C11orf95-RELA fusion drives aberrant gene expression through the unique epigenetic regulation for ependymoma formation

Recurrent C11orf95-RELA fusions (RELA(FUS)) are the hallmark of supratentorial ependymomas. The presence of RELA as the fusion partner indicates a close association of aberrant NF-κB activity with tumorigenesis. However, the oncogenic role of the C11orf95 has not been determined. Here, we performed ChIP-seq analyses to explore genomic regions bound by RELA(FUS) and H3K27ac proteins in human 293T and mouse ependymoma cells. We then utilized published RNA-Seq data from human and mouse RELA(FUS) tumors and identified target genes that were directly regulated by RELA(FUS) in these tumors. Subsequent transcription factor motif analyses of RELA(FUS) target genes detected a unique GC-rich motif recognized by the C11orf95 moiety, that is present in approximately half of RELA(FUS) target genes. Luciferase assays confirmed that a promoter carrying this motif is sufficient to drive RELA(FUS)-dependent gene expression. Further, the RELA(FUS) target genes were found to be overlapped with Rela target genes primarily via non-canonical NF-κB binding sites. Using a series of truncation and substitution mutants of RELA(FUS), we also show that the activation domain in the RELA(FUS) moiety is necessary for the regulation of gene expression of these RELA(FUS) target genes. Lastly, we performed an anti-cancer drug screening with mouse ependymoma cells and identified potential anti-ependymoma drugs that are related to the oncogenic mechanism of RELA(FUS). These findings suggested that RELA(FUS) might induce ependymoma formation through oncogenic pathways orchestrated by both C11orf95 and RELA target genes. Thus, our study unveils a complex gene function of RELA(FUS) as an oncogenic transcription factor in RELA(FUS) positive ependymomas. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40478-021-01135-4.