P01.17.A NOVEL FUSIONS AND CONCURRENT STRUCTURAL VARIANTS IN PEDIATRIC BRAIN TUMORS: INSIGHTS FROM A PEDIATRIC GLIOBLASTOMA H3/IDH WILD-TYPE, SUPRATENTORIAL EPENDYMOMA, AND GLIONEURONAL TUMOR DLGNT

Abstract BACKGROUND Pediatric brain tumors are a heterogeneous group of neoplasms with complex genetic and epigenetic alterations that define distinct molecular subtypes. Due to overlapping histopathological features, the accurate diagnosis often requires a multidisciplinary approach that integrates morphological, immunophenotypic, and molecular data. MATERIAL AND METHODS Following initial histological assessment, comprehensive molecular analyses were conducted on three pediatric brain tumor samples that lacked distinctive morphological and immunophenotypic features. To elucidate their genetic landscape, we employed RNA whole-transcriptome sequencing (RNA-seq), DNA methylation profiling (Illumina EPIC 850K array), and fluorescence in situ hybridization (FISH). This integrative approach aimed to detect a wide range of genetic alterations, including novel fusions and concurrent structural variants. RESULTS One tumor (sample #1), with histological and immunophenotypic profile suggestive of a pediatric glioma versus supratentorial ependymoma, tested negative for H3F3A/IDH mutations, and FISH did not reveal ZFTA/YAP1 rearrangements. DNA methylation profiling classified the tumor as pediatric glioblastoma H3/IDH wild-type, with a calibrated score of 0.9. Remarkably, RNA-seq identified a novel PAX5: : ATM fusion resulting from a t(9;11)(p13.2;q22.3) translocation. While PAX5 rearrangements are known in acute lymphoblastic leukemia and ATM mutations are common in lymphoid malignancies, this represents the first report of a PAX5: : ATM fusion in a brain tumor, revealing a novel genetic alteration with potential prognostic or therapeutic relevance. Interestingly, we also observed the presence of concurrent structural variants within single tumors. In one supratentorial ependymoma (sample #2), both ZFTA: : RELA and YAP1: : TYR fusions were detected, with TYR representing a previously unreported fusion partner for YAP1. In another case (sample #3), a diffuse leptomeningeal glioneuronal tumor (DLGNT) exhibited concurrent KIAA1549: : BRAF and MN1: : BEND2 fusions. These findings provide strong evidence of intratumoral genetic heterogeneity, demonstrating the coexistence of distinct genetic subclones within individual tumors and underscoring the complexity of pediatric brain tumor biology. CONCLUSION The identification of novel fusions and concurrent structural variants in pediatric brain tumors expands our understanding of their genetic landscape. These findings underscore the importance of comprehensive molecular profiling for accurate tumor classification, risk stratification, and therapeutic decision-making. Further investigation into the clinical implications of these structural alterations is essential for advancing pediatric neuro-oncology.