Genetic alterations in uncommon low-grade neuroepithelial tumors: BRAF, FGFR1, and MYB mutations occur at high frequency and align with morphology

Ibrahim Qaddoumi, Wilda Orisme, Ji Wen, Teresa Santiago, Kirti Gupta, James D. Dalton, Bo Tang, Kelly Haupfear, Chandanamali Punchihewa, John Easton, Heather Mulder, Kristy Boggs, Ying Shao, Michael Rusch, Jared Becksfort, Pankaj Gupta, Shuoguo Wang, Ryan P. Lee, Daniel Brat, V. Peter CollinsSonika Dahiya, David George, William Konomos, Kathreena M. Kurian, Kathryn McFadden, Luciano Neder Serafini, Hilary Nickols, Arie Perry, Sheila Shurtleff, Amar Gajjar, Fredrick A. Boop, Paul D. Klimo, Elaine R. Mardis, Richard K. Wilson, Suzanne J. Baker, Jinghui Zhang, Gang Wu, James R. Downing, Ruth G. Tatevossian, David W. Ellison

Research output: Contribution to journalArticle

137 Scopus citations

Abstract

Low-grade neuroepithelial tumors (LGNTs) are diverse CNS tumors presenting in children and young adults, often with a history of epilepsy. While the genetic profiles of common LGNTs, such as the pilocytic astrocytoma and ‘adult-type’ diffuse gliomas, are largely established, those of uncommon LGNTs remain to be defined. In this study, we have used massively parallel sequencing and various targeted molecular genetic approaches to study alterations in 91 LGNTs, mostly from children but including young adult patients. These tumors comprise dysembryoplastic neuroepithelial tumors (DNETs; n = 22), diffuse oligodendroglial tumors (d-OTs; n = 20), diffuse astrocytomas (DAs; n = 17), angiocentric gliomas (n = 15), and gangliogliomas (n = 17). Most LGNTs (84 %) analyzed by whole-genome sequencing (WGS) were characterized by a single driver genetic alteration. Alterations of FGFR1 occurred frequently in LGNTs composed of oligodendrocyte-like cells, being present in 82 % of DNETs and 40 % of d-OTs. In contrast, a MYB-QKI fusion characterized almost all angiocentric gliomas (87 %), and MYB fusion genes were the most common genetic alteration in DAs (41 %). A BRAF:p.V600E mutation was present in 35 % of gangliogliomas and 18 % of DAs. Pathogenic alterations in FGFR1/2/3, BRAF, or MYB/MYBL1 occurred in 78 % of the series. Adult-type d-OTs with an IDH1/2 mutation occurred in four adolescents, the youngest aged 15 years at biopsy. Despite a detailed analysis, novel genetic alterations were limited to two fusion genes, EWSR1-PATZ1 and SLMAP-NTRK2, both in gangliogliomas. Alterations in BRAF, FGFR1, or MYB account for most pathogenic alterations in LGNTs, including pilocytic astrocytomas, and alignment of these genetic alterations and cytologic features across LGNTs has diagnostic implications. Additionally, therapeutic options based upon targeting the effects of these alterations are already in clinical trials.

Original languageEnglish
Pages (from-to)833-845
Number of pages13
JournalActa Neuropathologica
Volume131
Issue number6
DOIs
StatePublished - Jun 1 2016

Keywords

  • BRAF
  • FGFR1
  • Glioma
  • Glioneuronal
  • MYB
  • RNA-seq

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    Qaddoumi, I., Orisme, W., Wen, J., Santiago, T., Gupta, K., Dalton, J. D., Tang, B., Haupfear, K., Punchihewa, C., Easton, J., Mulder, H., Boggs, K., Shao, Y., Rusch, M., Becksfort, J., Gupta, P., Wang, S., Lee, R. P., Brat, D., ... Ellison, D. W. (2016). Genetic alterations in uncommon low-grade neuroepithelial tumors: BRAF, FGFR1, and MYB mutations occur at high frequency and align with morphology. Acta Neuropathologica, 131(6), 833-845. https://doi.org/10.1007/s00401-016-1539-z