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

Simple Summary: Medulloblastoma is the most common malignant childhood brain tumor and it is considered poor immunogenic because of its low mutational burden. Nevertheless, several clinical trials are currently evaluating immunotherapy for medulloblastoma patients, since new treatment strategies for this entity are a matter of utmost urgency. Tumor specific antigens resulting from gene fusions are potentially highly immunogenic. In our study, we identified a new medulloblastoma-specific fusion transcript EPC2-GULP1.The resulting protein sequence produced a neoantigen, which was able to activate CD8(+) T cells. Thus, our data indicate an immunotherapeutic approach for pediatric medulloblastoma patients carrying the EPC2-GULP1 fusion or other fusions generating immunogenic neoantigens. 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.