Withdrawn 36th Lorne Cancer Conference 2024

A multi-omically guided approach to the treatment of diffuse midline gliomas. (NOT ATTENDING) (#101)

Izac J. Findlay 1 2 , Dilana Staudt 1 2 , Ryan J. Duchatel 1 2 , Evangeline R. Jackson 1 2 , Padraic Kearney 1 2 , Mika L. Persson 1 2 , Holly McEwen 1 2 , Nathan D. Smith 3 , Nicholas A. Vitanza 4 5 , Jason E. Cain 6 7 , Sebastian M. Waszak 8 9 , Mitchell Hansen 10 , Frank Alvaro 1 2 11 , Matthew D. Dun 1 2
  1. Precision Medicine Program, Hunter Medical Research Institute, Newcastle, NSW, Australia
  2. Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine & Wellbeing, University of Newcastle, Newcastle, NSW, Australia
  3. Analytical and Biomolecular Research Facility, University of Newcastle, Newcastle, NSW, Australia
  4. Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute , Seattle, WA, USA
  5. Division of Pediatric Hematology/Oncology, Department of Pediatrics, Seattle Children's Hospital, Seattle, WA, USA
  6. Hudson Institute of Medical Research, Melbourne, VIC, Australia
  7. Department of Paediatrics, Monash University, Melbourne, VIC, Australia
  8. Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway
  9. Department of Neurology, University of California, San Francisco, Ca, USA
  10. Surgical Department, John Hunter Hospital, Newcastle, NSW, Australia
  11. John Hunter Children's Hospital, Newcastle, NSW, Australia

Diffuse midline glioma (DMG) is a devastating paediatric central nervous system (CNS) tumour that localises along the midline region of the brain (pons, thalamus, midbrain, spine). DMG patients face a median OS of just 9–11 months, with <10% of patients with pontine tumours surviving two years post-diagnosis. Current approved treatments are centred on palliative radiotherapy. Patients enrolled on precision medicine clinical trials can be prescribed therapies targeting genetic alterations, however, for the most part, DMGs are populated with genetic changes that are either loss-of-function (LoF), or gain of function but currently lack effective, CNS-active therapeutics.

To improve patient outcomes, we are currently performing multi-omic analysis on 210 DMG, normal controls and other paediatric high-grade glioma (pHGG) samples to characterise the genomic landscape of these tumours and understand the protein-controlled functional consequences of their somatic alterations.

Genomic sequencing has been performed on 40 DMG/pHGG samples, identifying 290 unique mutations and several recurrent chromosomal alterations. Additionally, proteomic and phosphoproteomic profiling identified notably unique and similar landscapes across genotypes. To test predicted therapies, we proceeded to in vitro cell proliferation assays. Using the H3.3K27M DMG patient-derived cell-lines, SU-DIPG-XIII and UON-VIBE5, genomic sequencing identified 11 and 6 somatic alterations respectively, however, only UON-VIBE5 possessed a genomically-predicted target, being a PDGFRA D842V mutation, potentially targetable by Avapritinib. Conversely, investigation of proteome/phosphoproteome revealed several potential therapeutic vulnerabilities with SU-DIPG-XIII possessing high enrichment of HDAC/BRD and CDK pathways and UON-VIBE5, ATM-centric pathways. Proliferation assays of Avapritinib treated UON-VIBE5 failed to elicit a response at clinically relevant doses, while all proteomically predicted therapies (HDAC – Fimepinostat, BRD/BET – JQ1/iBET858, CDK – Ribociclib and ATM – WSD-0628) successfully influenced tumour cell growth whilst leaving microglia controls cells unaffected. Avapritinib and WSD-0628 drug predictions were further validated in the RA055 DMG model, which possesses similar genomic and proteomic features to UON-VIBE5. Avapritinib alone again failed to influence tumour cell growth while WSD-0628 notably reduced cell proliferation, however, the combination of these genomically-predicted and proteomically-predicted drugs synergistically inhibited RA055 proliferation.

These preliminary findings provide evidence highlighting the need to take a multi-omic approach in guiding the treatment of DMGs.