Understanding how ZFTA-RELA drives ependymoma

Background

Ependymoma, a type of brain and spinal cord tumour, is the third most common brain tumour in children. With 40% of the cases currently being incurable, this disease is a tricky one to research. While they are histologically similar, ependymomas from the different sites of the central nervous system differ in lineage, transcriptome, genetic alterations, and clinical outcome. To understand Ependymomas better, we completed a series of comprehensive genomic assays of human ependymomas, including whole-genome sequencing (WGS) experiments, and identified the ZFTA-RELA translocation as the most recurrent genetic alteration in any brain tumour. ZFTA-RELA is a highly potent oncogene, transforming mouse neural stem cells into brain tumours.

We have generated the first mouse models of supratentorial, posterior fossa and spinal ependymoma through a series of innovative, in vivo cross-species genomic and functional tumorigenesis assays. By testing the in vivo transforming power of the ZFTA-RELA translocation and genes located in ependymoma amplicons we have validated the ZFTA-RELA fusion as transforming as well as ZNF668, BCL7C,  RAB3A, RTBDN, the AKT2 oncogene and the putative oncogene PRDX2, which regulates oxidation-induced apoptosis. We also validated TMEM129 and the mitochondrial ribosomal protein MRPS17 as spinal and hindbrain oncogenes, respectively. 

In this manner, we have now generated mouse models of both main types of human supratentorial ependymoma. More than 70% of supratentorial ependymomas (ST-EP) contain translocations between ZFTA and RELA or, more rarely, between ZFTA and YAP1 or MAML2 (ZFTA–MAML2). Seven ZFTA-RELA fusion variants have been described: around two-thirds of cases is fusion 1.

Although we now know that ZFTA fusion proteins are transforming, how this gene cooperates with its various translocation partners to drive tumorigenesis remains to be determined. Our work has identified a tripartite transformation mechanism of ZFTA-containing fusions that include active nuclear trafficking; zinc finger (ZF)–dependent chromatin binding and remodelling; and promiscuous activation of gene expression. We now understand that ZFTA tethers fusion proteins across the genome, modifying chromatin to an active state and enabling its partner transcriptional coactivators to promote promiscuous expression of a transforming transcriptome.

Figure 1: Molecular and cancer phenotype characteristics of ZFTA–RELA^FUS1 protein domains. Schematic depicting the protein complexes that bind each ZFTA–RELA^FUS1 domain. Protein subunits identified in each domain interactome by qPLEX-RIME are coloured and labelled in complexes. Complex components not identified are white ovals/circles Source: R.Kupp et al, Cancer Discovery 2022.

Current research

We are currently focusing on three main research questions:

• 1) What is the role of ZFTA in normal development?
• 2)How does the transcriptome of these tumours alter during development and are these altered transcriptomes and proteomes druggable?
• 3) Can we target the ZFTA–RELA fusion protein or its downstream pathways for therapeutic benefit in ependymoma? 

To answer these we are using our mouse models and human-derived xenografts of ependymoma to conduct high-throughput drug screens and in vivo preclinical therapy studies of new treatments.

Further Reading

1. Taylor MD et al. Radial glia cells are candidate stem cells of ependymoma. Cancer Cell 8: 323–335, 2015.
2. Johnson RA et al. Cross-species genomics matches driver mutations and cell compartments to model ependymoma. Nature 466: 632–636, 2010.
3. Parker M., Kumarasamypet MM. et. al. C11orf95-RELA fusions drive oncogenic NF-kB signalling in ependymoma. Nature 506: 451-455, 2014.
4. Mohankumar M, et al., An in vivo screen identifies ependymoma oncogenes and tumour suppressor genes. Nature Genetics 8:878-87, 2015.
5. Atkinson J, et al., An integrated in vitro and in vivo high-throughput screen identifies treatment leads for ependymoma. Cancer Cell 20:384-99, 2011.
6. Kupp R et al., ZFTA Translocations Constitute Ependymoma Chromatin Remodeling and Transcription Factors. Cancer Discovery 2:2216-22