PXD008012

PXD008012 is an original dataset announced via ProteomeXchange.

Title	In vivo phosphoproteomics reveals kinase activity profiles that predict treatment outcome in triple-negative breast cancer
Description	Triple-negative breast cancer (TNBC) lacks prognostic and predictive markers. We used high-throughput phosphoproteomics to build a functional TNBC taxonomy. A cluster of 159 phosphosites was upregulated in relapsed cases of a training set (n=34 patients). Eleven hyperactive kinases accounted for this phosphoprofile. A massspectrometry-to-immunohistochemistry translation step that assessed 113 TNBC validation specimens revealed that 6/12 kinases (PRKCE, KIT, PNKP, ERK, CDK6, and P70S6K) preserved independent prognostic value. The kinases split the validation set into two patterns: one (0/6 hyperactive kinases; 29% of the patients) associated with a 93.5% cure rate. The other (≥1 hyperactive kinase; 37 subpatterns) was associated with a 9.5-fold higher relapse risk. Each kinase pattern agglutinated different mutational patterns. Drug regimens designed based on these six kinases showed synergistic activity in vitro and in vivo. Our results elucidated novel phosphosites/kinases that are implicated in TNBC and provide a ready-to-use, actionable target-based clinical classification system for TNBC
HostingRepository	PRIDE
AnnounceDate	2018-07-23
AnnouncementXML	Submission_2019-03-07_05:40:01.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Javier Muñoz
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2017-10-23 02:04:44	ID requested
1	2018-07-19 03:16:40	announced
2	2018-07-24 05:27:35	announced	Updated contact info
⏵ 3	2019-03-07 05:40:03	announced	Updated publication reference for PubMed record(s): 30158526.

Zagorac I, Fernandez-Gaitero S, Penning R, Post H, Bueno MJ, Mouron S, Manso L, Morente MM, Alonso S, Serra V, Mu, ñ, oz J, G, ó, mez-L, ó, pez G, Lopez-Acosta JF, Jimenez-Renard V, Gris-Oliver A, Al-Shahrour F, Pi, ñ, eiro-Ya, ñ, ez E, Montoya-Suarez JL, Apala JV, Moreno-Torres A, Colomer R, Dopazo A, Heck AJR, Altelaar M, Quintela-Fandino M, In vivo phosphoproteomics reveals kinase activity profiles that predict treatment outcome in triple-negative breast cancer. Nat Commun, 9(1):3501(2018) [pubmed]

ProteomeXchange project tag: PRIME-XS Project

curator keyword: Biomedical

submitter keyword: triple negative breast cancer, phophoproteomics, kinases

Miguel Quintela-Fandino
contact affiliation	Breast Cancer Clinical Research Unit, CNIO, Spanish National Cancer Research Centre, Spain
contact email	mquintela@cnio.es
lab head
Javier Muñoz
contact affiliation	Breast Cancer Clinical Research Unit, CNIO, Spanish National Cancer Research Centre, Spain
contact email	jmunozpe@cnio.es
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/2018/07/PXD008012

PRIDE project URI

• PRIDE
  1. PXD008012
     1. Label: PRIDE project
     2. Name: In vivo phosphoproteomics reveals kinase activity profiles that predict treatment outcome in triple-negative breast cancer