Poster Presentation 32nd Lorne Cancer 2020

Identification of targetable pathway dependencies in Diffuse Intrinsic Pontine Glioma. (#326)

Sarah Parackal 1 2 3 , Wai Chin Chong 1 2 3 , Enola Roussel 1 4 , Samantha Jayasekara 1 2 , Duncan Crombie 1 2 3 , Ron Firestein 1 2 3 , Jason Cain 1 2 3
  1. Centre for Cancer Research, Hudson Institute of Medical Research, Melbourne , VIC, Australia
  2. Department of Molecular and Translational Science, Monash University, Melbourne, VIC, Australia
  3. Hudson Monash Paediatric Precision Medicine Program, Melbourne, VIC, Australia
  4. Department of Genetics, Monash University, Melbourne, VIC, Australia

Diffuse Intrinsic Pontine Glioma (DIPG) is a highly aggressive paediatric brainstem tumour with a survival rate of 9-12 months1. Currently DIPG has no effective therapy and treatment is limited to palliative radiotherapy2. Recurrent heterozygous mutations (p.K27M) in Histone H3 variant genes, H3.1 (HIST1H3B, HIST1H3C) and H3.3 (H3F3A) have been identified in the majority of DIPG cases3,4. While the exact mechanism of H3K27M’s function is poorly understood, evidence suggests a role in epigenetic dysregulation in the pathogenesis of disease5,6. This study aims to use functional genomics to identify novel therapeutic dependencies in H3K27M DIPG.

DIPG drug sensitivity screening was carried out in twelve established and validated patient derived cell lines (10 H3.3K27M and 2 Wt) using an FDA approved drug (1480) library. Cell viability data following 72 hours treatment was z-transformed and potential compounds identified based on a z-score £-1.5 and no effect in a neural stem cell (NSC) control line. Highly prevalent targets identified from this primary screen include HDAC, microtubule, proteasome and CDK inhibitors of which several are currently in clinical trials for a variety of paediatric solid tumours. Additionally, a custom pooled CRISPR knockout library of druggable targets (300 genes, 1200 guide RNAs) was used to identify key DIPG cell survival pathways. To date, five DIPG cell lines (1 Wt; 1 H3.1; 3 H3.3) have undergone screening. Knockdown of known DIPG driver genes (TP53; PDGFRA; PIK3CA and PIK3CR1) resulted in reduced cell viability, consistent with their proposed function and validating knockout screen utility. Preliminary data indicates Wt vs H3K27M DIPGs cluster distinctly based on genes required for survival, suggesting differing tumorigenesis mechanisms and the potential for therapeutically targeting genotype specific pathways. We are currently correlating this data with drug screen and RNA-seq data to reveal H3-dependent pathways for potential therapeutic exploitation.

Collectively, we show a functional genomics approach is able to identify genotype-specific pathway dependencies in DIPG, potentially paving the way for molecularly informed personalized therapies for patients.

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