ZFTA–RELA Dictates Oncogenic Transcriptional Programs to Drive Aggressive Supratentorial Ependymoma

Abstract

More than 60% of supratentorial ependymomas harbor a ZFTA–RELA (ZRfus) gene fusion (formerly C11orf95–RELA). To study the biology of ZRfus, we developed an autochthonous mouse tumor model using in utero electroporation (IUE) of the embryonic mouse brain. Integrative epigenomic and transcriptomic mapping was performed on IUE-driven ZRfus tumors by CUT&RUN, chromatin immunoprecipitation sequencing, assay for transposase-accessible chromatin sequencing, and RNA sequencing and compared with human ZRfus-driven ependymoma. In addition to direct canonical NFκB pathway activation, ZRfus dictates a neoplastic transcriptional program and binds to thousands of unique sites across the genome that are enriched with PLAGL family transcription factor (TF) motifs. ZRfus activates gene expression programs through recruitment of transcriptional coactivators (Brd4, Ep300, Cbp, Pol2) that are amenable to pharmacologic inhibition. Downstream ZRfus target genes converge on developmental programs marked by PLAGL TF proteins, and activate neoplastic programs enriched in Mapk, focal adhesion, and gene imprinting networks. Significance: Ependymomas are aggressive brain tumors. Although drivers of supratentorial ependymoma (ZFTA- and YAP1-associated gene fusions) have been discovered, their functions remain unclear. Our study investigates the biology of ZFTA–RELA-driven ependymoma, specifically mechanisms of transcriptional deregulation and direct downstream gene networks that may be leveraged for potential therapeutic testing. This article is highlighted in the In This Issue feature, p. 2113

Cross-Species Genomics Reveals Oncogenic Dependencies in ZFTA/C11orf95 Fusion–Positive Supratentorial Ependymomas

“…The strong effect on the transcriptome could also be demonstrated for another ZFTA-RELA-driven mouse model generated by Arabzade et al (Supplementary Fig. S10A) (20) trimethylation and acetylation in our ZFTA fusion-driven mouse models corresponding well to respective levels in human tumors (Supplementary Fig. S10B-R) (20,21).…”

“…We suggest that these oncogenic alterations may affect cells that had remained in an early stemness state permissive for one-hit tumorigenesis and rendering possible the development of morphologically non-neuronal, non-glial elements. This is supported by data in a cosubmitted manuscript by Arabzade et al identifying transcriptional programs within fusion-driven ependymoma that are active during embryonic brain development (20).…”

“…Based on our findings together with two co-submitted studies by Kupp et al. and Arabzade et al (20,21), C11orf95 has now been officially designated ZFTA (zinc finger translocation associated) by the HUGO Gene Nomenclature Committee.…”

“…In our study, we did not observe NF-κB pathway activation in tumors without RELA as fusion partner. In keeping with this notion, Arabzade et al demonstrated that a major component of the fusion binding is tumor-specific and not observed in canonical NF-κB-related gene expression (20).…”

“…S12A-C). In addition, a comprehensive crossspecies analysis by Kupp et al comprising all mouse models deployed by the three independent co-submitted studies and the two largest published datasets of human ST-EPN-RELA identified a common fusion-associated signature of 93 genes that also included GLI2 and EPHB2 (6,7,20,21). To further explore potential direct interactions of ZFTA fusions with these genetic loci, we performed ChIP-seq with antibodies against HA and H3K27ac as well as ATAC-seq analyses on ZFTA-RELA-driven murine tumor cells (Supplementary Methods).…”