidesProteomeSialyltransferasesCell culture supernatantsExtracellular vesiclesN-glycomeProteome

Identifiers

PMID40301937
PMCPMC12042569

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.