Deep sequencing of a recurrent oligodendroglioma and the derived xenografts reveals new insights into the evolution of human oligodendroglioma and candidate driver genes
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Nadin D. Exner1,2, Jaime Alberto Campos Valenzuela3, Khalil Abou-El-Ardat1, Hrvoje Miletic4,5, Peter C. Huszthy6, Petra M. Radehaus2, Evelin Schröck1,7,8,9, Rolf Bjerkvig5,10, Lars Kaderali11, Barbara Klink1,7,8,9,12,* and Janice M. Nigro5,*
1 Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
2 University of Applied Sciences Mittweida, Department of Applied Informatics & Biosciences, Mittweida, Germany
3 Institut für Medizinische Informatik und Biometrie, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
4 Department of Pathology, Haukeland University Hospital, Bergen, Norway
5 Department of Biomedicine, University of Bergen, Bergen, Norway
6 Oslo University Hospital-Rikshospitalet, Department of Immunology, Oslo, Norway
7 German Cancer Consortium (DKTK), Dresden, Germany
8 German Cancer Research Center (DKFZ), Heidelberg, Germany
9 Center for Molecular Tumor Diagnostics, National Center for Tumor Diseases (NCT), Dresden, Germany
10 Oncology Department, Luxembourg Institute of Health, Val Fleuri, Luxembourg
11 University Medicine Greifswald, Institute of Bioinformatics, Greifswald, Germany
12 Centre national de Génétique, Laboratoire National de Santé, Dudelange, Luxembourg
* Co-senior authors
|Nadin D. Exner,||email:||firstname.lastname@example.org|
Keywords: exome sequencing; IDH1; oligodendroglioma; SNV; xenograft
Received: December 18, 2018 Accepted: May 04, 2019 Published: June 04, 2019
We previously reported the establishment of a rare xenograft derived from a recurrent oligodendroglioma with 1p/19q codeletion. Here, we analyzed in detail the exome sequencing datasets from the recurrent oligodendroglioma (WHO grade III, recurrent O2010) and the first-generation xenograft (xenograft1). Somatic SNVs and small InDels (n = 80) with potential effects at the protein level in recurrent O2010 included variants in IDH1 (NM_005896:c.395G>A; p. Arg132His), FUBP1 (NM_003902:c.1307_1310delTAGA; p.Ile436fs), and CIC (NM_015125:c.4421T>G; p.Val1474Gly). All but 2 of these 80 variants were also present in xenograft1, along with 7 new variants. Deep sequencing of the 87 SNVs and InDels in the original tumor (WHO grade III, primary O2005) and in a second-generation xenograft (xenograft2) revealed that only 11 variants, including IDH1 (NM_005896:c.395G>A; p. Arg132His), PSKH1 (NM_006742.2:c.650G>A; p.Arg217Gln), and SNX12 (NM_001256188:c.470G>A; p.Arg157His), along with a variant in the TERT promoter (C250T, NM_198253.2: c.-146G>A), were already present in primary O2005. Allele frequencies of the 11 variants were calculated to assess their potential as putative driver genes. A missense change in NDST4 (NM_022569:c.2392C>G; p.Leu798Val) on 4q exhibited an increasing allele frequency (~ 20%, primary O2005, 80%, recurrent O2010 and 100%, xenograft1), consistent with a selection event. Sequencing of NDST4 in a cohort of 15 oligodendrogliomas, however, revealed no additional cases with potential protein disrupting variants. Our analysis illuminated a tumor evolutionary series of events, which included 1p/19q codeletion, IDH1 R132H, and TERT C250T as early events, followed by loss of function of NDST4 and mutations in FUBP1 and CIC as late events.
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