Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level
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ABSTRACT:
PROVIDER: PRJNA1020062 | ENA |
REPOSITORIES: ENA
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Project description: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.
2024-04-22 | GSE243796 | GEO
Project description: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
2024-04-23 | GSE243795 | GEO
Project description: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.
2024-04-23 | GSE222478 | GEO
Project description: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.
2024-04-23 | GSE243768 | GEO
Project description:<p>Medulloblastomas (MBs) are malignant pediatric brain tumors that are molecularly and clinically very 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 reflect the phenotype of a tumor in a more direct way and thus hold the potential to discover clinically relevant phenotypes and targetable pathways. We compiled a harmonized proteome dataset of 167 MBs and integrated findings with DNA methylome and N-glycome data. Six proteome MB subtypes emerged, that could be assigned to two main molecular programs: transcription/translation (pSHHt, pWNT and pGroup3myc), and synapses/immunological processes (pSHHs, pGroup3 and pGroup4). Multiomic analysis revealed different conservation levels of proteome features across MB subtypes at the DNA methylome level. Aggressive pGroup3myc MBs and favourable 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 pGroup3myc tumors. Our results shed light on new targetable alterations in MB and set a foundation for potential immunotherapies targeting glycan structures.</p><p><br></p><p><strong>Metabolite profiling</strong> is reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS9830' rel='noopener noreferrer' target='_blank'><strong>MTBLS9830</strong></a>.</p><p><strong>Amino acid profiling</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS9836' rel='noopener noreferrer' target='_blank'><strong>MTBLS9836</strong></a>.</p>
2024-05-30 | MTBLS9830 | MetaboLights
Project description:<p>Medulloblastomas (MBs) are malignant pediatric brain tumors that are molecularly and clinically very 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 reflect the phenotype of a tumor in a more direct way and thus hold the potential to discover clinically relevant phenotypes and targetable pathways. We compiled a harmonized proteome dataset of 167 MBs and integrated findings with DNA methylome and N-glycome data. Six proteome MB subtypes emerged, that could be assigned to two main molecular programs: transcription/translation (pSHHt, pWNT and pGroup3myc), and synapses/immunological processes (pSHHs, pGroup3 and pGroup4). Multiomic analysis revealed different conservation levels of proteome features across MB subtypes at the DNA methylome level. Aggressive pGroup3myc MBs and favourable 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 pGroup3myc tumors. Our results shed light on new targetable alterations in MB and set a foundation for potential immunotherapies targeting glycan structures.</p><p><br></p><p><strong>Amino acid profiling</strong> is reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS9836' rel='noopener noreferrer' target='_blank'><strong>MTBLS9836</strong></a>.</p><p><strong>Metabolite profiling</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS9830' rel='noopener noreferrer' target='_blank'><strong>MTBLS9830</strong></a>.</p>
2024-05-30 | MTBLS9836 | MetaboLights
Project description:Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level [methylation 2]
| PRJNA1019779 | ENA
Project description:Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level [RNA-Seq]
| PRJNA1020067 | ENA
Project description:Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level [methylation 1]
| PRJNA922180 | ENA
Project description: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.
2024-06-05 | PXD039319 | Pride