PXD058805

PXD058805 is an original dataset announced via ProteomeXchange.

Title	Novel integration of spatial and single-cell omics data sets enables deeper insights into IPF pathogenesis
Description	Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease characterized by repetitive alveolar injuries with excessive deposition of extracellular matrix (ECM) proteins. A crucial need in understanding IPF pathogenesis is identifying cell types associated with histopathological regions, particularly local fibrosis centers known as fibroblast foci. To address this, we integrated published spatial transcriptomics and single-cell RNA sequencing (scRNA-seq) transcriptomics and adopted the Query method and the Overlap method to determine cell type enrichments in histopathological regions. Distinct fibroblast cell types are highly associated with fibroblast foci, and transitional alveolar type 2 and aberrant KRT5-/KRT17+ epithelial cells are associated with morphologically normal alveoli in human IPF lungs. Furthermore, we employed laser capture microdissection directed mass spectrometry to profile proteins. By comparing with another published similar dataset, common differentially expressed proteins and enriched pathways related to ECM structure organization and collagen processing were identified in fibroblast foci. Importantly, cell type enrichment results from innovative spatial proteomics and scRNA-seq data integration accord with those from spatial transcriptomics and scRNA-seq data integration, supporting the capability and versatility of the entire approach. In summary, we integrated spatial multi-omics with scRNA-seq data to identify disease-associated cell types and potential targets for novel therapies in IPF intervention. The approach can be further applied to other disease areas characterized by spatial heterogeneity.
HostingRepository	PRIDE
AnnounceDate	2025-01-27
AnnouncementXML	Submission_2025-01-27_09:09:16.180.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Fei Wang
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-12-12 00:37:30	ID requested
⏵ 1	2025-01-27 09:09:16	announced

Wang F, Jin L, Wang X, Cui B, Yang Y, Duggan L, Schwartz Sterman A, Lloyd SM, Hazelwood LA, Chaudhary N, Bawa B, Phillips LA, He Y, Tian Y, Novel Integration of Spatial and Single-Cell Omics Data Sets Enables Deeper Insights into IPF Pathogenesis. Proteomes, 13(1):(2025) [pubmed]

10.3390/proteomes13010003;

submitter keyword: Human,Idiopathic pulmonary fibrosis, lung, LCM-directed spatial proteomics, LC-MS/MS

Yu Tian
contact affiliation	Research & Development, AbbVie, North Chicago, IL, 60064
contact email	yu.tian@abbvie.com
lab head
Fei Wang
contact affiliation	AbbVie Inc.
contact email	wf199209@gmail.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/2025/01/PXD058805

PRIDE project URI

• PRIDE
  1. PXD058805
     1. Label: PRIDE project
     2. Name: Novel integration of spatial and single-cell omics data sets enables deeper insights into IPF pathogenesis