PXD045982

PXD045982 is an original dataset announced via ProteomeXchange.

Title	Proteomic profiling of cerebrospinal fluid for development of biomarker in medulloblastoma
Description	Cerebrospinal fluid (CSF) plays an important role in brain tumours, including medulloblastoma (MBL). CSF proteomics studies have mainly focused on extracellular vesicle (EV) proteins rather than the total CSF proteome. Recent advancements in mass spectrometry systems and �쁎mics�� data analysis methods enable unbiased, high proteome depth research. We conducted proteomic profiling of the total CSF in MBL patients with the purpose of finding a potential diagnostic biomarker for MBL. Methods CSF samples from patients with MBL (n=31) and hydrocephalus (HC, control, n=19) were analysed using liquid chromatography-tandem mass spectrometry (LC�묺S/MS). Enrichment analysis of canonical pathways and differentially expressed proteins (DEPs) was performed. Feature selection of the proteins was conducted using the analysis of variance F value and fast correlation-based filter methods. The selected proteins were validated through ELISA and EV characterization using ExoView systems. Results We quantified 1,112 proteins per CSF sample. We further investigated 273 DEPs extracted from a comparison of MBL and HC. Hierarchical clustering of DEPs between MBL and HC clearly showed classification into two groups. Feature selection identified four elevated soluble proteins (SPTBN1, HSP90AA1, TKT, and NME1-NME2) in MBL CSF. Validation with ELISA confirmed that TKT was significantly elevated in MBL compared to HC, as well as in Group 4 MBL and leptomeningeal seeding (LMS). Additionally, TKT-positive EVs were significantly enriched in MBL CSF compared to HC CSF and correlated with the burden of LMS. Conclusions Our results provide insights into the proteomics data of the total CSF of MBL patients. Furthermore, we identified the significance of TKT within the total CSF and its presence within circulating EVs in the CSF. We suggest that TKT may serve as a biomarker for MBL, particularly for the diagnosis of LMS.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:56:55.498.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Dohyun Han
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-10-09 03:24:06	ID requested
1	2024-08-28 20:26:52	announced
⏵ 2	2024-10-22 06:56:55	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: cerebrospinal fluid, medulloblastoma,Proteomics

Dohyun Han
contact affiliation	Proteomics core facility, Biomedical Research Institute, Seoul National University Hospital
contact email	hdh03@snu.ac.kr
lab head
Dohyun Han
contact affiliation	Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital
contact email	hdh03@snu.ac.kr
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD045982
     1. Label: PRIDE project
     2. Name: Proteomic profiling of cerebrospinal fluid for development of biomarker in medulloblastoma