PXD051205-1

PXD051205 is an original dataset announced via ProteomeXchange.

Title	Integrated multiomics implicates dysregulation of ECM and cell adhesion pathways as drivers of severe COVID-associated kidney injury
Description	COVID-19 has been a significant public health concern for the last four years; however, not much is known about the mechanisms that lead to severe COVID-19. In this multicenter study, we combine quantitative urinary proteomics and machine learning to predict severe outcomes in hospitalized COVID-19 patients. We further combine multiple omics datasets to understand the mechanisms that drive severe COVID-19 associated kidney injury. Functional overlap and network analysis of urinary proteomics, plasma proteomics and urine sediment single cell RNA sequencing analysis show extracellular matrix and autophagy associated pathways are highly impacted in severe COVID-19. Differentially abundant proteins associated with these pathways showed high expression in cells in the juxtamedullary nephron, endothelial cells, and podocytes, indicating these kidney cell types to be potentially impacted. Further, single cell transcriptomic analysis of kidney organoids infected with SARS-CoV-2 showed dysregulation of extracellular matrix organization indicating a cohesive fibrotic response across multiomic datasets. Receptor ligand interaction analysis of the podocyte and tubule clusters in the kidney organoids showed significant reduction and loss of integrin and glomerular basement membrane receptors in the infected kidney organoids. Collectively, these data uncover extracellular matrix, degradation and adhesion associated mechanisms as a driver of COVID associated kidney injury.
HostingRepository	PRIDE
AnnounceDate	2025-11-03
AnnouncementXML	Submission_2025-11-03_11:55:13.948.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD051205
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Tong Liu
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-04-04 14:21:41	ID requested
⏵ 1	2025-11-03 11:55:15	announced

10.1016/j.ekir.2025.07.021;

Anandakrishnan N, Yi Z, Sun Z, Liu T, Haydak J, Eddy S, Jayaraman P, DeFronzo S, Saha A, Sun Q, Yang D, Mendoza A, Mosoyan G, Wen HH, Fu J, Kehrer T, Menon R, Otto EA, Godfrey B, Yang J, Suarez-Farinas M, Leffters S, Twumasi A, Meliambro K, Charney AW, Garc, í, a-Sastre A, Campbell KN, Gusella GL, He JC, Miorin L, Nadkarni GN, Wisnivesky J, Li H, Kretzler M, Coca SG, Chan L, Zhang W, Azeloglu EU, Liquid Biopsy-Multiomics Link Adhesion Pathway Dysregulation to Kidney Injury Severity. Kidney Int Rep, 10(10):3592-3610(2025) [pubmed]

10.6019/PXD051205;

submitter keyword: multiomics,TMT-16machine learning, kidney organoids, COVID-19, urine proteomics

Evren U. Azeloglu
contact affiliation	Department of Medicine, Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
contact email	evren.azeloglu@mssm.edu
lab head
Tong Liu
contact affiliation	Rutgers University
contact email	linto@njms.rutgers.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/2025/11/PXD051205

PRIDE project URI

• PRIDE
  1. PXD051205
     1. Label: PRIDE project
     2. Name: Integrated multiomics implicates dysregulation of ECM and cell adhesion pathways as drivers of severe COVID-associated kidney injury