Pediatric-type high-grade neuroepithelial tumors with CIC gene fusion share a common DNA methylation signature

Sievers, Philipp; Sill, Martin; Schrimpf, Daniel; Abdullaev, Zied; Donson, Andrew M.; Lake, Jessica A.; Friedel, Dennis; Scheie, David; Tynninen, Olli; Rauramaa, Tuomas; Vepsäläinen, Kaisa L.; Samuel, David; Chapman, Rebecca; Grundy, Richard G.; Pajtler, Kristian W.; Tauziède-Espariat, Arnault; Métais, Alice; Varlet, Pascale; Snuderl, Matija; Jacques, Thomas S.; Aldape, Kenneth; Reuss, David E.; Korshunov, Andrey; Wick, Wolfgang; Pfister, Stefan M.; von Deimling, Andreas; Sahm, Felix; Jones, David T. W.

Abstract

Pediatric neoplasms in the central nervous system (CNS) show extensive clinical and molecular heterogeneity and are fundamentally different from those occurring in adults. Molecular genetic testing contributes to accurate diagnosis and enables an optimal clinical management of affected children. Here, we investigated a rare, molecularly distinct type of pediatric high-grade neuroepithelial tumor (n = 18), that was identified through unsupervised visualization of genome-wide DNA methylation array data, together with copy number profiling, targeted next-generation DNA sequencing, and RNA transcriptome sequencing. DNA and/or RNA sequencing revealed recurrent fusions involving the capicua transcriptional repressor (CIC) gene in 10/10 tumor samples analyzed, with the most common fusion being CIC::LEUTX (n = 9). In addition, a CIC::NUTM1 fusion was detected in one of the tumors. Apart from the detected fusion events, no additional oncogenic alteration was identified in these tumors. The histopathological review demonstrated a morphologically heterogeneous group of high-grade neuroepithelial tumors with positive immunostaining for markers of glial differentiation in combination with weak and focal expression of synaptophysin, CD56 and CD99. All tumors were located in the supratentorial compartment, occurred during childhood (median age 8.5 years) and typically showed early relapses. In summary, we expand the spectrum of pediatric-type tumors of the CNS by reporting a previously uncharacterized group of rare high-grade neuroepithelial tumors that share a common DNA methylation signature and recurrent gene fusions involving the transcriptional repressor CIC. Downstream functional consequences of the fusion protein CIC::LEUTX and potential therapeutic implications need to be further investigated.

Citation

Sievers, P., Sill, M., Schrimpf, D., Abdullaev, Z., Donson, A. M., Lake, J. A., …Jones, D. T. W. (in press). Pediatric-type high-grade neuroepithelial tumors with CIC gene fusion share a common DNA methylation signature. npj Precision Oncology, 7, Article 30. https://doi.org/10.1038/s41698-023-00372-1

• Journal Article Type: Article
• Acceptance Date: Mar 10, 2023
• Online Publication Date: Mar 24, 2023
• Deposit Date: Jun 7, 2023
• Publicly Available Date: Jun 8, 2023
• Journal: npj Precision Oncology
• Print ISSN: 2397-768X
• Electronic ISSN: 2397-768X
• Publisher: Nature Research
• Peer Reviewed: Peer Reviewed
• Volume: 7
• Article Number: 30
• DOI: https://doi.org/10.1038/s41698-023-00372-1
• Keywords: Cancer Research; Oncology
• Public URL: https://nottingham-repository.worktribe.com/output/18993273
• Publisher URL: https://www.nature.com/articles/s41698-023-00372-1#citeas
• Additional Information: Received: 5 December 2022; Accepted: 10 March 2023; First Online: 24 March 2023; : M. Sill, D. Schrimpf, M. Snuderl, S.M.P., A.V.D., F.S., and D.T.W. J. are co-founders and shareholders in Heidelberg Epignostix, GmbH. The remaining authors declare no competing interests.