PXD059176

PXD059176 is an original dataset announced via ProteomeXchange.

Title	Spatial proteomics to discover aging-associated alterations in the renal tubulointerstitium
Description	The preservation of tissue architecture and morphology, in formalin-fixed paraffin-embedded (FFPE) tissue enables spatial resolution at the cellular and sub-cellular level. Laser capture microdissection (LCM) combined with liquid chromatography mass spectrometry analysis has enabled the collection of tissue areas within a spatial context for proteome profiling of FFPE tissues. In this study, we performed proteome profiling of the renal normal tubulointerstitial tissue among cohorts of young (<40 years) and old (>70 years) individuals aiming to spatially correlating with these microstructural features to proteome profile. To gain in-depth understanding of kidney tubulointerstitial tissue and identify renal aging-associated proteins, a multiplexing strategy using tandem mass tag was employed, resulting in the quantitation of 7,371 proteins. We demonstrated that our approach allowed for identification kidney specific proteins with low abundance such as fibrocystin. In addition, 162 solute carrier proteins from 47 solute carrier families were identified, which are enriched in proximal and distal tubule cells. Finally, we discovered proteomic signature associated with renal aging, which includes metalloproteinase inhibitor 3, matrix metallopeptidase 7, phospholipase A2 group IIA, cytokine receptor like factor 1 and solute carrier family 23 member 1. Overall, we demonstrated the power of LCM combined with proteomics to leverage archived FFPE tissue samples to investigate renal aging because of its adaptability and sample backed compatibility.
HostingRepository	PRIDE
AnnounceDate	2025-10-20
AnnouncementXML	Submission_2025-10-19_17:06:20.934.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Akhilesh Pandey
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	monohydroxylated residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-12-22 23:32:32	ID requested
⏵ 1	2025-10-19 17:06:21	announced

Mun DG, Pujari GP, Sachdeva G, Madden BJ, Charlesworth MC, Johnson KL, Archila LR, Alexander MP, Denic A, Mullan AF, Sharma V, Larson NB, Luehrs AC, Rule AD, Pandey A, Spatial proteomics to discover aging-associated alterations in the renal tubulointerstitium. Clin Proteomics, 22(1):37(2025) [pubmed]

10.1186/s12014-025-09550-8;

submitter keyword: FFPE, LCM,Kidney, LC-MS/MS

Akhilesh Pandey
contact affiliation	Department of Laboratory Medicine and Pathology, Mayo Clinic
contact email	pandey.akhilesh@mayo.edu
lab head
Akhilesh Pandey
contact affiliation	Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905
contact email	pandey.akhilesh@mayo.edu
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/2025/10/PXD059176

PRIDE project URI

• PRIDE
  1. PXD059176
     1. Label: PRIDE project
     2. Name: Spatial proteomics to discover aging-associated alterations in the renal tubulointerstitium