Fusions involving BCOR and CREBBP are rare events in infiltrating glioma

Abstract

BCOR has been recognized as a recurrently altered gene in a subset of pediatric tumors of the central nervous system (CNS). Here, we describe a novel BCOR-CREBBP fusion event in a case of pediatric infiltrating astrocytoma and further probe the frequency of related fusion events in CNS tumors. We analyzed biopsy samples taken from a 15-year-old male with an aggressive, unresectable and multifocal infiltrating astrocytoma. We performed RNA sequencing (RNA-seq) and targeted DNA sequencing. In the index case, the fused BCOR-CREBBP transcript comprises exons 1-4 of BCOR and exon 31 of CREBBP. The fused gene thus retains the Bcl6 interaction domain of BCOR while eliminating the domain that has been shown to interact with the polycomb group protein PCGF1. The fusion event was validated by FISH and reverse transcriptase PCR. An additional set of 177 pediatric and adult primary CNS tumors were assessed via FISH for BCOR break apart events, all of which were negative. An additional 509 adult lower grade infiltrating gliomas from the publicly available TCGA dataset were screened for BCOR or CREBBP fusions. In this set, one case was found to harbor a CREBBP-GOLGA6L2 fusion and one case a CREBBP-SRRM2 fusion. In a third patient, both BCOR-L3MBTL2 and EP300-BCOR fusions were seen. Of particular interest to this study, EP300 is a paralog of CREBBP and the breakpoint seen involves a similar region of the gene to that of the index case; however, the resultant transcript is predicted to be completely distinct. While this gene fusion may play an oncogenic role through the loss of tumor suppressor functions of BCOR and CREBBP, further screening over larger cohorts and functional validation is needed to determine the degree to which this or similar fusions are recurrent and to elucidate their oncogenic potential.

Keywords: BCOR; CREBBP; Fusion; Infiltrating glioma.

Fig. 1

Radiological and histological characteristics of the index case. Preoperative brain MRIs for the primary tumor demonstrated a mass involving the right frontal lobe as well as the left occipital and temporal lobes (a, b). Representative histology of the primary tumor shows a diffusely infiltrating astrocytoma with predominantly lower grade features (c). Re-resection material met histologic criteria for glioblastoma (d)

Fig. 2

Description and validation of BCOR-CREBBP fusion product. Structure and functional domains of BCOR and CREBBP with the red line indicating the fusion point (a). The detected fusion joins exon 4 of BCOR on chromosome X with exon 31 of CREBBP on chromosome 16 (b). RNA sequencing demonstrated multiple reads in support of the fusion transcript (c). RT-PCR using primers for CREBBP and BCOR demonstrates a robust PCR product (d). Sanger sequencing confirmed the chimeric DNA transcript, with the black dashed line indicating the fusion point (e)

Fig. 3

Fluorescent in situ hybridization (FISH) assays for BCOR and CREBBP in the index case. Break-apart green and red signals for BCOR (a) and CREBBP (b) demonstrate gene rearrangement at the break points. For BCOR, only one allele is present, consistent with a single X chromosome in this male patient. Fusion FISH assay shows the overlapping red and green signals in one allele (yellow signal), confirming BCOR-CREBBP fusion (c)

Fig. 4

Fusion proteins detected in TCGA cohort with genes relevant to this study. BCOR-CREBBP fusion product in the index case (a). TCGA-DU-6404 is a 24-year-old female with IDH-wildtype high grade glioma harbored two fusions involving BCOR, namely BCOR-L3MBTL2 and BCOR-EP300 (b). TCGA-TM-A84I is a 30-year-old with IDH-mutant anaplastic astrocytoma harbored a CREBBP-SRRM2 fusion (c). TCGA-KT-A7W1 is 45-year-old with IDH-wildtype anaplastic astrocytoma harbored a CREBBP-GOLGA6L2 fusion (d)