HGG-21. ABERRANT SPLICING OF CLK1 IN PEDIATRIC HIGH-GRADE GLIOMAS DISRUPTS KEY ONCOGENIC TRANSCRIPTIONAL PROGRAMS

Abstract

Abstract While the majority of somatic DNA coding alterations in pediatric brain tumors have been profiled, studies exploring transcriptional mechanisms remain underexplored. We systematically characterized aberrant splicing in primary tumors of seven broad histologies of pediatric brain tumors. We obtained RNA-seq data (n = 792) from the Open Pediatric Brain Tumor Atlas and integrated rMATs splice event calls with UniProt Knowledgebase to quantify and prioritize differential alternative splicing events with proteomic potential. We identified three splicing-driven biological clusters and found pediatric high-grade gliomas (pHGGs) to be uniquely heterogeneous, spanning all three clusters. We also discovered that tumors with high splicing burden (SB) had significantly worse overall survival than tumors with low SB (p < 1x10-4). Furthermore, pHGGs (n = 154) displayed the greatest splicing heterogeneity with 20,620 exon splicing aberrations (pval/FDR < 0.05) in 3,294 genes that resulted in a gain or loss of known functional sites. We prioritized targetable kinases and found that CDC-like kinase 1 (CLK1), a known modulator of master splicing regulators, exhibited significantly increased exon 4 inclusion (p < 0.05, ΔPSI >= |.20|), and subsequent gain of two phosphorylation sites, in tumors compared to matched non-tumor tissue. Exon 4 inclusion was significantly correlated with increased CLK1 expression (r = 0.57, p = 7.8 x10-9), which we posit results in hyper-activity of CLK1 and aberrant splicing of its targets in these tumors. Furthermore, predicted CLK1 gene targets (n = 101) were enriched for cancer-related pathways, such as DNA repair (odds ratio > 2, p < 0.005). In summary, we describe aberrant splicing in pHGGs as an alternative mechanism that could drive tumorigenesis. Future work will focus on molecular validation and therapeutic targeting of CLK1 in available pHGG models, potentially opening new therapeutic strategies in children with brain tumors.