P13.03 Identification of novel gene fusions in glioblastomas with chromothripsis

Abstract

Abstract BACKGROUND Genomic rearrangements are thought to occur in a stepwise manner during cancer development. Recent findings, however, suggest an alternative mechanism, involving massive chromosome (chr) rearrangements in a one-step catastrophic event termed chromothripsis (CT). In this scenario, the chr shatters into tens to hundreds of pieces, some of which are then stitched together in a mosaic patchwork of genomic fragments. Such random stitching may give rise to fusion genes with oncogenic potential. CT has not been thoroughly studied in diffuse gliomas, such as glioblastomas (GB). The aim of the project was to detect CT in GB and identify novel fusion genes in CT regions. Those genes are potential therapeutic targets. MATERIAL AND METHODS 170 de novo IDH wild-type GB were screened for CT patterns using whole genome SNP arrays. RNA sequencing was performed in 52 cases with CT features to identify novel fusion genes within the rearranged genomic regions. Expression levels of transcripts were measured using FPKM (fragments per kilobase of exon per million fragments mapped) normalization method. Candidate fusion genes were validated by RT-PCR followed by Sanger sequencing. RESULTS Out of 66 GB with CT patterns (66/170, 38.8%), 40 cases (out of 52 RNA-sequenced cases, 77%) harbored at least one fusion gene within CT regions, which were mostly detected on chr 7, 9, and 12. Overall, 137 candidate fusion genes were identified, 26 of which with a predicted open reading frame. Twelve out of 26 fusions were validated by RT-PCR followed by Sanger sequencing (validation of the remaining fusions is ongoing). The fusions involved either well-known key oncogenes such as EGFR, MDM2, and MET or potential oncogenes (CPM, PPM1H, SEPT14, SEC61G) with a yet-to-discover role in GB pathogenesis. GB with CT on chr 12 (11/66, 16.7%) showed a distinct transcript expression profile at the locus 12q13-15, particularly in the vicinity of MDM2 and CDK4 genes. In our cohort, this so-called “multi-aberration region” recurrently harbored gene fusions, involving, among others, CPM (12q15). CPM, encoding an extracellular membrane-bound carboxypeptidase, is recurrently amplified in liposarcoma and is a potential oncogene involved in the EGFR signaling pathway. Three cases (3/26, 11.5%) harboring an in-frame gene fusion involving CPM showed higher levels of CPM transcripts and did not exhibit any EGFR amplification. Gene fusions involving CPM might constitute an alternative mechanism of EGFR pathway activation in de novo IDH wild-type GB. CONCLUSION The occurrence of CT points to underlying gene fusions in IDH wild-type GB. Such fusions may drive tumorigenesis and represent promising therapeutic targets. We identified CPM as a recurrent fusion partner and a potential alternative mechanism of EGFR signaling pathway activation in de novo IDH wild-type GB.