PXD060933-1

PXD060933 is an original dataset announced via ProteomeXchange.

Title	In-Depth Proteomic Analysis of Stage II Colorectal Cancer for the Identification of Recurrence Biomarkers in FFPE Tissue and Extracellular Vesicles
Description	Colorectal cancer (CRC) is a leading cause of cancer-related death worldwide, with stage II CRC patients presenting unique challenges due to their heterogeneous outcomes. Despite curative surgical resection, 15-20% of stage II CRC patients experience recurrence within five years of diagnosis. Current prognostic models, based on clinicopathologic features such as vascular invasion, poor differentiation, and adverse molecular profiles, lack precision in predicting recurrence, highlighting the need for other complementary tools. Advances in proteomics have positioned formalin-fixed paraffin-embedded (FFPE) tissues and small extracellular vesicles (sEVs) as promising sources for biomarker identification. FFPE tissues offer a wealth of retrospective diagnostic material, while sEVs, particularly exosomes, encapsulate tumor-derived proteins and nucleic acids, providing minimally invasive insights into the tumor microenvironment. Proteomic profiling of these samples should allow the identification of molecular alterations linked to tumor aggressiveness and recurrence, paving the way for novel diagnostic and prognostic applications. In this study, we here combine proteomics analyses of paired FFPE tissues and sEVs to identify stage II CRC associated biomarkers and tumor biopsies, plasma of CRC patients and controls, and immunohistochemistry and in vitro and in vivo analyses to validate proteomics results. Among the identified candidates, CDCA2 emerged as a interesting driver of tumor formation, progression, and metastasis in CRC. Transient knockdown experiments demonstrated that its depletion impaired key tumorigenic processes, including proliferation, adhesion, migration, and invasion. Additionally, this study validated MANF as a plasma biomarker capable of distinguishing recurrent from non-recurrent CRC patients, offering potential for improving patient stratification and personalized treatment strategies in combination with other markers. Interestingly, our multifaceted approach allowed the identification of dysregulated proteins associated to CRC recurrence.
HostingRepository	PRIDE
AnnounceDate	2026-05-03
AnnouncementXML	Submission_2026-05-03_06:51:06.004.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ana Montero Calle
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-02-18 15:59:28	ID requested
⏵ 1	2026-05-03 06:51:07	announced

10.1021/ACS.JPROTEOME.5C01148;

submitter keyword: None

Rodrigo Barderas
contact affiliation	Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
contact email	r.barderasm@isciii.es
lab head
Ana Montero Calle
contact affiliation	Instituto de Salud Carlos III
contact email	ana.monteroc@isciii.es
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/2026/05/PXD060933

PRIDE project URI

• PRIDE
  1. PXD060933
     1. Label: PRIDE project
     2. Name: In-Depth Proteomic Analysis of Stage II Colorectal Cancer for the Identification of Recurrence Biomarkers in FFPE Tissue and Extracellular Vesicles