PXD040812

PXD040812 is an original dataset announced via ProteomeXchange.

Title	Kidney Organoids treated with TNFa at 5 ng/mL and 50ng/mL for 24h and 48h
Description	This dataset serves as comparison for PXD029718 using a different organoid differentiation protocol – as requested by reviewers. Kidney organoids are a promising model to study kidney disease, but use is constrained by limited knowledge of their functional protein expression profile. We aimed to define the organoid proteome and transcriptome trajectories over culture duration and upon exposure to TNFα, a cytokine stressor. Older organoids increased deposition of extracellular matrix but decreased expression of glomerular proteins. Single cell transcriptome integration revealed that most proteome changes localized to podocytes, tubular and stromal cells. TNFα-treatment of organoids effected 320 differentially expressed proteins, including cytokines and complement components. Transcript expression of these 320 proteins was significantly higher in individuals with poorer clinical outcomes in proteinuric kidney disease. Key TNFα-associated protein (C3 and VCAM1) expression was increased in both human tubular and organoid kidney cell populations, highlighting the potential for organoids to advance biomarker development. By integrating kidney organoid omic layers, incorporating a disease-relevant cytokine stressor and comparing to human data, we provide crucial evidence of functional relevance of the kidney organoid model to human kidney disease.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:45:40.512.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Fatih Demir
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2023-03-13 07:44:37	ID requested
1	2023-05-12 09:13:20	announced
⏵ 2	2024-10-22 05:45:40	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: Human Organoids Kidney

Markus Matthias Rinschen
contact affiliation	Aarhus University Department of Biomedicine Høegh-Guldbergsgade 10 DK-8000 Aarhus C
contact email	rinschen@biomed.au.dk
lab head
Fatih Demir
contact affiliation	Aarhus University Department of Biomedicine Markus Rinschen Lab
contact email	fatih.demir@biomed.au.dk
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/2023/05/PXD040812

PRIDE project URI

• PRIDE
  1. PXD040812
     1. Label: PRIDE project
     2. Name: Kidney Organoids treated with TNFa at 5 ng/mL and 50ng/mL for 24h and 48h