The heterogeneous sensitivity of pediatric brain tumors to different oncolytic viruses is predicted by unique gene molecular profiles

Despite decades of research, the prognosis of high-grade pediatric brain tumors (PBTs) remains dismal, however, recent cases of favorable clinical responses were documented in clinical trials using oncolytic viruses (OVs). Therefore, we employ four different species of OVs: adenovirus Delta24-RGD, herpes simplex virus rQNestin34.5v1, reovirus R124 and the non-virulent Newcastle Disease Virus rNDV-F0-GFP against three entities of PBTs (high-grade gliomas, atypical teratoid/rhabdoid tumors and ependymomas) to determine their in vitro efficacy. These four OVs were screened on 14 patient-derived spheroids and the degree of oncolysis was assessed using an ATP-based assay. Subsequently, the observed viral efficacies were correlated to whole transcriptome data and Gene Ontology analysis was performed. Although no significant tumor type-specific OV efficacy was observed, whole transcriptome analysis revealed the intrinsic biological processes that associated with OV efficacy. The predictive power of those molecular profiles was further validated by screening the OV in vitro efficacy on additional PBTs. In summary, our results demonstrate OV susceptibility of multiple patient-derived PBT entities and the ability to predict in vitro responses to OVs using unique molecular profiles. Those profiles highlight the cellular intrinsic factors for potent oncolysis, that could potentially allow stratification of patients and lead to improved OV responses. To investigate the intrinsic factors that relate to Oncolytic virus (OV) oncolysis we used a panel of 14 patient derived pediatric brain tumor cell cultures (PBTs) which were infected with 4 different OVs: Delta24-RGD, rQNestin34.5v1, R124 and rNDV-F0-GFP. We then performed gene expression profiling using RNA seq data obtained from the 14 uninfected PBTs. The gene expression of the PBTs was correlated (using spearman correlation) with the concentration of each OV needed to kill 50% per PBT 5 days post infection (EC50s). Gene Ontology enrichment was performed using as input the significantly correlated genes to link specific factors to OV sensitivity and resistance. Additional PBTs were used for phenotypic profiling using the significantly correlating genes in order to predict their response to the OVs and those profiles were further validated through in vitro testing.