PXD062231-1

PXD062231 is an original dataset announced via ProteomeXchange.

Title	Single-cell spatial proteomics maps human liver zonation patterns and their vulnerability to disruption in tissue architecture
Description	Understanding protein distribution patterns across tissue architecture is crucial for deciphering organ function in health and disease. Here, we applied single-cell Deep Visual Proteomics to perform spatially-resolved proteome analysis of individual cells in native tissue. We built a robust framework comprising strategic cell selection and continuous protein gradient mapping, allowing the investigation of larger clinical cohorts. We generated a comprehensive spatial map of the human hepatic proteome by analyzing hundreds of isolated hepatocytes from 18 individuals. Among the 2,500 proteins identified per cell, about half exhibited zonated expression patterns. Cross-species comparison with male mice revealed conserved metabolic functions and human-specific features of liver zonation. Analysis of samples with disrupted liver architecture demonstrated widespread loss of protein zonation, with pericentral proteins being particularly susceptible. Our study provides a comprehensive and open-access resource of human liver organization while establishing a broadly applicable framework for spatial proteomics analyses along tissue gradients.
HostingRepository	PRIDE
AnnounceDate	2025-12-20
AnnouncementXML	Submission_2025-12-19_19:21:29.200.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mario Oroshi
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Astral

Revision	Datetime	Status	ChangeLog Entry
0	2025-03-25 18:05:30	ID requested
⏵ 1	2025-12-19 19:21:29	announced

Dataset with its publication pending

submitter keyword: Deep Visual Proteomics,single cell proteomics, spatial protein gradients, fibrosis,human liver zonation

Matthias Mann
contact affiliation	Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
contact email	mmann@biochem.mpg.de
lab head
Mario Oroshi
contact affiliation	Proteomics
contact email	oroshi@biochem.mpg.de
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/2025/12/PXD062231

PRIDE project URI

• PRIDE
  1. PXD062231
     1. Label: PRIDE project
     2. Name: Single-cell spatial proteomics maps human liver zonation patterns and their vulnerability to disruption in tissue architecture