PXD056096 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Dynamic multi-omics and mechanistic modeling approach uncovers novel mechanisms of kidney fibrosis progression |
Description | Kidney fibrosis, characterized by excessive extracellular matrix (ECM) deposition, is a progressive disease that, despite affecting 10% of the population, lacks specific treatments and suitable biomarkers. Aimed at unraveling disease mechanisms and identifying potential therapeutic targets, this study presents a comprehensive, time-resolved multi-omics analysis of kidney fibrosis using an in vitro model system based on human kidney PDGFRβ+ mesenchymal cells. Using computational network modeling we integrated transcriptomics, proteomics, phosphoproteomics, and secretomics with imaging of the extracellular matrix (ECM). We quantified over 14,000 biomolecules across seven time points following TGF-β stimulation, revealing distinct temporal patterns in the expression and activity of known and potential novel renal fibrosis markers and modulators. The resulting time-resolved multi-omic network models allowed us to propose mechanisms related to fibrosis progression through early transcriptional reprogramming. Using siRNA knockdowns and phenotypic assays, we validated predictions and elucidated regulatory mechanisms underlying kidney fibrosis. Notably, we demonstrate that several early-activated transcription factors, including FLI1 and E2F1, act as negative regulators of collagen deposition and propose underlying molecular mechanisms. This work advances our understanding of the pathogenesis of kidney fibrosis and provides a valuable resource for the organ fibrosis research community. |
HostingRepository | PRIDE |
AnnounceDate | 2025-04-08 |
AnnouncementXML | Submission_2025-04-08_04:58:05.093.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Frank Stein |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | TMT6plex-126 reporter+balance reagent acylated residue; phosphorylated residue; iodoacetamide derivatized residue |
Instrument | Orbitrap Fusion Lumos |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2024-09-23 08:35:21 | ID requested | |
⏵ 1 | 2025-04-08 04:58:05 | announced | |
Publication List
Dataset with its publication pending |
Keyword List
submitter keyword: time-points, network modeling, multi-omics, secretomics, proteomic, transcriptomics, phosphoproteomics,kidney fibrosis, extracellular matrix |
Contact List
Rainer Pepperkok |
contact affiliation | European Molecular Biology Laboratory (EMBL) Meyerhofstr 17 69117 Heidelberg Germany |
contact email | rainer.pepperkok@embl.org |
lab head | |
Frank Stein |
contact affiliation | EMBL |
contact email | frank.stein@embl.de |
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/2025/04/PXD056096 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD056096
- Label: PRIDE project
- Name: Dynamic multi-omics and mechanistic modeling approach uncovers novel mechanisms of kidney fibrosis progression