PXD024427

PXD024427 is an original dataset announced via ProteomeXchange.

Title	Proteomic analysis of IDHmut gliomas suggests novel classification with greater separation than 1p/19q codeletion status
Description	Glial cell-derived brain tumors (gliomas) are devastating diseases without effective curative therapies. Gliomas are classified according to various schemes including the cancer-initiating cell type, World Health Organization tumor grades, and genetic markers such as Isocitrate dehydrogenase (IDH) mutations and chromosomal 1p/19q codeletion status. Genomics, transcriptomics and methylomics approaches are emerging as powerful means to refine classification. However, various aspects of cancer biology are solely reflected on the proteomelevel. Here, we employ mass spectrometry (MS) to characterize the proteomes and phospho-proteomes of IDHmut glioma entities with and without 1p/19q codeletion, IDHwt gliomas and control tissue from a total of 42 patients. Our data-dependent acquisition MS workflow on average quantifies more than 5000 proteins and 3000 phospho-sites per sample of formalin-fixed paraffin-embedded (FFPE) brain sections. The tumor proteomes reflected genetic alterations such as the loss of chromosome 1p/19q proteins, the loss of ATRX in non-codeletion IDHmut glioma, and the frequent loss and amplification of chromosomes 10 and 7, respectively,in IDH-wild type glioma. Nevertheless, 1p/19q codeletion status was not the major determinant of IDHmut glioma proteomes. Instead, the proteome profiles suggest an alternative classification of IDHmut gliomas that correlates with the loss of mitochondrial DNA-encoded proteins, the abundance of respiratory chain proteins, a distinct tumor suppressor and oncoprotein profile, an extracellular matrix signature, and alterations in the phospho-proteome. Moreover, the glioma association of numerous proteins implicated in other cancers by this dataset provides a resource for further mechanistic investigation of glioma genesis and progression.
HostingRepository	PRIDE
AnnounceDate	2022-11-09
AnnouncementXML	Submission_2022-11-09_05:41:21.952.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	MarioOroshi
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF; Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2021-03-01 04:44:23	ID requested
⏵ 1	2022-11-09 05:41:22	announced

Dataset with its publication pending

submitter keyword: proteomics,Glioma, Glioblastoma, Isocitrate dehydrogenase, 1p/19q-codeletion

MatthiasMann
contact affiliation	Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
contact email	mmann@biochem.mpg.de
lab head
MarioOroshi
contact affiliation	Proteomics
contact email	oroshi@biochem.mpg.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD024427
     1. Label: PRIDE project
     2. Name: Proteomic analysis of IDHmut gliomas suggests novel classification with greater separation than 1p/19q codeletion status