PXD057692-2

PXD057692 is an original dataset announced via ProteomeXchange.

Title	Proteomic analysis of plasma and duodenal tissue in patients with celiac disease: identification of potential diagnostic noninvasive biomarkers
Description	The pathogenesis of celiac disease (CeD) remains incompletely understood. Traditional diagnostic techniques for CeD include serological testing and endoscopic examination; however, they have limitations. Therefore, there is a need to identify novel noninvasive biomarkers for CeD diagnosis. We analyzed duodenal and plasma samples from CeD patients by four-dimensional data-dependent acquisition (4D-DIA) proteomics. Differentially expressed proteins (DEPs) were identified for functional analysis and to propose blood biomarkers associated with CeD diagnosis. In duodenal and plasma samples, respectively, 897 and 140 DEPs were identified. Combining weighted gene co-expression network analysis(WGCNA) with the DEPs, five key proteins were identified across three machine learning methods. FGL2 and TXNDC5 were significantly elevated in the CeD group, while CHGA expression showed an increasing trend, but without statistical significance. The receiver operating characteristic curve results indicated an area under the curve (AUC) of 0.7711 for FGL2 and 0.6978 for TXNDC5, with a combined AUC of 0.8944. Exploratory analysis using Mfuzz and three machine learning methods identified four plasma proteins potentially associated with CeD pathological grading (Marsh classification): FABP, CPOX, BHMT, and PPP2CB. We conclude that FGL2 and TXNDC5 deserve exploration as potential sensitive, noninvasive diagnostic biomarkers for CeD.
HostingRepository	PRIDE
AnnounceDate	2024-12-03
AnnouncementXML	Submission_2024-12-03_06:50:37.592.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Feng Gao
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-11-08 21:28:56	ID requested
1	2024-11-15 09:17:59	announced
⏵ 2	2024-12-03 06:50:37	announced	2024-12-03: Updated project metadata.

10.1038/S41598-024-80391-5;

submitter keyword: celiac disease

4D-DIA proteomics

machine learning

WGCNA

Marsh classification

biomarker

Feng Gao
contact affiliation	Department of Gastroenterology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang Uygur Autonomous Region, China
contact email	xjgf@sina.com
lab head
Feng Gao
contact affiliation	Department of Gastroenterology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang Uygur Autonomous Region, China
contact email	xjgf@sina.com
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/2024/11/PXD057692

PRIDE project URI

• PRIDE
  1. PXD057692
     1. Label: PRIDE project
     2. Name: Proteomic analysis of plasma and duodenal tissue in patients with celiac disease: identification of potential diagnostic noninvasive biomarkers