PXD038518-1

PXD038518 is an original dataset announced via ProteomeXchange.

Title	Whole proteome and transcriptome analysis of cancer-derived extracellular vesicles overlap in specific pathways and distinct EV populations
Description	Extracellular Vesicles (EVs) are particles of different sizes, covered by a lipid bilayer membrane and containing highly heterogeneous cargo. Cancer cell-derived EVs have been the main object of an extensive investigation in the field because they carry cancer-specific molecular cargo and can promote cancer progression. Cancer-derived EVs include populations of atypically large EVs (L-EVs), which have been referred to as tumor microvesicles, large oncosomes, or simply L-EVs. While small EVs (S-EVs), which include exosomes, have been investigated by a plethora of reports, little is known about L-EVs. The paucity of studies comparing protein cargo of L- and S-EVs, of studies focused on protein coding RNA, and the absence of integrative analyses to compare the protein and gene expression in different EV fractions, prompted us to perform mass spectrometry to profile three different, size-based EV fractions generated by three cancer cell models (glioma, prostate and breast cancer). We identified protein signatures for L- and S-EVs either common to all cell types or specific to each of them individually. The proteins enriched in prostate cancer cell-derived L-EVs were also identified in L-EVs from patients with metastatic prostate cancer by a SWATH proteomic assay. We also performed RNA-Seq on the prostate cancer model and integrated proteomic and transcriptomic datasets. GSEA revealed that mitochondrial function was enriched in L-EVs versus S-EVs at both the RNA and protein level. The mitochondrial signature at the transcriptome level was confirmed by single cell RNA-Seq of L- EVs in vitro. The integrated L-EV proteomic and transcriptomic signature enabled distinction between benign and localized prostate cancer, as well as between localized cancer and metastatic castration-resistant cancer.
HostingRepository	PRIDE
AnnounceDate	2025-04-16
AnnouncementXML	Submission_2025-04-16_10:17:36.970.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Wei Yang
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-12-02 06:45:13	ID requested
⏵ 1	2025-04-16 10:17:37	announced

Dataset with its publication pending

submitter keyword: proteomics

label-free

large oncosomes

exosomes

extracellular vesicles;

Wei Yang
contact affiliation	Cedars-Sinai Medical Center
contact email	wei.yang@cshs.org
lab head
Wei Yang
contact affiliation	Stony Brook University
contact email	wei.yang@cshs.org
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD038518
     1. Label: PRIDE project
     2. Name: Whole proteome and transcriptome analysis of cancer-derived extracellular vesicles overlap in specific pathways and distinct EV populations