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

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.