PXD019037

PXD019037 is an original dataset announced via ProteomeXchange.

Title	Impact of extracellular matrix on breast cancer progression: a biomechanical and shotgun proteomic analysis . ver LC-MSMS
Description	It has become increasingly evident that the local microenvironment of breast cancer (BC) plays an important role in its development and progression. A major component of this microenvironment is the extracellular matrix (ECM) that impact tumor progression. We recently identified an ECM gene expression pattern (ECM3) in ~40 % of BCs significantly associated with high risk of relapse only in patients with grade III tumors. To unravel the characteristic of this BC subgroup, in this study we investigated the biomechemical characteristics of ECM3 matrix in human BC samples with different grade. A collagen-reach matrix with several dense areas and a significantly higher value of stiffness distinguished ECM3 grade III tumors from the other breast carcinomas. Proteins recovered from decellularized BC matrices were analyzed by a shotgun label free proteomic approach. Principal Component Analysis on the total matrix proteome showed a significantly different protein repertoire in ECM3 grade III tumors, reflecting a deranged program of matrix biosynthesis in these tumors. A bioinformatic analysis in terms of pathways and GO enrichment focusing on the proteins more expressed or only expressed in ECM3 grade III BCs showed the significant enrichment of molecules involved in the focal adhesion and integrin pathway, ECM-receptor interaction, Tricarboxylic acid (TCA) cycle, ribosome and RNA transport. Obtained results indicate a marked interaction between ECM3 and undifferentiated BC cells that justifies an increased ribosome biogenesis needed at sites where local translation is required as focal adhesions. Moreover, the enrichment in decellularized matrices of molecules implicated in TCA cycle is indicative of a metabolic shift of these carcinomas toward energy production that gives them a selective advantage.
HostingRepository	PRIDE
AnnounceDate	2025-06-03
AnnouncementXML	Submission_2025-06-03_06:30:11.736.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Simona Nonnis
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2020-05-07 03:22:02	ID requested
⏵ 1	2025-06-03 06:30:12	announced

10.1038/S41523-025-00769-0;

submitter keyword: proteomics;nano LC-MS/MS;breast cancer;extracellular matrix

simona nonnis
contact affiliation	Department of Veterinary Medecine, University of Milan, Milan
contact email	simona.nonnis@unimi.it
lab head
Simona Nonnis
contact affiliation	University of Milan
contact email	simona.nonnis@unimi.it
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/2025/06/PXD019037

PRIDE project URI

• PRIDE
  1. PXD019037
     1. Label: PRIDE project
     2. Name: Impact of extracellular matrix on breast cancer progression: a biomechanical and shotgun proteomic analysis . ver LC-MSMS