2. Academic Validation
  3. Characterization of aberrant splicing in pediatric central nervous system tumors reveals CLK1 as a candidate oncogenic dependency

Characterization of aberrant splicing in pediatric central nervous system tumors reveals CLK1 as a candidate oncogenic dependency

  • bioRxiv. 2024 Aug 22:2024.08.03.606419. doi: 10.1101/2024.08.03.606419.
Ammar S Naqvi 1 2,  Ryan J Corbett 1 2 3,  Priyanka Seghal 4,  Karina L Conkrite 3,  Komal S Rathi 1 2,  Brian M Ennis 1 2,  Katharina E Hayer 3 5,  Bo Zhang 1 2,  Miguel A Brown 1 2,  Daniel P Miller 1 2,  Adam A Kraya 1 2,  Joseph M Dybas 1 2,  Zhuangzhuang Geng 1 2,  Christopher Blackden 1 2,  Shehbeel Arif 1 2,  Antonia Chroni 1 2,  Aditya Lahiri 5,  Madison L Hollawell 1 2,  Phillip B Storm 1 2,  Jessica B Foster 3 6,  Mateusz Koptyra 1 2,  Peter J Madsen 1 2,  Sharon J Diskin 3 5 6,  Andrei Thomas-Tikhonenko 3 4 6 7,  Adam C Resnick 1 2,  Jo Lynne Rokita 1 2
Affiliations

Affiliations

  • 1 Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
  • 2 Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
  • 3 Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA.
  • 4 Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
  • 5 Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
  • 6 Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, USA.
  • 7 Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA.
PMID: 39149264 DOI: 10.1101/2024.08.03.606419
Abstract

Pediatric brain Cancer is the leading cause of disease-related mortality in children, and many aggressive tumors still lack effective treatment strategies. Despite extensive studies characterizing these tumor genomes, alternative transcriptional splicing patterns remain underexplored. Here, we systematically characterized aberrant alternative splicing across pediatric brain tumors, identifying pediatric high-grade gliomas (HGGs) among the most heterogeneous. Through integration with UniProt Knowledgebase annotations, we identified 12,145 splice events in 5,424 genes, leading to functional changes in protein activation, folding, and localization. We discovered that the master splicing factor and cell-cycle modulator, CDC-like kinase 1 (CLK1), is aberrantly spliced in HGGs to include exon 4, resulting in a gain of two phosphorylation sites and subsequent activation of CLK1. Inhibition of CLK1 with Cirtuvivint in the pediatric HGG KNS-42 cell line significantly decreased both cell viability and proliferation in a dose-dependent manner. Morpholino-mediated depletion of CLK1 exon 4 splicing reduced RNA expression, protein abundance, and cell viability. Notably, KNS-42 cells treated with the CLK1 exon 4 morpholino demonstrated differential expression 78 genes and differential splicing with loss or gain of a functional site in 193 genes annotated as oncogene or tumor suppressor genes (TSGs). These genes were enriched for cancer-associated pathways, with 20 identified as significant gene dependencies in pediatric HGGs. Our findings highlight a dependency of pediatric HGGs on CLK1 and its roles contributing to tumor splicing heterogeneity through transcriptional dysregulation of splicing factors and transcriptional modulation of oncogenes. Overall, aberrant splicing in HGGs and other pediatric brain tumors represents a potentially targetable oncogenic pathway contributing to tumor growth and maintenance.

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Products
  • Cat. No.
    Product Name
    Description
    Target
    Research Area
  • HY-137435
    98.28%, CLK Inhibitor
    CDK