PXD017025-2

PXD017025 is an original dataset announced via ProteomeXchange.

Title	Comprehensive proteomic characterization reveals subclass-specific molecular aberrations within triple-negative breast cancer
Description	Triple-negative breast cancer (TNBC) is regarded as the most aggressive subtype of breast cancer lacking targeted therapies. This is attributed to its high heterogeneity that complicates elucidation of its molecular aberrations. Here, we report identification of specific proteome expression profiles pertaining to two TNBC subclasses, basal A and basal B, through in-depth proteomics analysis of breast cancer cells. We observed that kinases and proteases displayed unique expression patterns within the subclasses, similar to whole proteome clusters. Systematic analyses of protein-protein interaction and co-regulation networks of these kinases and proteases unraveled dysregulated pathways and plausible targets for each TNBC subclass. Among these, we identified kinases AXL, PEAK1 and TGFBR2, and proteases FAP, UCHL1 and MMP2/14, as specific targets for basal B subclass, which represents the more aggressive TNBC cell lines. Our study thus highlights intricate mechanisms and distinct targets within TNBC, and emphasizes that these have to be exploited in a subclass-specific manner rather than a one-for-all TNBC therapy.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:59:48.532.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Asfa Alli Shaik
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2020-01-09 00:41:27	ID requested
1	2020-03-03 05:47:10	announced
⏵ 2	2024-10-22 04:59:50	announced	2024-10-22: Updated project metadata.

Kosok M, Alli-Shaik A, Bay BH, Gunaratne J, Comprehensive Proteomic Characterization Reveals Subclass-Specific Molecular Aberrations within Triple-negative Breast Cancer. iScience, 23(2):100868(2020) [pubmed]

10.1016/j.isci.2020.100868;

curator keyword: Biomedical

submitter keyword: triple-negative, TNBC, proteomics, mass spectrometry, protease,Breast cancer, kinase

Jayantha Gunaratne
contact affiliation	Translational Biomedical Proteomics, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, Singapore 138673
contact email	jayanthag@imcb.a-star.edu.sg
lab head
Asfa Alli Shaik
contact affiliation	IMCB
contact email	asfaas@imcb.a-star.edu.sg
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/2020/03/PXD017025

PRIDE project URI

• PRIDE
  1. PXD017025
     1. Label: PRIDE project
     2. Name: Comprehensive proteomic characterization reveals subclass-specific molecular aberrations within triple-negative breast cancer