PXD013397-1

PXD013397 is an original dataset announced via ProteomeXchange.

Title	Prognostic Markers in Triple-Negative Breast Cancer
Description	There are no widely-accepted prognostic markers currently available to predict outcomes in patients with triple-negative breast cancer (TNBC), and no targeted therapies with confirmed benefit. We have used MALDI mass spectrometry imaging (MSI) of tryptic peptides to compare regions of cancer and benign tissue in 10 formalin-fixed, paraffin-embedded sections of TNBC tumors. Proteins were identified by reference to a peptide library constructed by LC-MALDI-MS/MS analyses of the same tissues. The prognostic significance of proteins that distinguished between cancer and benign regions was estimated by Kaplan-Meier analysis of their gene expression from public databases. Among peptides that distinguished between cancer and benign tissue in at least 3 tissues with a ROC area under the curve >0.7, 14 represented proteins identified from the reference library, including proteins not previously associated with breast cancer. Initial network analysis using the STRING database showed no obvious functional relationships except among collagen subunits COL1A1, COL1A2, and COL63A, but manual curation, including the addition of EGFR to the analysis, revealed a unique network connecting 10 of the 14 proteins. Kaplan-Meier survival analysis to examine the relationship between tumor expression of genes encoding the 14 proteins, and recurrence-free survival (RFS) in patients with basal-like TNBC showed that, compared to low expression, high expression of nine of the genes was associated with significantly worse RFS, most with hazard ratios >2. In contrast, in estrogen receptor-positive tumors, high expression of these genes showed only low, or no, association with worse RFS. These proteins are proposed as putative markers of RFS in TNBC, and some may also be considered as possible targets for future therapies.
HostingRepository	PRIDE
AnnounceDate	2019-05-06
AnnouncementXML	Submission_2019-05-06_07:15:19.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Robert Baxter
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	ultrafleXtreme

Revision	Datetime	Status	ChangeLog Entry
0	2019-04-08 03:18:51	ID requested
⏵ 1	2019-05-06 07:15:19	announced
2	2019-06-03 01:24:11	announced	Updated publication reference for PubMed record(s): 31139569.
3	2024-10-22 03:59:53	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: Human, breast cancer, triple-negative, MALDI imaging

Robert Charles Baxter
contact affiliation	Hormones & Cancer Group, Kolling Institute, University of Sydney, Sydney 2065, Australia
contact email	robert.baxter@sydney.edu.au
lab head
Robert Baxter
contact affiliation	The University of Sydney
contact email	robert.baxter@sydney.edu.au
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/2019/05/PXD013397

PRIDE project URI

• PRIDE
  1. PXD013397
     1. Label: PRIDE project
     2. Name: Prognostic Markers in Triple-Negative Breast Cancer