PXD042671-1

PXD042671 is an original dataset announced via ProteomeXchange.

Title	Proteomics of cell-free patient-derived scaffolds from breast cancer identify clinically relevant imprinted proteins and cancer-progressing properties
Description	Breast cancer is a heterogenous disease that is difficult to model in vitro. Frozen primary breast cancers were decellularised to generate patient-derived scaffolds which are used to model 3D growth for cancer cell lines. The cell-free cancer microenvironments in the patient-derived scaffolds influence breast cancer cell line phenotypes and enrich for cells with cancer stem cell characteristics. Growth in patient-derived scaffold cultures also influenced the expression of epithelial-to-mesenchymal transition-related genes, and several gene expression changes in the model could be associated to clinical parameters of the original tumors and corresponding patients. Previous studies also demonstrated that the relative protein composition in the cell-free cancers were related to tumor grade and proliferation in cancer cells, suggesting that the relative proteomic composition varies between individual microenvironments. Therefore, we decellularised a larger breast cancer cohort to better characterize the cell-free microenvironments and potentially link to clinical features of the tumors and patients, which could be used to identify novel processes and targets that could be used to better model the disease or targeted in drug discovery.
HostingRepository	PRIDE
AnnounceDate	2024-04-18
AnnouncementXML	Submission_2024-04-18_04:58:35.418.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Johannes Fuchs
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2023-06-02 07:44:37	ID requested
⏵ 1	2024-04-18 04:58:36	announced

Gustafsson A, Jonasson E, St, å, hlberg A, Landberg G, Proteomics of cell-free breast cancer scaffolds identify clinically relevant imprinted proteins and cancer-progressing properties. Cancer Commun (Lond), 44(6):695-699(2024) [pubmed]

10.1002/cac2.12542;

submitter keyword: patient-derived scaffold,Breast cancer, 3D model, quantitative liquid chromatography-mass spectrometry/mass spectrometry, tumor microenvironment

Göran Landberg
contact affiliation	Department of Pathology, Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, 405 30 Gothenburg, Sweden
contact email	goran.landberg@gu.se
lab head
Johannes Fuchs
contact affiliation	Gothenburg University
contact email	johannes.fuchs@gu.se
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/2024/04/PXD042671

PRIDE project URI

• PRIDE
  1. PXD042671
     1. Label: PRIDE project
     2. Name: Proteomics of cell-free patient-derived scaffolds from breast cancer identify clinically relevant imprinted proteins and cancer-progressing properties