PXD042342

PXD042342 is an original dataset announced via ProteomeXchange.

Title	Fibroblast-derived matrix models desmoplastic properties and forms a prognostic signature in cancer progression
Description	The desmoplastic reaction observed in many cancers is a hallmark of disease progression and prognosis, particularly in breast and pancreatic cancer. Stromal-derived extracellular matrix (ECM) is significantly altered in desmoplasia, and as such plays a critical role in driving cancer progression. Using fibroblast-derived matrices (FDMs), we show that cancer cells have increased growth on cancer-associated FDMs, comparing to FDMs derived from non-malignant tissue (normal) fibroblasts. We assess the changes in ECM characteristics from normal to cancer-associated stroma at the primary tumor site. Compositional, structural, and mechanical analyses reveal significant differences, with an increase in abundance of core ECM proteins, coupled with an increase in stiffness and density in cancer-associated FDMs. From compositional changes of FDM we derived a 36-ECM proteins’ signature, which we show largely matching the changes in pancreatic ductal adenocarcinoma (PDAC) tumor and metastases progression, as well as at the transcriptomic level in multiple cancer types in patients, predictive of their survival. Together, our results show relevance of FDMs for cancer modelling and identification of desmoplastic ECM components for further mechanistic studies.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:54:06.516.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Erwin Schoof
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	acetylated residue; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2023-05-18 12:53:36	ID requested
1	2023-07-17 08:27:46	announced
2	2023-08-08 00:53:13	announced	2023-08-08: Updated project metadata.
3	2023-08-08 01:21:41	announced	2023-08-08: Updated project metadata.
4	2023-11-14 09:04:42	announced	2023-11-14: Updated project metadata.
⏵ 5	2024-10-22 05:54:07	announced	2024-10-22: Updated project metadata.

Penner I, Dejung M, Freiwald A, Butter F, Chen JX, Plachter B, Proteome changes of fibroblasts and endothelial cells upon incubation with human cytomegalovirus subviral Dense Bodies. Sci Data, 10(1):517(2023) [pubmed]

10.1038/s41597-023-02418-2;

submitter keyword: cancer,lc-ms, matrix, mouse

Janine Erler
contact affiliation	Biotech Research and Innovation Centre (BRIC), University of Copenhagen (UCPH), Copenhagen, Denmark
contact email	janine.erler@bric.ku.dk
lab head
Erwin Schoof
contact affiliation	Technical University of Denmark
contact email	erws@dtu.dk
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/2023/07/PXD042342

PRIDE project URI

• PRIDE
  1. PXD042342
     1. Label: PRIDE project
     2. Name: Fibroblast-derived matrix models desmoplastic properties and forms a prognostic signature in cancer progression