Significance of molecular classification of ependymomas: C11orf95-RELA fusion-negative supratentorial ependymomas are a heterogeneous group of tumors

Abstract

Extensive molecular analyses of ependymal tumors have revealed that supratentorial and posterior fossa ependymomas have distinct molecular profiles and are likely to be different diseases. The presence of C11orf95-RELA fusion genes in a subset of supratentorial ependymomas (ST-EPN) indicated the existence of molecular subgroups. However, the pathogenesis of RELA fusion-negative ependymomas remains elusive. To investigate the molecular pathogenesis of these tumors and validate the molecular classification of ependymal tumors, we conducted thorough molecular analyses of 113 locally diagnosed ependymal tumors from 107 patients in the Japan Pediatric Molecular Neuro-Oncology Group. All tumors were histopathologically reviewed and 12 tumors were re-classified as non-ependymomas. A combination of RT-PCR, FISH, and RNA sequencing identified RELA fusion in 19 of 29 histologically verified ST-EPN cases, whereas another case was diagnosed as ependymoma RELA fusion-positive via the methylation classifier (68.9%). Among the 9 RELA fusion-negative ST-EPN cases, either the YAP1 fusion, BCOR tandem duplication, EP300-BCORL1 fusion, or FOXO1-STK24 fusion was detected in single cases. Methylation classification did not identify a consistent molecular class within this group. Genome-wide methylation profiling successfully sub-classified posterior fossa ependymoma (PF-EPN) into PF-EPN-A (PFA) and PF-EPN-B (PFB). A multivariate analysis using Cox regression confirmed that PFA was the sole molecular marker which was independently associated with patient survival. A clinically applicable pyrosequencing assay was developed to determine the PFB subgroup with 100% specificity using the methylation status of 3 genes, CRIP1, DRD4 and LBX2. Our results emphasized the significance of molecular classification in the diagnosis of ependymomas. RELA fusion-negative ST-EPN appear to be a heterogeneous group of tumors that do not fall into any of the existing molecular subgroups and are unlikely to form a single category.Electronic supplementary materialThe online version of this article (10.1186/s40478-018-0630-1) contains supplementary material, which is available to authorized users.

Invited Review: DNA methylation‐based classification of paediatric brain tumours

“…The ependymal classes constituted the known PFA and PFB groups as well as the previously described supratentorial RELA ‐fusion‐positive ependymoma , and three new molecular classes consisting of supratentorial YAP1 ‐fusion‐positive ependymomas, a benign spinal ependymoma class and a class closely related to the histological group of myxopapillary ependymoma . Several series of histologically diagnosed ependymomas that were additionally classified by DNA methylation profiling have demonstrated a high rate of histological misdiagnoses, in particular within histologically diagnosed supratentorial ependymomas or ependymomas of the non‐classical histological subtypes . In contrast, a missed diagnosis of an ependymoma seems to be a rare event .…”

“…Therefore, for ependymoma the most central role of DNA methylation profiling may be the validation of the histological diagnosis, in particular for supratentorial cases. A second observation from histology validation studies is that a substantial number of cases cannot be molecularly classified yet . This may indicate further rare molecular classes of ependymal tumours not yet established as methylation classes of their own and the requirement for further improvement of DNA methylation‐based classification.…”

“…DNA methylation profiling offers some guidance for additional molecular testing for ependymomas. In particular the tight association of RELA and YAP1 fusion proteins with certain molecular classes strongly indicates which tumours to test for these gene fusions and in which tumours testing can be omitted . Among ependymomas, recurrent mutations in EZHIP , HIST1H3C , HIST1H2B and H3F3A seem to be specific for PFA ependymomas and thus for other ependymoma classes testing may likely be less relevant .…”

Emerging entities in NUTM1‐rearranged neoplasms

“…60 It is also a putative tumor suppressor gene and inactivating mutations have been detected in a range of myeloid malignancies. 61 Like CIC, BCORL1 has also been associated with other oncogenic fusion partners [62][63][64][65] although only one of these cases has found BCORL1 as the N-terminal partner, with BCORL1 exons 1-11 fused to ELF4 exon 8 in a hepatocellular carcinoma. 62 Interestingly, in the single reported BCORL1-NUTM1 fusion case 22 inactivation, is commonly observed in tumorigenesis.…”

Intracranial ependymomas: molecular insights and translation to treatment

“…Approximately 72% of supratentorial ependymomas contain RELA gene fusions, falling within the ST‐EPN‐RELA subgroup . These tumors are more common in children over the age of 4 and adults and have one of the poorest prognoses, among the subgroups .…”