PXD039258

PXD039258 is an original dataset announced via ProteomeXchange.

Title	Proteomics characterization of clear cell renal cell carcinoma
Description	The aims of the study was to explore the tumor proteome of patients diagnosed with localized ccRCC and treated with surgery and the identification of altered pathways that could be the target of new treatments. A total of 165 FFPE tumor samples from patients diagnosed with ccRCC were analyzed using DIA-proteomics. Proteomics ccRCC subtypes were defined using a Consensus Cluster Algorithm (CCA) and characterized by a functional approach using probabilistic graphical models and survival analyses. Two proteomics subtypes of ccRCC (CCA1 and CCA2) were identified by CCA using the high confidence proteins only. Characterization of molecular differences between CCA1 and CCA2 was performed in two steps. First, we defined 514 proteins showing differential expression between the two subtypes using a significance analysis of microarrays analysis. Proteins overexpressed in CCA1 were mainly related to translation and ribosome, while proteins overexpressed in CCA2 were mainly related to focal adhesion and membrane. Second, a functional analysis using probabilistic graphical models was performed. The CCA1 subtype is characterized by an increased expression of proteins related to glycolysis, mitochondria, translation, adhesion proteins related to cytoskeleton and actin, nucleosome, and spliceosome, while CCA2 subtype showed higher expression o proteins involved in focal adhesion, extracellular matrix and collagen organization.
HostingRepository	PRIDE
AnnounceDate	2025-05-09
AnnouncementXML	Submission_2025-05-09_05:40:34.096.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Lucia Trilla-Fuertes
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2023-01-04 04:32:46	ID requested
⏵ 1	2025-05-09 05:40:35	announced

Pinto-Mar, í, n Á, Trilla-Fuertes L, Miranda Poma J, Vasudev NS, Garc, í, a-Fern, á, ndez E, L, ó, pez-Vacas R, Miranda N, Wilson M, L, ó, pez-Camacho E, Pertejo A, Dittmann A, Kunz L, Brown J, Pedroche-Just Y, Zapater-Moros A, de Velasco G, Castellano D, Gonz, á, lez-Peramato P, Espinosa E, Banks RE, Fresno Vara J Á, G, á, mez-Pozo A, A prognostic microRNA-based signature for localized clear cell renal cell carcinoma: the Bio-miR study. Br J Cancer, ():(2025) [pubmed]

10.1038/s41416-025-03008-2;

ProteomeXchange project tag: EPIC-XS

submitter keyword: DIA

molecular subtypes,localized clear cell renal cancer, FFPE, probabilistic graphical models, ccRCC

Angelo Gámez-Pozo
contact affiliation	Molecular Oncology Lab, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
contact email	angelo.gamez@salud.madrid.org
lab head
Lucia Trilla-Fuertes
contact affiliation	Molecular Oncology Lab, Hospital Universitario La Paz-IdiPAZ
contact email	lucia.lt30@gmail.com
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/2025/05/PXD039258

PRIDE project URI

• PRIDE
  1. PXD039258
     1. Label: PRIDE project
     2. Name: Proteomics characterization of clear cell renal cell carcinoma