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

Abstract

Abstract 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.

Keywords

• Ependymoma
• Fusion gene
• NF-κB signaling
• Transcription factor motif