Delineation of Two Clinically and Molecularly Distinct Subgroups of Posterior Fossa Ependymoma

Abstract

Summary Despite the histological similarity of ependymomas from throughout the neuroaxis, the disease likely comprises multiple independent entities, each with a distinct molecular pathogenesis. Transcriptional profiling of two large independent cohorts of ependymoma reveals the existence of two demographically, transcriptionally, genetically, and clinically distinct groups of posterior fossa (PF) ependymomas. Group A patients are younger, have laterally located tumors with a balanced genome, and are much more likely to exhibit recurrence, metastasis at recurrence, and death compared with Group B patients. Identification and optimization of immunohistochemical (IHC) markers for PF ependymoma subgroups allowed validation of our findings on a third independent cohort, using a human ependymoma tissue microarray, and provides a tool for prospective prognostication and stratification of PF ependymoma patients.

Epigenetic modification in chromatin machinery and its deregulation in pediatric brain tumors: Insight into epigenetic therapies

“…Genomic abnormalities have often been observed in ependymoma, including genomic gains and losses or translocations within the ependymoma genome, but these genomic aberrations are more frequent in adult ependymomas. Methylated genes and gene expression profiles are associated with tumor location, patient age at disease onset, grade, and retrospective risk for relapse 57 (also reviewed in 56 ). For example, deregulation of genes involved in neural differentiation and maintenance, particularly ion transport and synaptogenesis, highlights the importance of these events in the formation of this supratentorial ependymoma subgroup.…”

Molecular Characterization of Choroid Plexus Tumors Reveals Novel Clinically Relevant Subgroups

“…Differential gene expression analysis was conducted with PGS 6.5 (see Supplementary Appendix). Gene set enrichment analysis (GSEA) was performed as previously described (11), and its visualization was obtained by Cytoscape and Enrichment Map using an in-house-curated database containing freely available NCI, Kyoto Encyclopedia of Genes and Genomes (KEGG), Protein families database (PFAM), Biocarta, and GO databases as described in Witt and colleagues (12). Differences in DNA methylation status were analyzed with the Illumina GenomeStudio software (see Supplementary Appendix).…”

Therapeutic targeting of ependymoma as informed by oncogenic enhancer profiling

“…Greater than 70% of supratentorial ependymomas are defined by highly recurrent gene fusions in the NFκB subunit RELA (ST-EPN-RELA), and less frequently involve fusion of the gene encoding the transcriptional activator YAP1 (ST-EPN-YAP1). 1,3,4 Subependymomas, a distinct histologic variant, can also be found within the ST and PF compartments accounting for the majority of tumours in the molecular subgroups ST-EPN-SE and PF-EPN-SE, respectively 1 . Here, we mapped active chromatin landscapes in 42 primary ependymomas in two non-overlapping primary ependymoma cohorts with the goal of identifying essential super enhancer associated genes on which tumour cells were dependent.…”

“…Ependymomas are chemotherapy-resistant brain tumours, which, despite genomic sequencing, lack effective molecular targets. Intracranial ependymomas are segregated based on anatomical location – supratentorial region (ST) or posterior fossa (PF) – and further divided into distinct molecular subgroups that reflect differences in age of onset, gender predominance, and response to therapy 1–3 . The most common and aggressive subgroup, Posterior Fossa Ependymoma Group A (PF-EPN-A), occurs in young children and appears to lack recurrent somatic mutations 2 .…”

“…The most common and aggressive subgroup, Posterior Fossa Ependymoma Group A (PF-EPN-A), occurs in young children and appears to lack recurrent somatic mutations 2 . Conversely, Posterior Fossa Ependymoma Group B (PF-EPN-B) tumours display frequent large-scale copy number gains and losses yet favourable clinical outcomes 1,3 . Greater than 70% of supratentorial ependymomas are defined by highly recurrent gene fusions in the NFκB subunit RELA (ST-EPN-RELA), and less frequently involve fusion of the gene encoding the transcriptional activator YAP1 (ST-EPN-YAP1).…”