PXD044246

PXD044246 is an original dataset announced via ProteomeXchange.

Title	Dissection of prognostic traits in colorectal cancer using multi-dimensional proteomics
Description	Colorectal cancer (CRC) is the third most commonly diagnosed cancer worldwide and the second leading cause of cancer death globally. The molecular mechanisms underlying CRC have been investigated using different omics technologies including genomics, proteomics, and metabolomics. Resulting molecular signatures can be employed to stratify CRC patients and aid decisions about therapies or evaluate prognostic outcome. However, molecular biomarkers for identification of patients at increased risk of disease recurrence are currently lacking. Here, we present a comprehensive multi-omics analysis of a Danish colorectal cancer tumor cohort composed of 412 biopsies from tumors of 371 patients diagnosed at stage II or III. We identified microsatellite instability and tumor stage as the two main clinical traits statistically linked to the risk of relapse. Integrating proteomics and transcriptomics data, we classified the tumors into four consensus molecular subtypes, and found that stage III tumors showed higher epithelial-to-mesenchymal transition signature than stage II. As the mesenchymal-like subtype is the one with most invasive and metastatic phenotype, we focused on proteins over-expressed in this subtype and evaluated their potential as relapse-free survival markers. Specifically, we studied on the role of CAVIN1 in the formation and progression of colorectal cancer in a 3D in vitro model. Finally, using hybrid-DIA phosphoproteomics profiling we identified an mTOR kinase activity footprint that was specific to patients that suffered post-surgery relapse. Compared to previous omics analysis of CRC, our multi-omics classification provided deeper insights into the mesenchymal-like subtypes with stronger correlations with risk of relapse.
HostingRepository	PRIDE
AnnounceDate	2025-03-27
AnnouncementXML	Submission_2025-03-26_17:31:30.236.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ana Martinez-Val
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2023-07-31 21:46:25	ID requested
⏵ 1	2025-03-26 17:31:30	announced

Dataset with its publication pending

submitter keyword: proteomics,Colorectal cancer, phosphoproteomics

Jesper V. Olsen
contact affiliation	Vice Director, Professor Novo Nordisk Foundation Center for Protein Research Proteomics Program University of Copenhagen Faculty of Health and Medical Sciences Blegdamsvej 3b DK-2200 Copenhagen Denmark
contact email	jesper.olsen@cpr.ku.dk
lab head
Ana Martinez-Val
contact affiliation	Novo Nordisk Foundation Center for Protein Research
contact email	ana.mdval@cpr.ku.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/2025/03/PXD044246

PRIDE project URI

• PRIDE
  1. PXD044246
     1. Label: PRIDE project
     2. Name: Dissection of prognostic traits in colorectal cancer using multi-dimensional proteomics