Medulloblastoma is a highly malignant paediatric brain tumour currently treated with a combination of surgery, radiation and chemotherapy, posing a considerable burden of toxicity to the developing child. Genomics has illuminated the extensive intertumoral heterogeneity of medulloblastoma, identifying four distinct molecular subgroups. Group 3 and group 4 subgroup medulloblastomas account for most paediatric cases; yet, oncogenic drivers for these subtypes remain largely unidentified. Here we describe a series of prevalent, highly disparate genomic structural variants, restricted to groups 3 and 4, resulting in specific and mutually exclusive activation of the growth factor independent 1 family proto-oncogenes, GFI1 and GFI1B. Somatic structural variants juxtapose GFI1 or GFI1B coding sequences proximal to active enhancer elements, including super-enhancers, instigating oncogenic activity. Our results, supported by evidence from mouse models, identify GFI1 and GFI1B as prominent medulloblastoma oncogenes and implicate ‘enhancer hijacking’ as an efficient mechanism driving oncogene activation in a childhood cancer.
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Short-read sequencing data have been deposited at the European Genome-Phenome Archive (EGA, http://www.ebi.ac.uk/ega/) hosted by the EBI, under accession number EGAS00001000215.
For technical support and expertise we thank: the DKFZ Genomics and Proteomics Core Facility; B. Haase, D. Pavlinic and B. Baying (EMBL Genomics Core Facility); M. Knopf (NCT Heidelberg); the Sanford-Burnham Animal Facility and Cell Imaging, Tissue & Histopathology Shared Resource; and the UCSD Flow Cytometry Core Facility. We also thank Active Motif for the preparation of histone ChIP libraries. This work was principally supported by the PedBrain Tumor Project contributing to the International Cancer Genome Consortium, funded by the German Cancer Aid (109252) and by the German Federal Ministry of Education and Research (BMBF, grants 01KU1201A, MedSys 0315416C and NGFNplus 01GS0883). Additional support came from the German Cancer Research Center–Heidelberg Center for Personalized Oncology (DKFZ-HIPO), the EMBL International PhD Programme (T.Z.), Dutch Cancer Foundations KWF (2010-4713) and KIKA (M.Ko.), the US National Institutes of Health, National Center for Research Resources (P41 GM103504; G.D.B.), the CancerSys grant MYC-NET (German Federal Ministry of Education and Research, BMBF, 0316076A), the European Commission (Health-F2-2010-260791), and the Helmholtz Alliance PCCC (grant number HA-305). PAN is a Roman Herzog Postdoctoral Fellow funded by the Hertie Foundation and the DKFZ. R.J.W.-R. is the recipient of a Research Leadership Award from the California Institute for Regenerative Medicine (CIRM LA1-01747) and obtained additional support from the National Cancer Institute (5P30CA030199 and R01 CA159859), and the CureSearch for Children's Cancer Foundation.
Extended data figures
This file contains the details on the sequencing cohorts included in the main paper.
RNA-seq analysis did not disclose evidence for possible GFI1 fusion genes (data not shown), suggesting that the detected rearrangements contribute to GFI1 activation by alternative mechanisms. This table shows that observed translocation partners showed no apparent preference for intragenic or intergenic breakpoints.