PXD057700

PXD057700 is an original dataset announced via ProteomeXchange.

Title	Uncovering biological heterogeneity in endometrial carcinoma molecular subtypes by proteomic analysis
Description	While endometrial cancer (EC) has an overall favorable prognosis, some patients do poorly and may benefit from refinements of current classification systems. Molecular classification stratifies ECs into four prognostic groups: POLEmut, MMRd (mismatch repair deficient), p53abn, and NSMP (no specific molecular profile), where POLEmut has the best prognosis and p53abn has the worst prognosis. We used proteomic profiling to provide additional prognostic or predictive information for EC patients, across or within molecular subtypes. Global proteome profiling of formalin fixed, paraffin embedded samples, that had clinicopathologic and outcome data, was performed on 184 ECs encompassing all four molecular subtypes, including replicate samples of the same tumor, and both biopsy and final hysterectomy specimens. To ensure representation of each subtype, we profiled an approximately equal distribution in the 148 unique tumors; 34 (23%) POLEmut, 40 (23%) MMRd, 35 (24%) p53abn and 39 (26%) NSMP, rather than the population-based distributions. There was high reproducibility in the proteomic profiles of intra-tumor replicate samples, and between matched biopsy and hysterectomy tumor samples. Consensus clustering identified four clusters with different prognosis, named ‘Adhesion’, ‘Immune’, ‘Proliferation’, and ‘Metabolic’ based on proteins enriched in each cluster. We correlated protein expression with common mutations, molecular subtypes, and outcomes. Proteomic analysis of EC identified candidate prognostic markers that may further refine current molecular classification and help guide treatment decisions. These data offer insights into new therapeutic interventions that could be developed to target proteins and pathways identified by EC proteomic profiling.
HostingRepository	PRIDE
AnnounceDate	2025-10-07
AnnouncementXML	Submission_2025-10-06_16:30:05.950.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Gian Luca Negri
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2024-11-09 13:11:47	ID requested
⏵ 1	2025-10-06 16:30:06	announced

10.1016/j.neo.2025.101229;

Cochrane DR, Negri GL, Huvila J, Kalantari F, Farnell DA, Mohammad N, Thompson E, Yang W, Lum A, Spencer SE, Riley R, Jamieson A, Leung S, Chiu D, Chow C, Lim JLP, K, ö, bel M, Kommoss S, Kommoss F, Gilks B, Hoang L, Huntsman DG, Morin GB, McAlpine JN, Proteomic analysis uncovers biological diversity in molecularly defined endometrial carcinomas. Neoplasia, 69():101229(2025) [pubmed]

submitter keyword: ffpe,endometrial carcinoma, tmt

Gregg Morin
contact affiliation	Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada.
contact email	gmorin@bcgsc.ca
lab head
Gian Luca Negri
contact affiliation	Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada.
contact email	gnegri@bcgsc.ca
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/PXD057700

PRIDE project URI

• PRIDE
  1. PXD057700
     1. Label: PRIDE project
     2. Name: Uncovering biological heterogeneity in endometrial carcinoma molecular subtypes by proteomic analysis