PXD064643 is an
original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Biopsy-derived colonoid monolayers reveal a range of persistent mucosal defects in patients with ulcerative colitis |
| Description | Rationale: Ulcerative colitis (UC) is characterized by colonic mucosal inflammation and barrier dysfunction. We hypothesize that UC causes persistent defects in mucosal homeostasis, evident even in the absence of inflammation, contributing to disease chronicity. Objective: To test this, we grew patient biopsy-derived sigmoid colonoids into air-liquid interface (ALI) monolayers, characterizing them through microscopy, proteomics, bulk RNAseq, and their susceptibility to UC patient-isolated Escherichia coli pathobiont p19A. Findings: Non-IBD ALI monolayers formed uniform crypt-like structures, mature goblet cells and a thick mucus layer containing all epithelial-derived proteins previously identified in human colonic mucus. In contrast, ALI monolayers from UC patients displayed a range of impairments, from distorted crypt-like structures and a thinner and more permeable mucus layer to severe defects in cellular differentiation and crypt development. Transcriptome analysis identified activated pathways associated with extracellular matrix formation and cell signaling, including numerous cancer-associated genes in UC ALI monolayers, which also proved significantly more susceptible to E. coli p19A. Conclusions: The culturing of patient biopsies into ALI colonoid monolayers provides a powerful model to assess human mucosal development, healing, homeostasis and mucus barrier function, revealing that UC-derived colonoids display a range of developmental and functional defects that persist in the absence of inflammation. |
| HostingRepository | PRIDE |
| AnnounceDate | 2026-01-29 |
| AnnouncementXML | Submission_2026-01-29_11:09:26.969.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Dominique Levesque |
| SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; |
| ModificationList | iodoacetamide derivatized residue |
| Instrument | timsTOF Pro |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|
| 0 | 2025-06-04 12:45:24 | ID requested | |
| ⏵ 1 | 2026-01-29 11:09:27 | announced | |
Publication List
Keyword List
| submitter keyword: Mucus, Air-liquid interface, Pathobiont,Ulcerative colitis, Mucosal homeostasis |
Contact List
| Bruce A. Vallance |
|---|
| contact affiliation | Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada |
| contact email | bvallance@cw.bc.ca |
| lab head | |
| Dominique Levesque |
|---|
| contact affiliation | University of Sherbrooke, FM Boisvert lab |
| contact email | dominique.levesque@usherbrooke.ca |
| dataset submitter | |
Full Dataset Link List
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/2026/01/PXD064643 |
| PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD064643
- Label: PRIDE project
- Name: Biopsy-derived colonoid monolayers reveal a range of persistent mucosal defects in patients with ulcerative colitis
