Medulloblastoma (MB) comprises a group of heterogeneous paediatric embryonal neoplasms of the hindbrain with strong links to early development of the hindbrain1-4. Mutations that activate Sonic hedgehog signalling lead to Sonic hedgehog MB in the upper rhombic lip (RL) granule cell lineage5-8. By contrast, mutations that activate WNT signalling lead to WNT MB in the lower RL9,10. However, little is known about the more commonly occurring group 4 (G4) MB, which is thought to arise in the unipolar brush cell lineage3,4. Here we demonstrate that somatic mutations that cause G4 MB converge on the core binding factor alpha (CBFA) complex and mutually exclusive alterations that affect CBFA2T2, CBFA2T3, PRDM6, UTX and OTX2. CBFA2T2 is expressed early in the progenitor cells of the cerebellar RL subventricular zone in Homo sapiens, and G4 MB transcriptionally resembles these progenitors but are stalled in developmental time. Knockdown of OTX2 in model systems relieves this differentiation blockade, which allows MB cells to spontaneously proceed along normal developmental differentiation trajectories. The specific nature of the split human RL, which is destined to generate most of the neurons in the human brain, and its high level of susceptible EOMES+KI67+ unipolar brush cell progenitor cells probably predisposes our species to the development of G4 MB.

• MeSH
• Ki-67 Antigen metabolism   MeSH
• Cell Differentiation * genetics   MeSH
• Cell Lineage MeSH
• Histone Demethylases MeSH
• Humans MeSH
• Medulloblastoma * classification   genetics   pathology   MeSH
• Metencephalon * embryology   pathology   MeSH
• Cerebellum embryology   pathology   MeSH
• Mutation MeSH
• Cerebellar Neoplasms * classification   genetics   pathology   MeSH
• Hedgehog Proteins metabolism   MeSH
• T-Box Domain Proteins metabolism   MeSH
• Repressor Proteins MeSH
• Muscle Proteins MeSH
• Otx Transcription Factors deficiency   genetics   MeSH
• Core Binding Factor alpha Subunits genetics   MeSH
• Transcription Factors MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Research Support, N.I.H., Extramural MeSH
• Names of Substances
• Ki-67 Antigen MeSH
• CBFA2T2 myeloid-transforming gene-related protein MeSH Browser
• CBFA2T3 protein, human MeSH Browser
• core binding factor alpha MeSH Browser
• EOMES protein, human MeSH Browser
• Histone Demethylases MeSH
• KDM6A protein, human MeSH Browser
• OTX2 protein, human MeSH Browser
• PRDM6 protein, human MeSH Browser
• Hedgehog Proteins MeSH
• T-Box Domain Proteins MeSH
• Repressor Proteins MeSH
• Muscle Proteins MeSH
• Otx Transcription Factors MeSH
• Core Binding Factor alpha Subunits MeSH
• Transcription Factors MeSH

Embryonal tumours with multilayered rosettes (ETMRs) are aggressive paediatric embryonal brain tumours with a universally poor prognosis1. Here we collected 193 primary ETMRs and 23 matched relapse samples to investigate the genomic landscape of this distinct tumour type. We found that patients with tumours in which the proposed driver C19MC2-4 was not amplified frequently had germline mutations in DICER1 or other microRNA-related aberrations such as somatic amplification of miR-17-92 (also known as MIR17HG). Whole-genome sequencing revealed that tumours had an overall low recurrence of single-nucleotide variants (SNVs), but showed prevalent genomic instability caused by widespread occurrence of R-loop structures. We show that R-loop-associated chromosomal instability can be induced by the loss of DICER1 function. Comparison of primary tumours and matched relapse samples showed a strong conservation of structural variants, but low conservation of SNVs. Moreover, many newly acquired SNVs are associated with a mutational signature related to cisplatin treatment. Finally, we show that targeting R-loops with topoisomerase and PARP inhibitors might be an effective treatment strategy for this deadly disease.

• MeSH
• DEAD-box RNA Helicases genetics   MeSH
• DNA Topoisomerases, Type I genetics   MeSH
• Neoplasms, Germ Cell and Embryonal diagnosis   genetics   MeSH
• Polymorphism, Single Nucleotide MeSH
• Humans MeSH
• MicroRNAs genetics   MeSH
• Mutation MeSH
• Poly(ADP-ribose) Polymerase Inhibitors MeSH
• Poly(ADP-ribose) Polymerases genetics   MeSH
• Recurrence MeSH
• Ribonuclease III genetics   MeSH
• RNA, Long Noncoding MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Research Support, N.I.H., Extramural MeSH
• Names of Substances
• DEAD-box RNA Helicases MeSH
• DICER1 protein, human MeSH Browser
• DNA Topoisomerases, Type I MeSH
• MicroRNAs MeSH
• MIR17HG, human MeSH Browser
• Poly(ADP-ribose) Polymerase Inhibitors MeSH
• Poly(ADP-ribose) Polymerases MeSH
• Ribonuclease III MeSH
• RNA, Long Noncoding MeSH
• TOP1 protein, human MeSH Browser

While molecular subgrouping has revolutionized medulloblastoma classification, the extent of heterogeneity within subgroups is unknown. Similarity network fusion (SNF) applied to genome-wide DNA methylation and gene expression data across 763 primary samples identifies very homogeneous clusters of patients, supporting the presence of medulloblastoma subtypes. After integration of somatic copy-number alterations, and clinical features specific to each cluster, we identify 12 different subtypes of medulloblastoma. Integrative analysis using SNF further delineates group 3 from group 4 medulloblastoma, which is not as readily apparent through analyses of individual data types. Two clear subtypes of infants with Sonic Hedgehog medulloblastoma with disparate outcomes and biology are identified. Medulloblastoma subtypes identified through integrative clustering have important implications for stratification of future clinical trials.

• Keywords
• copy number, gene expression, integrative clustering, medulloblastoma, methylation, subgroups,
• MeSH
• Genomics MeSH
• Precision Medicine * MeSH
• Cohort Studies MeSH
• Humans MeSH
• Medulloblastoma classification   genetics   therapy   MeSH
• DNA Methylation MeSH
• Cluster Analysis MeSH
• Gene Expression Profiling MeSH
• DNA Copy Number Variations MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Research Support, N.I.H., Extramural MeSH

The development of targeted anti-cancer therapies through the study of cancer genomes is intended to increase survival rates and decrease treatment-related toxicity. We treated a transposon-driven, functional genomic mouse model of medulloblastoma with 'humanized' in vivo therapy (microneurosurgical tumour resection followed by multi-fractionated, image-guided radiotherapy). Genetic events in recurrent murine medulloblastoma exhibit a very poor overlap with those in matched murine diagnostic samples (<5%). Whole-genome sequencing of 33 pairs of human diagnostic and post-therapy medulloblastomas demonstrated substantial genetic divergence of the dominant clone after therapy (<12% diagnostic events were retained at recurrence). In both mice and humans, the dominant clone at recurrence arose through clonal selection of a pre-existing minor clone present at diagnosis. Targeted therapy is unlikely to be effective in the absence of the target, therefore our results offer a simple, proximal, and remediable explanation for the failure of prior clinical trials of targeted therapy.

• MeSH
• Clone Cells drug effects   metabolism   pathology   MeSH
• Molecular Targeted Therapy methods   MeSH
• Drosophila melanogaster cytology   genetics   MeSH
• Genome, Human genetics   MeSH
• Craniospinal Irradiation MeSH
• Humans MeSH
• Neoplasm Recurrence, Local genetics   pathology   therapy   MeSH
• Medulloblastoma genetics   pathology   radiotherapy   surgery   therapy   MeSH
• Disease Models, Animal MeSH
• DNA Mutational Analysis MeSH
• Mice MeSH
• Cerebellar Neoplasms genetics   pathology   radiotherapy   surgery   therapy   MeSH
• Radiotherapy, Image-Guided MeSH
• Selection, Genetic drug effects   MeSH
• Signal Transduction MeSH
• Xenograft Model Antitumor Assays MeSH
• Animals MeSH
• Check Tag
• Humans MeSH
• Male MeSH
• Mice MeSH
• Female MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Research Support, N.I.H., Extramural MeSH