PXD038011

PXD038011 is an original dataset announced via ProteomeXchange.

Title	Integration of the whole proteome and transcriptome reveals a strong correlation between the protein and mRNA in a distinct population of cancer-derived EVs
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) that can be pelleted by a low/medium speed centrifugation, which have been referred to as tumor microvesicles, large oncosomes, or simply L-EVs. While small EVs (S-EVs), which pellet at a high speed centrifugation and include exosomes, have been investigated by a plethora of reports, little is known about the cargo of 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 general as well as cancer type-specific protein signatures for L- and S-EVs. A subset of the proteins enriched in prostate cancer cell-derived L-EVs was also identified in L-EVs from plasma of patients with metastatic prostate cancer by an independent Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH) mass spectrometry analysis. Proteomic and transcriptomic analyses of the prostate cancer-derived EVs revealed an enrichment of mitochondrial functions in L-EVs versus S-EVs at both the protein and RNA level. The mitochondrial signature was confirmed in L-EVs by single EV RNA-Seq. 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_08:44:48.056.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sarah Parker
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2022-11-07 09:56:57	ID requested
⏵ 1	2025-04-16 08:44:48	announced

Silva TF, Hutchins E, Zhao W, Ciani Y, Kim M, Mariscal J, Qiu Z, Kittel A, Zhou B, Wang Y, Hall M, Galasso F, Reiman R, Freeman MR, Parker S, Van Eyk J, Yang W, Posadas E, Guarnerio J, Nolan J, Thery C, Zijlstra A, Stott S, You S, Demichelis F, Boutros P, Van Keuren-Jensen K, Di Vizio D, Extracellular Vesicles heterogeneity through the lens of multiomics. bioRxiv, ():(2024) [pubmed]

10.1101/2024.08.14.607999;

submitter keyword: Cancer-derived EV, Transcriptomics, Proteomics, Prostate Cancer

Doloros DiVisio
contact affiliation	Associate Professor, Cedars-Sinai Medical Center, Surgery
contact email	doloros.divisio@cshs.org
lab head
Sarah Parker
contact affiliation	Cedars-Sinai Medical Center
contact email	sarah.parker@cshs.org
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/04/PXD038011

PRIDE project URI

• PRIDE
  1. PXD038011
     1. Label: PRIDE project
     2. Name: Integration of the whole proteome and transcriptome reveals a strong correlation between the protein and mRNA in a distinct population of cancer-derived EVs