PXD052341-1

PXD052341 is an original dataset announced via ProteomeXchange.

Title	Deep Visual Proteomics advances human colon organoid models by revealing a switch to an in vivo-like phenotype upon xenotransplantation
Description	Intestinal epithelial damage predisposes to chronic disorders like inflammatory bowel disease. The organoid model allows the cultivation, expansion and analysis of primary intestinal epithelial cells and has been instrumental in studying epithelial behavior in homeostasis and disease. Recent advances in organoid transplantation lay the base for studies of human epithelial cell behavior within the intestinal tissue context. It remained unclear how organoid transplantation into the colon affects epithelial phenotypes, which is key to assessing the model’s suitability to study human epithelial cells. We employed Deep Visual Proteomics, integrating AI-guided cell classification, laser microdissection, and an improved proteomics pipeline to study the human colon mucosa. Thereby, we created the first cell type-resolved proteomics dataset of human intestinal epithelial cells within human tissue, in vitro organoids, and the murine colon post-xenotransplantation. Our findings reveal that in vitro conditions induce a proliferative organoid phenotype, which is reversible upon transplantation and adjustment of organoid culturing conditions.
HostingRepository	PRIDE
AnnounceDate	2025-09-14
AnnouncementXML	Submission_2025-09-14_09:03:22.009.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mario Oroshi
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Astral

Revision	Datetime	Status	ChangeLog Entry
0	2024-05-17 05:09:26	ID requested
⏵ 1	2025-09-14 09:03:22	announced

Dataset with its publication pending

submitter keyword: Colon, Spatial Proteomics, Deep Visual Proteomics, Organoids,Proteomics

Matthias Mann
contact affiliation	Novo Nordisk Foundation Center for Protein Research, UCPH, DK; Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
contact email	mmann@biochem.mpg.de
lab head
Mario Oroshi
contact affiliation	Proteomics
contact email	oroshi@biochem.mpg.de
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/2025/09/PXD052341

PRIDE project URI

• PRIDE
  1. PXD052341
     1. Label: PRIDE project
     2. Name: Deep Visual Proteomics advances human colon organoid models by revealing a switch to an in vivo-like phenotype upon xenotransplantation