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Series GSE243796 Query DataSets for GSE243796
Status Public on Apr 22, 2024
Title Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Methylation profiling by array
Expression profiling by high throughput sequencing
Summary Medulloblastomas (MBs) are malignant pediatric brain tumors that are molecularly and clinically heterogenous. The application of omics technologies – mainly studying nucleic acids – has significantly improved MB classification and stratification, but treatment options are still unsatisfactory. The proteome and their N-glycans hold the potential to discover clinically relevant phenotypes and targetable pathways. We compile a harmonized proteome dataset of 167 MBs and integrate findings with DNA methylome, transcriptome and N-glycome data. We show six proteome MB subtypes, that can be assigned to two main molecular programs: transcription/translation (pSHHt, pWNT and pGroup3myc), and synapses/immunological processes (pSHHs, pGroup3 and pGroup4). Multiomic analysis reveals different conservation levels of proteome features across MB subtypes at the DNA methylome level. Aggressive pGroup3myc MBs and favourable pWNT MBs are most similar in cluster hierarchies concerning overall proteome patterns but show different protein abundances of the vincristine resistance-associated multiprotein complex TriC/CCT and of N-glycan turnover-associated factors. The N-glycome reflects proteome subtypes and complex-bisecting N-glycans characterize pGroup3myc tumors. Our results shed light on targetable alterations in MB and set a foundation for potential immunotherapies targeting glycan structures.
This SuperSeries is composed of the SubSeries listed below.
 
Overall design Refer to individual Series
 
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Submission date Sep 22, 2023
Last update date Apr 23, 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 (3)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
GPL23976 Illumina Infinium HumanMethylation850 BeadChip
GPL30173 NextSeq 2000 (Homo sapiens)
Samples (90)
GSM6924294 genomic DNA from FFPE material of MB patient biopsie 1
GSM6924295 genomic DNA from FFPE material of MB patient biopsie 2
GSM6924296 genomic DNA from FFPE material of MB patient biopsie 3
This SuperSeries is composed of the following SubSeries:
GSE222478 Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level [methylation 1]
GSE243768 Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level [methylation 2]
GSE243795 Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level [RNA-Seq]
Relations
BioProject PRJNA1020062

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
GSE243796_RAW.tar 1.1 Gb (http)(custom) TAR (of IDAT)
SRA Run SelectorHelp
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