PXD023023-1

PXD023023 is an original dataset announced via ProteomeXchange.

Title	Proteomic profiling of stromal reprogramming in canine simple mammary carcinomas using laser-capture microdissected FFPE tissue
Description	Cancer-associated stroma (CAS) profoundly influences development and progression of tumours including mammary carcinoma (mCA). Spontaneous canine simple mCA represent relevant models of human mCA, notably also with respect to CAS reprogramming. While transcriptomic changes in CAS of mCA are well described, it remains unclear to what extent these differences translate to the protein level. Therefore, we sought to gain insight into the proteomic changes in CAS and compare them with transcriptomic changes in the same tissue. To this end, we analysed CAS and matched normal stroma isolated by laser-capture microdissection (LCM) by LC-MS/MS in a cohort of 14 Formalin-fixed paraffin embedded (FFPE) canine mCAs that we had previously characterized using LCM-RNAseq. Our results reveal clear differences in protein abundance between CAS and normal stroma, which are characterised by changes in the extracellular matrix, the cytoskeleton, and cytokines such as TNF. While the proteomics-based analysis of LCM-FFPE tissue detects fewer targets than RNAseq, the protein and RNA levels show a decent degree of correlation, especially for the most deregulated targets. Moreover, the results from both approaches reveal a comparable picture with regards to pathway activation. Finally, we validate transcriptomic upregulation of LTBP2, IGFBP2, COL6A5, POSTN, FN1, COL4A1, COL12A1, PLOD2, COL4A2, and IGFBP7 in CAS on the protein level and demonstrate their adverse prognostic value for human breast cancer. Given the relevance of canine mCA as model for the human disease, our analysis substantiates these targets as disease-promoting stromal components with implications for breast cancer in both humans and dogs.
HostingRepository	PRIDE
AnnounceDate	2021-03-30
AnnouncementXML	Submission_2021-03-30_11:53:08.814.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Laura Kunz
SpeciesList	scientific name: Canis lupus familiaris; NCBI TaxID: 9615;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2020-12-09 08:28:27	ID requested
⏵ 1	2021-03-30 11:53:09	announced

Dataset with its publication pending

submitter keyword: Tumour microenvironment, cancer-associated stroma, cancer-associated fibroblasts, comparative oncology, breast cancer, tumour stroma, canine breast cancer

Enni Markkanen
contact affiliation	Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zürich, Winterthurerstr. 260, 8057 Zürich, Switzerland
contact email	enni.markkanen@vetpharm.uzh.ch
lab head
Laura Kunz
contact affiliation	ETH
contact email	laura.kunz@fgcz.ethz.ch
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/2021/03/PXD023023

PRIDE project URI

• PRIDE
  1. PXD023023
     1. Label: PRIDE project
     2. Name: Proteomic profiling of stromal reprogramming in canine simple mammary carcinomas using laser-capture microdissected FFPE tissue