Identification of an Immunogenic Medulloblastoma-Specific Fusion Involving EPC2 and GULP1

Abstract

Medulloblastoma is the most common malignant brain tumor in children. Immunotherapy is yet to demonstrate dramatic results in medulloblastoma, one reason being the low rate of mutations creating new antigens in this entity. In tumors with low mutational burden, gene fusions may represent a source of tumor-specific neoantigens. Here, we reviewed the landscape of fusions in medulloblastoma and analyzed their predicted immunogenicity. Furthermore, we described a new in-frame fusion protein identified by RNA-Seq. The fusion involved two genes on chromosome 2 coding for the enhancer of polycomb homolog 2 (EPC2) and GULP PTB domain containing engulfment adaptor 1 (GULP1) respectively. By qRT-PCR analysis, the fusion was detected in 3 out of 11 medulloblastoma samples, whereby 2 samples were from the same patients obtained at 2 different time points (initial diagnosis and relapse), but not in other pediatric brain tumor entities. Cloning of the full-length sequence indicated that the fusion protein contains the N-terminal enhancer of polycomb-like domain A (EPcA) of EPC2 and the coiled-coil domain of GULP1. In silico analyses predicted binding of the neoantigen-derived peptide to HLA-A*0201. A total of 50% of the fusions described in the literature were also predicted to produce an immunogenic peptide. The EPC2-GULP1 fusion peptide was able to induce a de novo T cell response characterized by interferon gamma release of CD8+ cytotoxic T cells in vitro. While the functional relevance of this fusion in medulloblastoma biology remains to be clarified, our data support an immunotherapeutic approach for pediatric medulloblastoma patients carrying the EPC2-GULP1 fusion and other immunogenic fusions.

Non-Canonical Splicing and Its Implications in Brain Physiology and Cancer

“…Recently, a novel trans-splicing-mediated fusion transcript generated from the enhancer of polycomb homolog 2 (EPC2) and GULP PTB domain containing engulfment adaptor 1 (GULP1) loci has been identified in MB [ 192 ]. Although the EPC2-GULP1 chimera did not show MB subgroup-specificity, it was detected in 3 out of 11 MB patients analysed and not in other paediatric brain tumours [ 192 ].…”

“…Recently, a novel trans-splicing-mediated fusion transcript generated from the enhancer of polycomb homolog 2 (EPC2) and GULP PTB domain containing engulfment adaptor 1 (GULP1) loci has been identified in MB [ 192 ]. Although the EPC2-GULP1 chimera did not show MB subgroup-specificity, it was detected in 3 out of 11 MB patients analysed and not in other paediatric brain tumours [ 192 ]. Importantly, the peptide encoded by the EPC2-GULP1 fusion transcript presented immunogenic potential, as demonstrated by its ability to induce a CD8+ T-cell-mediated immune response [ 192 ].…”

“…Although the EPC2-GULP1 chimera did not show MB subgroup-specificity, it was detected in 3 out of 11 MB patients analysed and not in other paediatric brain tumours [ 192 ]. Importantly, the peptide encoded by the EPC2-GULP1 fusion transcript presented immunogenic potential, as demonstrated by its ability to induce a CD8+ T-cell-mediated immune response [ 192 ]. This observation has extremely relevant clinical implications, suggesting that neo-antigens depending on trans-splicing for their biogenesis, as is the case for EPC2-GULP1 fusion peptide, may represent optimal candidates for immunotherapy, especially in a tumour context, such as that of MB, with minimal mutational load and low immunogenicity [ 193 ].…”

New Strategies in Diagnosis and Treatments for Brain Tumors

“…This, they believe, is a consequence of the rather low mutation rate in these tumors. Their data suggests, however, that immunogenic fusions, such as the EPC2-GULP1 fusion, might provide alternative targets for immunotherapeutic approaches [26].…”