Investigating the Cellular and Molecular Effects of the Subventricular Zone on Hosted Glioblastoma Cells

AIMS The subventricular zone (SVZ) is a unique zone of the brain located along the wall of the lateral ventricles. Glioblastomas (GBM) in contact with the SVZ are associated with a poorer prognosis. In mouse models, GBM cells migrate towards the SVZ, where they are more protected against treatments. In the SVZ, GBM cells are in contact with the cerebrospinal fluid (CSF). In this context, we aim to investigate the interactions between the SVZ including the CSF, and the nested GBM cells to better understand their roles in tumor persistence and relapses. METHODS RNA sequencing was performed on four primary GBM cultures plated in CSF or control medium, to assess the effects on their transcriptome. Single-cell RNA sequencing was also performed on primary GBM cells ortho- topically injected in mice. The SVZ and tumor mass (TM) were microdissected, dissociated, mCherry+ GBM cells were FACSorted and analyzed to evaluate the transcriptomic differences between the two zones. RESULTS Numerous differentially expressed genes in CSF compared to control medium were highlighted, 138 being com- mon to all GBM cultures. Downstream gene set enrichment analysis (GSEA) and Ingenuity Pathway Analysis showed an activation of different pathways such as the epithelial-to-mesenchymal transition, ID1 pathway and migrative functions in CSF. Between SVZ and TM, 239 genes were differentially expressed. GSEA depicted an activation of the TNFa signaling via NKkB, p53 pathway and hypoxia. A comparison of the downstream GSEA of both experiments showed that those pathways are also activated in the CSF in vitro. CONCLUSION GBM cells are influenced both by CSF and the SVZ localization. CSF activates the epithelial-to-mesenchymal transition, the ID1 pathway and migrative functions, which may be associated with a more aggressive pheno- type. TNFa signaling via NFkB, p53 pathway and hypoxia are modulated both in vitro and in vivo, suggesting that they may be important in SVZ-associated tumor persistence.