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Cited by 189Extracellular vesicles in diseaseCellular transport and secretionAdvanced Proteomics Techniques and Applications

Quantitative Proteomics Identifies Proteins Enriched in Large and Small Extracellular Vesicles

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Lischnig, Anna, Bergqvist, Markus, Ochiya, Takahiro, Lässer, Cecilia·2022·Molecular & Cellular Proteomics
DOI 10.1016/j.mcpro.2022.100273PMC PMC9486130
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Abstract

There is a long-held consensus that several proteins are unique to small extracellular vesicles (EVs), such as exosomes. However, recent studies have shown that several of these markers can also be present in other subpopulations of EVs to a similar degree. Furthermore, few markers have been identified as enriched or uniquely present in larger EVs, such as microvesicles. The aim of this study was to address these issues by conducting an in-depth comparison of the proteome of large and small EVs. Large (16,500g) and small EVs (118,000g) were isolated from three cell lines using a combination of differential ultracentrifugation and a density cushion and quantitative mass spectrometry (tandem mass tag-liquid chromatography-tandem mass spectrometry) was used to identify differently enriched proteins in large and small EVs. In total, 6493 proteins were quantified, with 818 and 1567 proteins significantly enriched in small and large EVs, respectively. Tetraspanins, ADAMs and ESCRT proteins, as well as SNAREs and Rab proteins associated with endosomes were enriched in small EVs compared with large EVs, whereas ribosomal, mitochondrial, and nuclear proteins, as well as proteins involved in cytokinesis, were enriched in large EVs compared with small EVs. However, Flotillin-1 was not differently expressed in large and small EVs. In conclusion, our study shows that the proteome of large and small EVs are substantially dissimilar. We validated several proteins previously suggested to be enriched in either small or large EVs (e.g., ADAM10 and Mitofilin, respectively), and we suggest several additional novel protein markers.

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  • The particle-to-protein ratio of NTERA2-derived EV preparations is consistent with values reported for large EV fractions of similar size, isolated from other cancer cell lines (e.g., breast) either after 16,500× g sedimentation alone or followed by density cushioning.

    “Notably, the particle-to-protein ratio of NTERA2-derived EV preparations is consistent with values reported for large EV fractions of similar size, isolated from other cancer cell lines (e.g., breast) either after 16,500× g sedimentation alone or followed by density cushioning [53].”

    From Optimized Wound Healing Assay to Study Extracellular Vesicle-Driven Glioblastoma Cell Migration (2026) · cites this paper as [53]

    The Experimental Procedures describe large EVs from breast cancer cell lines collected at 16,500g, with subsequent density-cushion purification. The Results report particle-to-protein ratios for crude and cushion-purified large EVs (Supplemental Fig. S1C and Fig. 3C). Our copy does not give numerical ratios in the text, so it cannot establish whether the NTERA2 preparations have consistent values or similar sizes. (LLM, conf=0.79)

    Experimental — accuracy not yet measured

  • The ratio of our extracellular vesicle batches aligns with the ratio reported for large extracellular vesicle fractions of similar size isolated from breast cancer cell lines.

    “The ratio of our EV batches aligns with the ratio reported for large EV fractions of a similar size isolated from breast cancer cell lines, either after 16,500× g sedimentation alone or followed by density cushion centrifugation [53].”

    From Optimized Wound Healing Assay to Study Extracellular Vesicle-Driven Glioblastoma Cell Migration (2026) · cites this paper as [53]

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Authors
Lischnig, A., Bergqvist, M., Ochiya, T., & Lässer, C.
Affiliations
  • University of Gothenburg (SE)
  • Tokyo Medical University (JP)
  • National Cancer Center Research Institute (JP)
Corresponding author
Lässer, Cecilia
ORCID
Venue
Molecular & Cellular Proteomics
Publisher
Elsevier BV
Published
2022-09
Volume
21
Issue
9
Pages
100273
ISSN
1535-9476 (ISSN-L)
DOI
10.1016/j.mcpro.2022.100273
PMC
PMC9486130
OpenAlex
W4288885853
Cited by
189
References
94
Citations by year
2026: 41 · 2025: 55 · 2024: 59 · 2023: 31 · 2022: 3
FWCI
12.08
Type
journal article
Language
en
Update notices
erratum (2023-03-01)
Open access
Licence
Locations
  • Molecular & Cellular Proteomics (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Extracellular vesicles in disease
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Cellular transport and secretion
  • Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
Keywords
extracellular vesicles, microvesicles, exosomes, EV proteome, protein biomarkers, tetraspanins, ADAMS, ESCRT proteins, snares, Rab GTPases, endosomes, flotillin-1, ADAM10, mitofilin
MeSH terms
Extracellular Vesicles, Nuclear Proteins, Biomarkers, Proteome, Proteomics, SNARE Proteins, Endosomal Sorting Complexes Required for Transport

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