PXD014414-1

PXD014414 is an original dataset announced via ProteomeXchange.

Title	Quantitative proteomic landscape of metaplastic breast carcinoma pathological subtypes and their relationship to triple-negative tumors
Description	Metaplastic breast carcinoma (MBC) is the most aggressive form of triple-negative cancer (TNBC), defined by the presence of “metaplastic” components of spindle, squamous, or sarcomatoid histology. The protein profiles underpinning the pathological subtypes and metastatic behavior of MBC are unknown. Using multiplex quantitative tandem mass tag-based proteomics we quantified 5,798 proteins in MBC, TNBC, and normal breast from 27 patients. MBC showed increased epithelial-to-mesenchymal transition and extracellular matrix, and reduced metabolic pathways compared to TNBC. MBC subtypes exhibited distinct upregulated profiles; translation and ribosomal events in spindle, inflammation and apical junctions in squamous, and extracellular matrix in sarcomatoid. Comparison of the proteomes of spindle MBC with MMTV-cre;Ccn6fl/fl spindle MBC tumors revealed a shared spindle-specific signature of 17 upregulated proteins involved in translation (e.g. RPL4,6,18, P3H1, PYCR1) and 19 downregulated proteins with roles in cell metabolism (e.g. ADH1B, ADH1C, LIPE, SOD1, FABP4). These data identify subtype specific MBC protein profiles providing biomarkers and therapeutic targets.
HostingRepository	PRIDE
AnnounceDate	2020-04-22
AnnouncementXML	Submission_2020-04-22_03:13:20.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sabra Djomehri
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2019-06-27 08:37:25	ID requested
⏵ 1	2020-04-22 03:13:22	announced
2	2024-10-22 05:02:29	announced	2024-10-22: Updated project metadata.

Djomehri SI, Gonzalez ME, da Veiga Leprevost F, Tekula SR, Chang HY, White MJ, Cimino-Mathews A, Burman B, Basrur V, Argani P, Nesvizhskii AI, Kleer CG, Quantitative proteomic landscape of metaplastic breast carcinoma pathological subtypes and their relationship to triple-negative tumors. Nat Commun, 11(1):1723(2020) [pubmed]

submitter keyword: metaplastic breast carcinoma, LC-MS/MS shotgun proteomics, tandem mass tag (TMT) labeling, triple-negative breast cancer, precision therapy, CCN6, WISP3

Celina G. Kleer
contact affiliation	Harold Oberman Collegiate Professor of Pathology Director, Breast Pathology Program University of Michigan Medical School
contact email	kleer@umich.edu
lab head
Sabra Djomehri
contact affiliation	University of Michigan
contact email	djomehri@umich.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/2020/04/PXD014414

PRIDE project URI

• PRIDE
  1. PXD014414
     1. Label: PRIDE project
     2. Name: Quantitative proteomic landscape of metaplastic breast carcinoma pathological subtypes and their relationship to triple-negative tumors