PXD048564

PXD048564 is an original dataset announced via ProteomeXchange.

Title	Identification of mechanistic chronic kidney disease biomarkers by comprehensive bulk RNA-seq transcriptomics and SWATH proteomics of the rat sub-total nephrectomy (SNx) model of kidney fibrosis
Description	The rat sub-total nephrectomy (SNx) is a functional model of chronic kidney disease (CKD), where the main pathological driver is glomerular hypertension. Comprehensive transcriptomics and proteomics analyses on the rat SNx model were performed to identify biomarkers in plasma or urine that correlate with kidney disease and functional kidney loss. SWATH proteomics and bulk RNA-sequencing transcriptomics (RNA-seq), with SWATH also performed on plasma and urine. Differential expression analysis demonstrated significant dysregulation of genes and proteins involved in fibrosis, metabolism, and immune response in the SNx rats compared to controls. Gene ontology analysis of the intersecting genes and proteins from both studies demonstrated common biology between animal cohorts that reached the predefined kidney disease thresholds (serum creatinine >2-fold or proteinuria >3-fold increase over sham-operated). About a dozen significantly differential molecules were detected with consistent directional changes in both transcriptomics and proteomics datasets. These molecules were detected independently in kidney (both RNA and protein) and urine (protein only), but not in plasma. The bioinformatics analysis enabled the identification of mechanistic CKD biomarkers whose co-expression have previously been both implicated in fibrosis and detected in urine in CKD patients.
HostingRepository	PRIDE
AnnounceDate	2025-04-25
AnnouncementXML	Submission_2025-04-25_15:20:50.992.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Karin Barnouin
SpeciesList	scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116;
ModificationList	iodoacetamide derivatized residue
Instrument	TripleTOF 6600

Revision	Datetime	Status	ChangeLog Entry
0	2024-01-15 07:50:45	ID requested
⏵ 1	2025-04-25 15:20:51	announced

10.1038/S41598-025-93894-6;

submitter keyword: SNx, DIA, SWATH, Subtotal nephrectomy,Chronic Kidney Disease, Rat, LCMS, Biomarkers

Karin Nathalie Barnouin
contact affiliation	UCB Biopharma (where the work was done) MSD UK (current)
contact email	kbarnouin@bioapicem.com
lab head
Karin Barnouin
contact affiliation	MSD UK
contact email	kbarnouin@bioapicem.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/PXD048564

PRIDE project URI

• PRIDE
  1. PXD048564
     1. Label: PRIDE project
     2. Name: Identification of mechanistic chronic kidney disease biomarkers by comprehensive bulk RNA-seq transcriptomics and SWATH proteomics of the rat sub-total nephrectomy (SNx) model of kidney fibrosis