SRA

Medulloblastoma is the most frequent malignant pediatric brain tumor and is divided into at least four subgroups known as Wnt, SHH, Group 3 and Group 4. Here we characterized gene regulation mechanisms in the most aggressive subtype, Group 3 tumors, through genome-wide chromatin and expression profiling. Our results show that most active distal sites in these tumors are occupied by the transcription factor OTX2. Highly active OTX2 bound enhancers are often arranged as clusters of adjacent peaks and are also bound by the transcription factor NEUROD1. These sites are responsive to OTX2 and NEUROD1 knockdown and could also be generated de novo upon ectopic OTX2 expression in primary cells, showing that OTX2 cooperates with NEUROD1 and plays a major role in maintaining and possibly establishing regulatory elements as a pioneer factor. Among OTX2 target genes we identified the kinase NEK2, whose knockdown and pharmacological inhibition decreased cell viability. Our studies thus show that OTX2 controls the regulatory landscape of Group 3 medulloblastoma through cooperative activity at enhancer elements and contributes to the expression of critical target genes. Overall design: ChIP-seq for of 4 histone modifications (H3K27ac, H3K4me1, H3K4me3 and H3K27me3) in primary Group 3 Medulloblastomas tumor samples, cell lines (D341 and D283) and mesenchymal stem cells (MSC). ChIP-seq for the transcription factors OTX2 and NEUROD1 in Group 3 medulloblastoma cell lines (D341 and D283) and mesenchymal stem cells (MSC). OTX2 and NEUROD1 were knocked-down with lentiviral shRNA or knocked-out using Cas9 in Group 3 medulloblastoma cell lines. OTX2 and NEUROD1 were expressed in MSCs with lentiviral expression vectors. Raw data not provided for primary Medulloblastoma samples due to patient privacy concerns. Submitter states that the raw data for these samples will be submitted to dbGaP.