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Series GSE243768 Query DataSets for GSE243768
Status Public on Apr 23, 2024
Title Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level [methylation 2]
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary Medulloblastomas (MBs) are malignant pediatric brain tumors that are molecularly and clinically very heterogenous. To unravel phenotypically relevant MB subtypes, we compiled a harmonized proteome dataset of 167 MBs and integrated findings with DNA methylation and N-glycome data. Six proteome MB subtypes emerged, that could be assigned to two main molecular programs: transcription/translation (pSHHt, pWNT and pGroup3-Myc), and synapses/immunological processes (pSHHs, pGroup3 and pGroup4). Multiomic analysis revealed different conservation levels of proteome features across MB subtypes at the DNA-methylation level. Aggressive pGroup3-Myc MBs and favorable pWNT MBs were most similar in cluster hierarchies concerning overall proteome patterns but showed different protein abundances of the vincristine resistance associated multiprotein complex TriC/CCT and of N-glycan turnover associated factors. The N-glycome reflected proteome subtypes and complex-bisecting N-glycans characterized pGroup3-Myc tumors. Our results shed light on new targetable alterations in MB and set a foundation for potential immunotherapies targeting glycan structures.To biologicallyy validate these results we further generated methylome and proteome data for 29 samples.
 
Overall design Bisulphite converted DNA from the 29 samples were hybridised to the Illumina Infinium 850k Human Methylation Beadchip
 
Contributor(s) Shweta G, Julia N
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Submission date Sep 21, 2023
Last update date Apr 24, 2024
Contact name Julia Elisabeth Neumann
Organization name University Hospital Hamburg Eppendorf
Department ZMNH
Street address Martinistrasse 52
City Hamburg
ZIP/Postal code 20251
Country Germany
 
Platforms (1)
GPL23976 Illumina Infinium HumanMethylation850 BeadChip
Samples (29)
GSM7795496 genomic DNA from FFPE material of MB patient biopsy 1
GSM7795497 genomic DNA from FFPE material of MB patient biopsy 2
GSM7795498 genomic DNA from FFPE material of MB patient biopsy 3
This SubSeries is part of SuperSeries:
GSE243796 Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level
Relations
BioProject PRJNA1019779

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE243768_RAW.tar 407.8 Mb (http)(custom) TAR (of IDAT)
GSE243768_non-normalized.txt.gz 263.6 Mb (ftp)(http) TXT

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