Abstract 1505: Platelet derived growth factor receptor alpha oncogene dependency in glioblastoma
Authors: Berezovsky Artem D. , Irtenkauf Susan M. , Transou Andrea D. , Hasselbach Laura A. , Mikkelsen Tom , deCarvalho Ana C. 
Published: September 2020

Abstract
Platelet-derived growth factor receptor alpha (PDGFRA) is a ligand-activated receptor tyrosine kinase (RTK) involved in neurodevelopment. In pediatric and adult glioblastoma (GBM), PDGFRA downstream signaling promotes tumor cell proliferation, stemness and survival. Deregulated oncogenic PDGFRA signaling in these tumors occurs by gene amplification (15% of cases), often times as extrachromosomal elements (ecDNA), or by mutations and transcriptional upregulation. Lack of biomarker-based patient selection has contributed to failure of PDGFRA inhibitors in clinical trials. To provide experimental evidence for selection of patients that can benefit from PDGFRA targeted therapy, we have investigated the mode of PDGFRA deregulation in patient-derived GBM models, which we hypothesize determines the degree of dependency on PDGFRA signaling. PDGFRA copy number and mRNA levels in a panel of 13 GBM tumors, derived cancer stem cells (CSC) and xenografts (PDX) were determined by DNA and RNA seq, respectively. EcDNA location of PDGFRA-amplified CSCs was determined by FISH. Levels of total PDGFRA and activated (phospho-PDGFRA Y754) protein were determined by IHC and reverse phase protein array (RPPA). PDGFRA mRNA overexpression was observed for 3 GBM tumors and their derived models: one GBM carrying PDGFRA ecDNA amplification (HF3253), and two non-amplified GBMs (Tukey p=0.60, 0.37). Messenger RNA correlated to total protein levels for all cases, but corresponding PDGFRA activation was observed only for HF3253. High levels of PDGFRA activation in HF3253 PDX was retained in recurrent tumors after temozolomide treatment. Exploiting intra-tumoral heterogeneity, we have isolated 2 single cell clones from HF3253 CSCs which do not carry PDGFRA ecDNA(-) and tested their self-renewal and tumorigenic potential against the parental ecDNA(+) cells. Reduced self-renewal in both ecDNA(-) clones was observed (p=1e-03, p=0.01). Tumor growth in mouse orthotopic xenografts, measured by symptom-free survival, was extraordinarily reduced in the two ecDNA(-) clones (log-rank, p=1e-03, 2e-04). In contrast to parental HF3253, ecDNA(-) tumors demonstrated diffuse tumor morphology and weak PDGFRA activation. Using RPPA data from four in vitro media conditions (normal growth, minus EGF/FGF, 2% and 10% FBS) in eight GBM CSC models, the effect of growth conditions on PDGFRA activation was significant and strongest under growth factor-depleted conditions (p=5e-04, 2-way ANOVA). In conclusion, we demonstrated the dependency on PDGFRA signaling in a patient-derived GBM model carrying ecDNA PDGFRA amplification. PDGFRA over-expression was observed for 2 GBMs in absence of gene amplification, but it did not result in protein activation, which our data suggest is a determinant of oncogene dependency. PDGFRA activity is preserved by endogenous stressors (removal of growth factors) and exogenous stressors (TMZ). Our data validates PDGFRA as a therapeutic target in a subset of GBM patients and demonstrates that detection of ecDNA-amplified PDGFRA has the potential to be a predictive biomarker of future PDGFRA targeted therapies.
Citation Format: Artem D. Berezovsky, Susan M. Irtenkauf, Andrea D. Transou, Laura A. Hasselbach, Tom Mikkelsen, Ana C. deCarvalho. Platelet derived growth factor receptor alpha oncogene dependency in glioblastoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1505.