PXD062934

PXD062934 is an original dataset announced via ProteomeXchange.

Title	Proteomic landscapes of 3D and 2D models of High-Grade Serous Ovarian Carcinoma: Implications for Carboplatin Response
Description	High-Grade Serous Ovarian Carcinoma (HGSOC) is is the most common form of ovarian cancer and finding new treatments remains an unmet need. While drug discovery is typically performed in two-dimensional (2D) monolayers, three-dimensional (3D) culture systems better mimic in vivo conditions. However, a comprehensive comparison of 3D vs 2D ovarian cancer models is lacking. Here, we quantitatively compared the whole cell proteomic signatures of 4 ovarian cell lines—PEO1, PEO4, UWB1.289, and UWB1.289+BRCA1— with different status of BRCA genes grown, in 2D and in 3D. Using isobaric labeling proteomics, we quantified 6,668 proteins and identified 412 significantly altered proteins between 2D and 3D. Proteins upregulated in 3D were enriched for transmembrane transport and oxidoreductase activity, while energy metabolism and cell growth pathways also showed dimensionality-dependent changes. Notably, membrane-associated proteins such as EGFR were downregulated in spheroids, particularly in PEO1 and PEO4. Furthermore, 3D culture modulated the response to carboplatin, with increased expression of drug resistance-associated proteins, including NDUF family members and ATP6V0A2, in all spheroid models. These findings underscore how culture dimensionality influences both the molecular landscape and chemotherapeutic response of HGSOC cells and highlight candidate targets for overcoming carboplatin resistance.
HostingRepository	PRIDE
AnnounceDate	2025-10-13
AnnouncementXML	Submission_2025-10-13_02:39:20.456.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Graeme Benstead-Hume
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Ascend

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-14 06:56:24	ID requested
⏵ 1	2025-10-13 02:39:21	announced

10.1021/acs.jproteome.5c00391;

Maillard J, Roumeliotis TI, Paranjape E, Pickard L, Ingles R Garces A, Choudhary JS, Banerji U, Proteomic Landscapes of 3D and 2D Models of High-Grade Serous Ovarian Carcinoma: Implications for Carboplatin Response. J Proteome Res, 24(10):5071-5082(2025) [pubmed]

submitter keyword: High-Grade Serous Ovarian Carcinoma

Jyoti Choudhary
contact affiliation	Functional Proteomics, ICR
contact email	jyoti.choudhary@icr.ac.uk
lab head
Graeme Benstead-Hume
contact affiliation	ICR
contact email	ghume@icr.ac.uk
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/2025/10/PXD062934

PRIDE project URI

• PRIDE
  1. PXD062934
     1. Label: PRIDE project
     2. Name: Proteomic landscapes of 3D and 2D models of High-Grade Serous Ovarian Carcinoma: Implications for Carboplatin Response