PXD007767-2

PXD007767 is an original dataset announced via ProteomeXchange.

Title	Novel stool-based protein biomarkers for improved colorectal cancer screening
Description	Fecal immunochemical tests (FIT) detecting hemoglobin in stool are widely used for non-invasive colorectal cancer (CRC) screening, but their sensitivity leaves room for improvement. Our aim is to identify novel protein biomarkers in stool that outperform or complement hemoglobin in detecting CRCs and advanced adenomas (AAs). Stool samples (one series of 12 CRCs and 10 controls, and a second series of 81 CRCs, 40 AAs, 43 non-advanced adenomas and 129 controls) were analyzed by mass-spectrometry and searched for human proteins. Classification and regression tree and logistic regression analyses were performed to identify protein combinations that differentiated CRCs and/or AAs from controls. Antibody-based assays for four selected proteins were performed on an independent series of FIT samples (14 CRCs, 16 AAs, 18 non-advanced adenomas and 24 controls) Results: In total, 834 human proteins were identified, of which 29 were significantly enriched in CRCs versus controls in both stool sample series. Combinations of four proteins reached sensitivities of 80% and 45% for detecting CRCs and AAs, at 95% specificity, which was higher than hemoglobin alone.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:05:05.265.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sander Piersma
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	LTQ FT; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-09-18 03:42:27	ID requested
1	2020-05-26 13:24:00	announced
⏵ 2	2024-10-22 05:05:13	announced	2024-10-22: Updated project metadata.

10.1002/path.5369;

Komor MA, Bosch LJ, Coup, é VM, Rausch C, Pham TV, Piersma SR, Mongera S, Mulder CJ, Dekker E, Kuipers EJ, van de Wiel MA, Carvalho B, Fijneman RJ, Jimenez CR, Meijer GA, de Wit M, Proteins in stool as biomarkers for non-invasive detection of colorectal adenomas with high risk of progression. J Pathol, 250(3):288-298(2020) [pubmed]

curator keyword: Biomedical

submitter keyword: Human, screening, CRC, label-free, stool, biomarker, colorectal cancer

Connie Ramona Jimenez
contact affiliation	OncoProteomics Laboratory, Dept of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
contact email	c.jimenez@vumc.nl
lab head
Sander Piersma
contact affiliation	OncoProteomics Laboratory, dept of Medical Oncology, VUmc Medical Center, Amsterdam, The Netherlands
contact email	s.piersma@vumc.nl
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/2020/05/PXD007767

PRIDE project URI

• PRIDE
  1. PXD007767
     1. Label: PRIDE project
     2. Name: Novel stool-based protein biomarkers for improved colorectal cancer screening