PXD048388-1

PXD048388 is an original dataset announced via ProteomeXchange.

Title	Comparison of the inflammatory niches of CF and COPD and the differences to healthy controls
Description	This study aimed to compare – at a multi-omics level, inflammation, protease abundance and activity, microbiome, and proteome in sputum samples from patients with cystic fibrosis (CF, n=38) or chronic obstructive pulmonary disease (COPD, n=18) and healthy controls (n=10) to identify shared and unique pathways between these respiratory conditions. Sputum analysis revealed elevated inflammatory cell counts in both CF and COPD patients, with neutrophils being the dominant cell type. Key inflammatory markers, including IL-1β, TNF-α, TGF-β1, IL-8, and LTB4, were increased in both disease groups, with the highest levels observed in CF. Conversely, COPD patients exhibited higher levels of IL-5, IL-6, and IL-10. Microbiome analysis showed distinct clusters for each group, with CF patients often characterized by a preponderance of Pseudomonas. Hierarchical clustering unveiled robust interdependencies between microbiome parameters and inflammation, a richer and more diverse microbiome was associated with a healthier microbial community. This study uncovered significant disparities in inflammation, microbiome composition, and proteome profiles among CF, COPD, and healthy control cohorts. Neutrophilic inflammation and protease activity emerged as common factors in both diseases highlighting proteases as good targets for both indications, while distinct microbial signatures were identified. These findings offer valuable insights into the underlying mechanisms of CF and COPD and may inform future clinical strategies.
HostingRepository	PRIDE
AnnounceDate	2025-09-08
AnnouncementXML	Submission_2025-09-08_02:15:13.817.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Marcel Schilling
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-01-10 09:35:11	ID requested
⏵ 1	2025-09-08 02:15:14	announced

Dataset with its publication pending

submitter keyword: COPD,CF, human, Proteome, LC-MS/MS

Prof. Dr. Ursula Klingmüller
contact affiliation	Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
contact email	u.klingmueller@dkfz.de
lab head
Marcel Schilling
contact affiliation	Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg
contact email	m.schilling@dkfz.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/2025/09/PXD048388

PRIDE project URI

• PRIDE
  1. PXD048388
     1. Label: PRIDE project
     2. Name: Comparison of the inflammatory niches of CF and COPD and the differences to healthy controls