PXD021984

PXD021984 is an original dataset announced via ProteomeXchange.

Title	Proteomic characterization of cerebrospinal fluid in patients with brain malignancies
Description	Recent technological advances in molecular diagnostics through liquid biopsies hold the promise to monitor tumor evolution and treatment response of brain malignancies without the need of invasive surgical tissue accrual. Here, we implemented a new mass spectrometry-based protein analysis pipeline and analyzed 251 cerebrospinal fluid (CSF) samples from patients with four types of brain malignancies (glioblastoma, lymphoma, brain metastasis and meningeal disease) as well as from healthy individuals. On average, we identified 511 ± 121 proteins per CSF sample. 169 proteins were commonly deregulated in all four types of brain malignancies compared to controls. CSF analysis of glioblastoma patients identified two proteomic clusters that correlated with tumor size and patient survival. By integrating CSF data with proteomic analyses of matching glioma tumor tissue and primary glioma cells, we identified potential CSF biomarkers for glioblastoma, in particular chitinase-3-like protein 1 (CHI3L1) and glial fibrillary acidic protein (GFAP). Results were validated in a prospective cohort with 35 glioblastoma patients. Response of a patient with meningeal disease to combinatorial drug treatment was associated with a complex shift of the proteomic signature, including detection of potential drug resistance mechanisms. Therefore, proteomic analysis of CSF in brain malignancies has the potential to reveal biomarkers for diagnosis and therapy monitoring.
HostingRepository	PRIDE
AnnounceDate	2021-03-25
AnnouncementXML	Submission_2021-03-25_15:36:21.477.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tobias Kessker
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	2020-10-14 23:29:49	ID requested
⏵ 1	2021-03-25 15:36:22	announced

Schmid D, Warnken U, Latzer P, Hoffmann DC, Roth J, Kutschmann S, Jaschonek H, R, ü, bmann P, Foltyn M, Vollmuth P, Winkler F, Seliger C, Felix M, Sahm F, Haas J, Reuss D, Bendszus M, Wildemann B, von Deimling A, Wick W, Kessler T, Diagnostic biomarkers from proteomic characterization of cerebrospinal fluid in patients with brain malignancies. J Neurochem, 158(2):522-538(2021) [pubmed]

submitter keyword: Proteome, Glioblastoma, Brain Tumor, Biomarker

Wolfgang Wick
contact affiliation	Department of Neurology and Neurooncology Program of the National Center for Tumor Diseases, Heidelberg University Hospital, Germany
contact email	wolfgang.wick@med.uni-heidelberg.de
lab head
Tobias Kessker
contact affiliation	DKFZ Heidelberg
contact email	t.kessler@dkfz-heidelberg.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/2021/03/PXD021984

PRIDE project URI

• PRIDE
  1. PXD021984
     1. Label: PRIDE project
     2. Name: Proteomic characterization of cerebrospinal fluid in patients with brain malignancies