Supratentorial non-RELA, ZFTA-fused ependymomas: a comprehensive phenotype genotype correlation highlighting the number of zinc fingers in ZFTA-NCOA1/2 fusions

Abstract

The cIMPACT-NOW Update 7 has replaced the WHO nosology of “ependymoma, RELA fusion positive” by “Supratentorial-ependymoma, C11orf95-fusion positive”. This modification reinforces the idea that supratentorial-ependymomas exhibiting fusion that implicates the C11orf95 (now called ZFTA) gene with or without the RELA gene, represent the same histomolecular entity. A hot off the press molecular study has identified distinct clusters of the DNA methylation class of ZFTA fusion-positive tumors. Interestingly, clusters 2 and 4 comprised tumors of different morphologies, with various ZFTA fusions without involvement of RELA. In this paper, we present a detailed series of thirteen cases of non-RELA ZFTA-fused supratentorial tumors with extensive clinical, radiological, histopathological, immunohistochemical, genetic and epigenetic (DNA methylation profiling) characterization. Contrary to the age of onset and MRI aspects similar to RELA fusion-positive EPN, we noted significant histopathological heterogeneity (pleomorphic xanthoastrocytoma-like, astroblastoma-like, ependymoma-like, and even sarcoma-like patterns) in this cohort. Immunophenotypically, these NFκB immunonegative tumors expressed GFAP variably, but EMA constantly and L1CAM frequently. Different gene partners were fused with ZFTA: NCOA1/2, MAML2 and for the first time MN1. These tumors had epigenetic homologies within the DNA methylation class of ependymomas-RELA and were classified as satellite clusters 2 and 4. Cluster 2 (n = 9) corresponded to tumors with classic ependymal histological features (n = 4) but also had astroblastic features (n = 5). Various types of ZFTA fusions were associated with cluster 2, but as in the original report, ZFTA:MAML2 fusion was frequent. Cluster 4 was enriched with sarcoma-like tumors. Moreover, we reported a novel anatomy of three ZFTA:NCOA1/2 fusions with only 1 ZFTA zinc finger domain in the putative fusion protein, whereas all previously reported non-RELA ZFTA fusions have 4 ZFTA zinc fingers. All three cases presented a sarcoma-like morphology. This genotype/phenotype association requires further studies for confirmation. Our series is the first to extensively characterize this new subset of supratentorial ZFTA-fused ependymomas and highlights the usefulness of ZFTA FISH analysis to confirm the existence of a rearrangement without RELA abnormality.

Molecular Stratification of Childhood Ependymomas as a Basis for Personalized Diagnostics and Treatment

“…ZFTA (non- RELA )-fused EPNs have an especially dismal prognosis, with EFS rates significantly lower compared with classical ZFTA – RELA -fused EPNs, while the corresponding OS rates are comparable [ 26 ]. However, these findings are preliminary, given the small number of cases reported so far.…”

“…However, IHC is not sufficient on its own: the results require confirmation by independent alternative methods since neither of the antibodies (anti-p65, anti-L1CAM, anti-cyclin D1) has enough sensitivity and/or specificity to reliably verify the ST-EPN-ZFTA group [ 20 , 22 ]. The diagnosis of ST-EPN-ZFTA with alternative (non- RELA ) fusion gene can be suspected if tumor cells show immunopositivity for L1CAM and negativity for p65 [ 26 ].…”

“…The archetypal chimeric transcript harbored by ZFTA-rearranged ependymomas is ZFTA-RELA, hence the ST-EPN-RELA is a traditional designation for this group [14]. Alternative ZFTA fusions (non-RELA, e.g., ZFTA-NCOA1, ZFTA-NCOA2, ZFTA-MAML2 [23][24][25][26][27][28], and MN1-ZFTA [28]) are less common.…”

“…Despite the heterogeneous morphology, these tumors are (epi)genetically similar and tend to resemble the classic ZFTA-RELA-fused EPNs, as revealed by methylome assay. A detailed analysis of DNA methylation profiles allows subdivision of these tumors into two clusters, one of them comprising tumors with histological features of astroblastomas and xanthoastrocytomas, harboring ZFTA-MAML2 and MN1-ZFTA rearrangements; the second cluster comprises tumors histologically resembling small-cell sarcomatoid carcinomas and undifferentiated sarcomas, harboring ZFTA-NCOA1 and ZFTA-NCOA2 rearrangements [24][25][26][27][28].…”

Cell-of-Origin and Genetic, Epigenetic, and Microenvironmental Factors Contribute to the Intra-Tumoral Heterogeneity of Pediatric Intracranial Ependymoma

“…Pediatric supratentorial RELA fusion-negative EPNs show other fusion events, the majority involving ZFTA as a partner gene, such as ZFTA-mastermind like transcriptional coactivator 2 (MAML2) or ZFTA-nuclear receptor coactivator 1 ( NCOA1) . These tumors exhibit histopathological heterogeneity, no nuclear NF-κB expression, and epigenetic proximity to the RELA methylation class in some cases [ 44 , 45 ]. Recently, recurrent fusions involving the pleomorphic adenoma gene-like 1 ( PLAGL1 ) gene have been discovered in a group of histopathologically diagnosed ST EPNs exhibiting a distinct DNA methylation profile [ 46 ], that occur mostly in children.…”