PXD055306-1

PXD055306 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Multi-omics analysis of triple-negative breast cancers
Description	Abstract The triple-negative breast cancer (TNBC) accounts for approximately 15% of all Breast Cancer (BC) cases. However, the prognosis and clinical outcomes of TNBC are worse than those of other BC subtypes due to a greater tumor and few therapeutically targetable oncogenic drivers. Numerous studies have employed genomic and transcriptomic approaches to identify clinically actionable TNBC subtypes in a comprehensive and unbiased manner using. While these analyses have advanced our knowledge of the molecular changes underlying TNBC, their clinical utility remains limited thus far. Given that proteins are the principal effector molecules of cellular signaling and function, we use a proteomic approach to quantitatively compare the abundances of 6,306 proteins across 55 formalin-fixed and paraffin-embedded (FFPE) TNBC tumors to reveal actionable pathways for anti-cancer treatment. We identified four major TNBC clusters by unsupervised clustering analysis of protein abundances. In addition, analyses of clinicopathological characteristics revealed associations between proteomic results and clinical phenotypes exhibited by each subtype. We validate the findings of our proteomics analysis, by inferring immune and stromal cell type composition from genome-wide DNA methylation profiles. Finally, quantitative proteomics on TNBC cell lines was conducted to identify representative in vitro models for each subtype. Collectively, our multi-omics data provide novel subtype-specific insights such as potential biomarkers, molecular drivers, and pharmacologic vulnerabilities for further investigations.
HostingRepository	MassIVE
AnnounceDate	2025-02-02
AnnouncementXML	Submission_2025-02-02_09:16:57.962.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Arminja Nadine Kettenbach
SpeciesList	scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-28 17:33:35	ID requested
⏵ 1	2025-02-02 09:16:58	announced

Publication List

no publication

no publication

Keyword List

submitter keyword: TNBC, cancer, tumor, subtypes

submitter keyword: TNBC, cancer, tumor, subtypes

Contact List

Arminja Kettenbach
contact affiliation	Geisel School of Medicine at Dartmouth
contact email	Arminja.N.Kettenbach@Dartmouth.edu
lab head
Arminja Nadine Kettenbach
contact affiliation	Dartmouth
contact email	Arminja.N.Kettenbach@Dartmouth.edu
dataset submitter

Full Dataset Link List

MassIVE dataset URI
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://massive.ucsd.edu/v08/MSV000095715/

MassIVE dataset URI

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://massive.ucsd.edu/v08/MSV000095715/