Supratentorial ependymoma in childhood: more than just RELA or YAP

Abstract

Two distinct genetically defined entities of ependymoma arising in the supratentorial compartment are characterized by the presence of either a C11orf95-RELA or a YAP-MAMLD1 fusion, respectively. There is growing evidence that supratentorial ependymomas without these genetic features exist. In this study, we report on 18 pediatric non-RELA/non-YAP supratentorial ependymomas that were systematically characterized by means of their histology, immunophenotype, genetics, and epigenomics. Comprehensive molecular analyses included high-resolution copy number analysis, methylation profiling, analysis of fusion transcripts by Nanostring technology, and RNA sequencing. Based upon histological and immunohistochemical features two main patterns were identified-RELA-like (n = 9) and tanycytic ependymomas (n = 6). In the RELA-like group histologically assigned to WHO grade III and resembling RELA-fused ependymomas, tumors lacked nuclear expression of p65-RelA as a surrogate marker for a pathological activation of the NF-κB pathway. Three tumors showed alternative C11orf95 fusions to MAML2 or NCOA1. A methylation-based brain tumor classifier assigned two RELA-like tumors to the methylation class "EP, RELA-fusion"; the others demonstrated no significant similarity score. Of the tanycytic group, 5/6 tumors were assigned a WHO grade II. No gene fusions were detected. Methylation profiling did not show any association with an established methylation class. We additionally identified two astroblastoma-like tumors that both presented with chromothripsis of chromosome 22 but lacked MN1 breaks according to FISH analysis. They revealed novel fusion events involving genes in chromosome 22. One further tumor with polyploid cytogenetics was interpreted as PFB ependymoma by the brain tumor methylation classifier but had no relation to the posterior fossa. Clinical follow-up was available for 16/18 patients. Patients with tanycytic and astroblastoma-like tumors had no relapse, while 2 patients with RELA-like ependymomas died. Our data indicate that in addition to ependymomas discovered so far, at least two more supratentorial ependymoma types (RELA-like and tanycytic) exist.

Keywords: Brain tumor; C11orf95 fusion; Childhood; Ependymoma; Methylation profiling; Pediatric; Supratentorial; Tanycytic.

Fig. 1

Clinical, histological, and genetic features of NRNY tumors. Histological class, WHO grade, gender, localization, and immunohistochemical features of all 18 tumors are shown in the top columns. The most frequent copy number alterations [detected with molecular inversion probe assay (MIP)] and gene fusion events (RNA-NGS) are shown in the middle panel. In the bottom, results from the methylation analysis are outlined

Fig. 2

Histological and genetic characteristics of RELA-like, tanycytic, and astroblastoma-like tumors. a Haematoxylin/eosin (HE) staining of case 3 (RELA-like group). b RelA immunohistochemistry displaying no nuclear accumulation of the p65-RelA protein. c EMA positivity in some tumor cells. d genomic copy number profile of case 3 showing gains of chromosomes 17 and 19 but an otherwise balanced genome. e, f HE staining of a tanycytic ependymoma (case 14) with typical elongated cell processes highlighted in the GFAP immunohistochemistry (g). h copy number profile of this case showing copy number losses of 1p and 3p as well as chromosomes 13, 14, and 22, and chromothripsis of chromosome 16. i, j HE of case 17 illustrating the astroblastoma-like appearance, strongly highlighted in the GFAP immunohistochemistry (k). l copy number profile of case 17 showing structural alterations of chromosomes 20 and 22 (chromothripsis) (scale bars in a, e, i: 50 µm; scale bars in b, c, f, g, j, k: 20 µm)

Fig. 3

Survival analysis (Kaplan–Meier plots)