PXD061015

PXD061015 is an original dataset announced via ProteomeXchange.

Title	Quantitative proteomics and phosphoproteomics analysis of patient-derived ovarian cancer stem cells
Description	High-grade serous ovarian carcinoma (HGSOC) is the deadliest gynecologic cancer. Key to the progression and ultimate lethality of this subtype is the intra-tumoral heterogeneity (ITH), which is defined as the coexistence of different cell types and populations within a single tumor. Among those, ovarian cancer stem cells (OCSCs) are a distinct subpopulation of tumor cells endowed with stem-like properties, which can survive current standard therapies, resulting in tumor recurrence. Here, we generated ex vivo primary OCSC-enriched three-dimensional (3D) spheres from ten distinct treatment naive patient-derived adherent (2D) cultures. We used state-of-the-art quantitative mass spectrometry to characterize the molecular events associated with OCSCs by analyzing their phosphoproteome and proteome. Our data revealed a stemness-related protein signature, shared within a heterogeneous patient cohort, which correlates with chemo-refractoriness in a clinical proteomics dataset. Moreover, we identified targetable deregulated kinases and aberrant PDGF receptor activation in OCSCs. Pharmacological inhibition of PDGFR in adherent OC cells reduced the stemness potential, measured by sphere formation assay. Overall, we provide a valuable resource to identify new OCSC markers and putative targets for OCSC-directed therapies.
HostingRepository	PRIDE
AnnounceDate	2025-04-24
AnnouncementXML	Submission_2025-04-24_03:28:07.906.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Giulia Franciosa
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-02-20 11:48:21	ID requested
⏵ 1	2025-04-24 03:28:11	announced

Nieddu V, Melocchi V, Battistini C, Franciosa G, Lupia M, Stellato C, Bertalot G, Olsen JV, Colombo N, Bianchi F, Cavallaro U, Matrix Gla Protein drives stemness and tumor initiation in ovarian cancer. Cell Death Dis, 14(3):220(2023) [pubmed]

10.1038/s41419-023-05760-w;

10.1016/j.mcpro.2025.100965;

Franciosa G, Nieddu V, Battistini C, Caffarini M, Lupia M, Colombo N, Fusco N, Olsen JV, Cavallaro U, Quantitative Proteomics and Phosphoproteomics Analysis of Patient-Derived Ovarian Cancer Stem Cells. Mol Cell Proteomics, 24(5):100965(2025) [pubmed]

submitter keyword: Cancer stem cells, Orbitrap exploris 480,Ovarian cancer

Jesper V. Olsen
contact affiliation	University of Copenhagen Faculty of Health and Medical Sciences Novo Nordisk Foundation Center for Protein Research Proteomics Program
contact email	Jesper.Olsen@cpr.ku.dk
lab head
Giulia Franciosa
contact affiliation	Novo Nordisk Foundation Center For Protein Research, Copenhagen University, Copenhagen
contact email	giulia.franciosa@cpr.ku.dk
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/PXD061015

PRIDE project URI

• PRIDE
  1. PXD061015
     1. Label: PRIDE project
     2. Name: Quantitative proteomics and phosphoproteomics analysis of patient-derived ovarian cancer stem cells