Journal Article

Fusion genes with ALK as recurrent partner in ependymoma-like gliomas: a new brain tumor entity?

Thale Kristin Olsen, Ioannis Panagopoulos, Torstein R. Meling, Francesca Micci, Ludmila Gorunova, Jim Thorsen, Bernt Due-Tønnessen, David Scheie, Marius Lund-Iversen, Bård Krossnes, Cathrine Saxhaug, Sverre Heim and Petter Brandal

in Neuro-Oncology

Published on behalf of Society for Neuro-Oncology

Volume 17, issue 10, pages 1365-1373
Published in print October 2015 | ISSN: 1522-8517
Published online March 2015 | e-ISSN: 1523-5866 | DOI: https://dx.doi.org/10.1093/neuonc/nov039
Fusion genes with ALK as recurrent partner in ependymoma-like gliomas: a new brain tumor entity?

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Background

We have previously characterized 19 ependymal tumors using Giemsa banding and high-resolution comparative genomic hybridization. The aim of this study was to analyze these tumors searching for fusion genes.

Methods

RNA sequencing was performed in 12 samples. Potential fusion transcripts were assessed by seed count and structural chromosomal aberrations. Transcripts of interest were validated using fluorescence in situ hybridization and PCR followed by direct sequencing.

Results

RNA sequencing identified rearrangements of the anaplastic lymphoma kinase gene (ALK) in 2 samples. Both tumors harbored structural aberrations involving the ALK locus 2p23. Tumor 1 had an unbalanced t(2;14)(p23;q22) translocation which led to the fusion gene KTN1-ALK. Tumor 2 had an interstitial del(2)(p16p23) deletion causing the fusion of CCDC88A and ALK. In both samples, the breakpoint of ALK was located between exons 19 and 20. Both patients were infants and both tumors were supratentorial. The tumors were well demarcated from surrounding tissue and had both ependymal and astrocytic features but were diagnosed and treated as ependymomas.

Conclusions

By combining karyotyping and RNA sequencing, we identified the 2 first ever reported ALK rearrangements in CNS tumors. Such rearrangements may represent the hallmark of a new entity of pediatric glioma characterized by both ependymal and astrocytic features. Our findings are of particular importance because crizotinib, a selective ALK inhibitor, has demonstrated effect in patients with lung cancer harboring ALK rearrangements. Thus, ALK emerges as an interesting therapeutic target in patients with ependymal tumors carrying ALK fusions.

Keywords: anaplastic lymphoma kinase; chromosomal aberrations; ependymoma; fusion genes; RNA sequencing

Journal Article.  5470 words.  Illustrated.

Subjects: Medical Oncology ; Neurology

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