PXD017210

PXD017210 is an original dataset announced via ProteomeXchange.

Title	Predictive protein biomarker signatures and the corresponding transcriptional cell state changes in human lung fibrosis (Plasma)
Description	Single cell genomics enables characterization of disease specific cell states, while improvements in mass spectrometry workflows bring the clinical use of body fluid proteomics within reach. However, the correspondence of peripheral protein signatures to changes in cell state in diseased organs is currently unknown. Here, we leverage single cell RNA-seq and proteomics from large patient cohorts of pulmonary fibrosis to establish that predictive protein signatures in body fluids correspond to specific cellular changes in the lung. We determined transcriptional changes in 45 cell types across three patient cohorts and quantified bronchoalveolar lavage fluid and plasma proteins to discover protein signatures and associated cell state changes that were linked to diagnosis, lung function, smoking and injury status. Altered expression of the novel marker of lung health CRTAC1 in alveolar epithelium is robustly reported in patient plasma. With further improvements of this concept and deeper coverage of plasma proteomes, we envision future longitudinal profiling of body fluid signatures coupled to machine learning for non-invasive prediction and monitoring of pathological cell state changes in patient organs.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:12:30.068.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christoph Mayr
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-01-20 08:20:26	ID requested
1	2020-09-18 01:48:17	announced
⏵ 2	2024-10-22 05:12:33	announced	2024-10-22: Updated project metadata.

Mayr CH, Simon LM, Leuschner G, Ansari M, Schniering J, Geyer PE, Angelidis I, Strunz M, Singh P, Kneidinger N, Reichenberger F, Silbernagel E, B, ö, hm S, Adler H, Lindner M, Maurer B, Hilgendorff A, Prasse A, Behr J, Mann M, Eickelberg O, Theis FJ, Schiller HB, Integrative analysis of cell state changes in lung fibrosis with peripheral protein biomarkers. EMBO Mol Med, 13(4):e12871(2021) [pubmed]

10.15252/emmm.202012871;

submitter keyword: data integration, proteomics,fibrosis, single cell RNA-seq, systems medicine, biomarker

Herbert B. Schiller
contact affiliation	Helmholtz Zentrum München, Institute of Lung Biology and Disease, Group Systems Medicine of Chronic Lung Disease, Member of the German Center for Lung Research (DZL), Munich, Germany
contact email	herbert.schiller@helmholtz-muenchen.de
lab head
Christoph Mayr
contact affiliation	CPC/ILBD HemholtzZentrum München
contact email	Christoph.Mayr@helmholtz-muenchen.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/2020/09/PXD017210

PRIDE project URI

• PRIDE
  1. PXD017210
     1. Label: PRIDE project
     2. Name: Predictive protein biomarker signatures and the corresponding transcriptional cell state changes in human lung fibrosis (Plasma)