PXD050655-1

PXD050655 is an original dataset announced via ProteomeXchange.

Title	Biopsy proteome score performs well as an effect measure in a gluten-challenge trial of coeliac disease
Description	Objective Development of novel treatments for coeliac disease (CeD) is dependent on precise tools to monitor changes in gluten-induced mucosal damage. Current histology measures are subjective and difficult to standardise. Biopsy proteome scoring is an objective alternative to histology which is based on robust changes in biological pathways that directly reflect gluten-induced mucosal damage. In this study we aimed to evaluate biopsy proteome scoring as effect measure in a clinical trial setting by measuring intestinal remodeling in response to oral gluten challenge. Design We analyzed biopsies from a gluten challenge trial of treated CeD patients that consumed 3 g (n=6) or 10 g (n=7) gluten per day for 14 days. Sections from individually embedded biopsies collected before and after challenge were processed for proteome scoring (n = 109) and measurement of Vh:Cd ratio (n = 58). Proteome scores were compared to histology, intraepithelial lymphocyte (IEL) frequency and plasma interleukin-2 (IL-2). Results Change in proteome scores were significant for the group of patients who consumed 10 g gluten, but not for the group who consumed 3 g gluten. Altogether, 8 of 13 patients had changes in delta proteome scores above cut-off. Proteome scores correlated with Vh:Cd ratios both at run-in and at day 15. Proteome scores at day 15 correlated with IEL frequency and with serum IL-2 levels measured 4 hours post gluten intake. Conclusion Biopsy proteome scoring is a simple and reliable measure of gluten-induced mucosal remodeling in response to 14-day oral gluten challenge.
HostingRepository	PRIDE
AnnounceDate	2025-04-08
AnnouncementXML	Submission_2025-04-08_05:14:55.958.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	glennda Smithson
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF fleX

Revision	Datetime	Status	ChangeLog Entry
0	2024-03-15 07:03:01	ID requested
⏵ 1	2025-04-08 05:14:56	announced

10.1016/j.cgh.2024.08.005;

Johansen A, Sandve GKF, Maxwell JR, Smithson G, Sollid LM, Stamnaes J, Biopsy Proteome Score Performs Well as an Effect Measure in a Gluten Challenge Trial of Celiac Disease. Clin Gastroenterol Hepatol, 23(5):758-765.e8(2025) [pubmed]

submitter keyword: Human, proteome score, gut biopsy, Evosep, timsTOFfleX, clinical trial

Jorunn Stamnæs
contact affiliation	Department of Immunology, University of Oslo, Norway
contact email	jorunn.stamnas@medisin.uio.no
lab head
glennda Smithson
contact affiliation	Takeda Pharmaceuticals
contact email	glennda.smithson@takeda.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/2025/04/PXD050655

PRIDE project URI

• PRIDE
  1. PXD050655
     1. Label: PRIDE project
     2. Name: Biopsy proteome score performs well as an effect measure in a gluten-challenge trial of coeliac disease