Optimising biomarkers for accurate ependymoma diagnosis, prognostication and stratification within International Clinical Trials: A BIOMECA study

Chapman, Rebecca J.; Ghasemi, David R.; Andreiuolo, Felipe; Zschernack, Valentina; Tauziede Espariat, Arnault; Buttarelli, Francesca R.; Giangaspero, Felice; Grill, Jacques; Haberler, Christine; Paine, Simon M.L.; Scott, Ian; Jacques, Thomas S.; Sill, Martin; Pfister, Stefan; Kilday, John-Paul; Leblond, Pierre; Massimino, Maura; Witt, Hendrik; Modena, Piergiorgio; Varlet, Pascale; Pietsch, Torsten; Grundy, Richard G.; Pajtler, Kristian W.; Ritzmann, Timothy A.; Biomarkers of Ependymoma in Childhood and Adolescence (BIOMECA) Consortium

Abstract

Background Accurate identification of brain tumour molecular subgroups is increasingly important. We aimed to establish the most accurate and reproducible ependymoma subgroup biomarker detection techniques, across 147 cases from International Society of Pediatric Oncology (SIOP) Ependymoma II trial participants, enrolled in the pan-European “Biomarkers of Ependymoma in Children and Adolescents (BIOMECA)” study. Methods Across six European BIOMECA laboratories we evaluated epigenetic profiling (DNA methylation array); immunohistochemistry (IHC) for nuclear p65-RELA, H3K27me3, and Tenascin-C; copy number analysis via FISH and MLPA (1q, CDKN2A), and MIP and DNA methylation array (genome-wide copy number evaluation); analysis of ZFTA- and YAP1-fusions by RT-PCR and sequencing, Nanostring and break-apart FISH. Results DNA Methylation profiling classified 65.3% (n=96/147) of cases as EPN-PFA and 15% (n=22/147) as ST-ZFTA fusion-positive. Immunohistochemical loss of H3K27me3 was a reproducible and accurate surrogate marker for EPN-PFA (sensitivity 99-100% across three centres). IHC for p65-RELA, FISH, and RNA-based analyses effectively identified ZFTA- and YAP1- fused supratentorial ependymomas. Detection of 1q gain using FISH exhibited only 57% inter-centre concordance and low sensitivity and specificity whilst MIP, MLPA and DNA methylation-based approaches demonstrated greater accuracy. Conclusions We confirm, in a prospective trial cohort, that H3K27me3 immunohistochemistry is a robust EPN-PFA biomarker. Tenascin-C should be abandoned as a PFA marker. DNA methylation and MIP arrays are effective tools for copy number analysis of 1q gain, 6q and CDKN2A loss whilst FISH is inadequate. Fusion detection was successful, but rare novel fusions need more extensive technologies. Finally, we propose test sets to guide future diagnostic approaches.

Citation

Chapman, R. J., Ghasemi, D. R., Andreiuolo, F., Zschernack, V., Tauziede Espariat, A., Buttarelli, F. R., …Biomarkers of Ependymoma in Childhood and Adolescence (BIOMECA) Consortium. (2023). Optimising biomarkers for accurate ependymoma diagnosis, prognostication and stratification within International Clinical Trials: A BIOMECA study. Neuro-Oncology, 25(10), 1871–1882. https://doi.org/10.1093/neuonc/noad055

• Journal Article Type: Article
• Acceptance Date: Mar 2, 2023
• Online Publication Date: Mar 14, 2023
• Publication Date: 2023-10
• Deposit Date: Mar 23, 2023
• Publicly Available Date: Mar 27, 2023
• Journal: Neuro-Oncology
• Print ISSN: 1522-8517
• Electronic ISSN: 1523-5866
• Publisher: Oxford University Press
• Peer Reviewed: Peer Reviewed
• Volume: 25
• Issue: 10
• Pages: 1871–1882
• DOI: https://doi.org/10.1093/neuonc/noad055
• Keywords: Cancer Research; Neurology (clinical); Oncology
• Public URL: https://nottingham-repository.worktribe.com/output/18530191
• Publisher URL: https://academic.oup.com/neuro-oncology/advance-article/doi/10.1093/neuonc/noad055/7076995