Revealing and targeting metabolic drivers contributing to treatment escape in diffuse midline glioma.
Authors: Frederico Stephen C. , Neyazi Sina , Gowda Pruthvi , Nguyen Cuong , Trissal Maria , Portero Erika P. , Haley-Read John-Paul , Anderson Emily P. , Thomas Craig J. , Danial Nika N. , Filbin Mariella G. 
Published: June 2024

10038

Background: Diffuse midline glioma (DMG) is an aggressive pediatric brain tumor that predominately affects children, with a median survival of 9-11 months. DMGs are driven by self-renewing, stem-like glioma cells that have been stalled in an oligodendrocyte precursor cell (OPC)-like state and that highly express PDGFRA. This overexpression of PDGFRA has been shown to be pivotal in DMG development. Thus, targeting PDGFRA may serve as a viable treatment approach for DMG. In our previous studies, we revealed that avapritinib, a next generation tyrosine kinase inhibitor of PDGFRA, is highly effective in DMG cells. While a subset of patients receiving treatment with avapritinib experienced a promising clinical response, all patients eventually experienced tumor progression due to treatment escape. In this study, we investigated which mechanisms DMG cells use to escape avapritinib treatment, and how we can therapeutically exploit these resistance mechanisms. Methods: Transcriptomic profiling and functional assays were performed on patient-derived DMG cell lines. A combinatorial drug screening identified drug candidates evaluated in this study. Results: Bulk RNA sequencing analysis of two patient derived DMG cell lines revealed an upregulation of genes associated with both fatty acid metabolism and oxidative phosphorylation (OXPHOS) following avapritinib treatment. Functional assays confirmed elevated OXPHOS in avapritinib-treated cells with significant increases in mitochondrial energy transduction, palmitate- (a product of fatty acid metabolism) driven oxygen consumption rates, and incorporation of palmitate-derived carbons into the tricarboxylic acid (TCA) cycle. CRISPR-Cas9-mediated knockout of PDGFRAin one DMG cell line confirmed the metabolic changes observed following avapritinib treatment. Analysis of bulk RNA sequencing data revealed an upregulation of key fatty acid- related transcription factors in avapritinib-treated DMG cells. Specifically, Peroxisome Proliferator-Activated Receptor alpha (PPAR-alpha), Sterol Regulatory Binding Element Binding Transcription Factors 1 and 2, and Fatty Acid Synthase (FASN) were most prominently upregulated. To determine which therapies could target the dependency of avapritinib-treated cells on fatty acid metabolism, we performed a combinatorial drug screening and found three lipid pathway inhibitors that have synergistic cytotoxic effects with avapritinib. Specifically, a FASN inhibitor, cholesterol pathway inhibitor, and PPAR-alpha inhibitor. Conclusions: In this study, we revealed metabolic drivers that may contribute to avapritinib resistance in DMG cells, and identified compounds capable of inhibiting these drivers that demonstrate synergy with avapritinib. We now intend on testing these combination therapies in vivo as we aim to provide a long-term clinical benefit to DMG patients receiving avapritinib.