Impact of genomic background and developmental state on signaling pathways and response to therapy in glioblastoma patient-derived cells

Glioblastoma (GBM) tumors encompass several subgroups, reflecting diversity in the genomic epigenomic, and transcriptional landscape. Additionally, remarkable intratumoral heterogeneity, a hallmark of glioblastomas, poses significant challenges to the standard of care, comprised of treatment with radiation (RT) and with the DNA-alkylating agent temozolomide (TMZ). In this study, using targeted proteomics we determined the response of a genomically-diverse panel of patient-derived GBM cells to neural stem and differentiation-inducing culture conditions, unveiling complex crosstalk in key oncogenic signaling. Furthermore, we show both common and tumor specific aspects of transcriptional and epigenetic reprograming accompanying differentiation of cancer stem cells (CSCs). We report the relative impact that differentiation and genomic background have on sensitivity and transcriptional response of GBM cells to TMZ and RT. Importantly, we show that the differentiation of GBM cancer stem cells increased sensitivity to temozolomide but not to radiation treatment. Transcriptional response to treatment was largely dependent on p53 status, while treatment-induced p53 activity was also influenced by the differentiation state of wildtype p53 cells. Interferon response was activated in CSC differentiation and in response to TMZ and RT. The modeling of GBM differentiation states in vitro is a powerful tool for optimizing treatments, emphasizing the necessity of evaluating gene expression patterns associated with cellular adaptations.