PXD021491

PXD021491 is an original dataset announced via ProteomeXchange.

Title	Molecular characterization of triple negative breast cancer formaldehyde-fixed paraffin-embedded samples by DIA proteomics
Description	Triple negative breast cancer (TNBC) accounts for 15-20% of all breast carcinomas and it is clinically characterized by an aggressive phenotype and bad prognosis. TNBC does not benefit from any targeted therapy, so further characterization is needed to define subgroups with potential therapeutic value. In this work, the proteomes of one hundred twenty-five formalin-fixed paraffin-embedded samples from patients diagnosed with triple negative breast cancer were analyzed by mass spectrometry using data-independent acquisition. Hierarchical clustering, probabilistic graphical models and Significance Analysis of Microarrays were used to characterize molecular groups. Additionally, a predictive signature related with relapse was defined. Two molecular groups with differences in several biological processes as glycolysis, translation and immune response, were defined in this cohort, and a prognostic signature based on the abundance of proteins RBM3 and NIPSNAP1 was defined. This predictor split the population into low-risk and high-risk groups. The differential processes identified between the two molecular groups may serve to design new therapeutic strategies in the future and the prognostic signature could be useful to identify a population at high-risk of relapse that could be directed to clinical trials.
HostingRepository	PRIDE
AnnounceDate	2022-02-14
AnnouncementXML	Submission_2022-02-14_03:57:13.404.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Cristina Chiva
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2020-09-15 09:30:20	ID requested
1	2022-02-14 03:40:47	announced
⏵ 2	2022-02-14 03:57:14	announced	2022-02-14: Updated project metadata.

Garc, í, a-Adri, á, n S, Trilla-Fuertes L, G, á, mez-Pozo A, Chiva C, L, ó, pez-Vacas R, L, ó, pez-Camacho E, Zapater-Moros A, Lumbreras-Herrera MI, Hardisson D, Y, é, benes L, Zamora P, Sabid, ó E, Fresno Vara J Á, Espinosa E, Molecular characterization of triple negative breast cancer formaldehyde-fixed paraffin-embedded samples by data-independent acquisition proteomics. Proteomics, 22(3):e2100110(2022) [pubmed]

ProteomeXchange project tag: EPIC-XS

submitter keyword: DIA, FFPE,breast cancer, DIA+

Juan Ángel Fresno Vara
contact affiliation	Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain
contact email	juanangel.fresno@salud.madrid.org
lab head
Cristina Chiva
contact affiliation	University Pompeu Fabra
contact email	cristina.chiva@upf.edu
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/2022/02/PXD021491

PRIDE project URI

• PRIDE
  1. PXD021491
     1. Label: PRIDE project
     2. Name: Molecular characterization of triple negative breast cancer formaldehyde-fixed paraffin-embedded samples by DIA proteomics