PXD015151

PXD015151 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Histone Modification Analysis of Oligodendroglioma and Astrocytoma Brain Cancer Samples
Description	WHO classification for tumors of the central nervous system strongly endorses molecular tests for the precise diagnosis of diffuse gliomas. While alterations in the DNA methylation status of gliomas are already well documented and used in specialised clinical centers to distinguish between brain tumor entities, changes to the epigenetic layer at the level of histone modifications are only poorly characterised. Here, we applied a recently developed data-independent acquisition (DIA) - mass spectrometry method to generate a comprehensive histone epi-proteomic map that documents the abundance of almost all characterized and many uncharacterized histone modifications to a series of IDH-mutant oligodendroglioma and astrocytoma samples. Our analysis documented significant abundance differences in almost one-third of the 144 quantified histone peptides. Among them are lower abundance levels of the polycomb repressive mark H3K27me3 in oligodendroglioma samples compared to astrocytomas. We validated this finding by immunohistochemistry using the C36B11 antibody. Surprisingly, we observed inconsistencies with another widely applied H3K27me3 antibody (07-449), providing a warning flag for immunohistochemistry of brain cancers. An unbiased unsupervised clustering analysis of the proteomic dataset separated the two IDH-mutant glioma subtypes in full accordance to the EPIC DNA methylation classifier and the 1p/19q status. The clustering also revealed at least two histone epi-proteomic subgroups of oligodendroglioma, a feature not observable in the DNA methylation dataset. Our results indicate that histone epi-proteomic profiling at the depth of the current method has the capacity to identify clinically-relevant glioma sub-groups. In addition to being of use for diagnostic purposes, this could also provide novel insights in glioma biology and may identify new therapeutic targets.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:57:39.358.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christian Feller
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monomethylated residue; phosphorylated residue; acetylated residue
Instrument	Q Exactive HF

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2019-08-25 23:54:03	ID requested
1	2020-01-17 05:41:01	announced
⏵ 2	2024-10-22 04:57:45	announced	2024-10-22: Updated project metadata.

Publication List

Feller C, Felix M, Weiss T, Herold-Mende C, Zhang F, Kockmann T, Sahm F, Aebersold R, von Deimling A, Reuss DE, Histone epiproteomic profiling distinguishes oligodendroglioma, IDH-mutant and 1p/19q co-deleted from IDH-mutant astrocytoma and reveals less tri-methylation of H3K27 in oligodendrogliomas. Acta Neuropathol, 139(1):211-213(2020) [pubmed]
10.1007/s00401-019-02096-8;

Feller C, Felix M, Weiss T, Herold-Mende C, Zhang F, Kockmann T, Sahm F, Aebersold R, von Deimling A, Reuss DE, Histone epiproteomic profiling distinguishes oligodendroglioma, IDH-mutant and 1p/19q co-deleted from IDH-mutant astrocytoma and reveals less tri-methylation of H3K27 in oligodendrogliomas. Acta Neuropathol, 139(1):211-213(2020) [pubmed]

10.1007/s00401-019-02096-8;

Keyword List

curator keyword: Biomedical
submitter keyword: Oligodendroglioma,histone modifications, brain cancer, Astrocytoma, histone epi-proteome

curator keyword: Biomedical

submitter keyword: Oligodendroglioma,histone modifications, brain cancer, Astrocytoma, histone epi-proteome

Contact List

Ruedi Aebersold
contact affiliation	Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Otto Stern Weg 3, 8093, Zürich, Switzerland
contact email	aebersold@imsb.biol.ethz.ch
lab head
Christian Feller
contact affiliation	ETH Zurich
contact email	feller.christian@gmail.com
dataset submitter

Full Dataset Link List

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/2020/01/PXD015151
PRIDE project URI

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/2020/01/PXD015151

PRIDE project URI

Repository Record List

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