digital transcriptome profiling of normal and glioblastoma-derived neural stem cells identifies genes associated with patient survival

background: glioblastoma multiforme, the most common type of primary brain tumor in adults, is driven by cellswith neural stem (ns) cell characteristics. using derivation methods developed for ns cells, it is possible to expandtumorigenic stem cells continuously in vitro. although these glioblastoma-derived neural stem (gns) cells arehighly similar to normal ns cells, they harbor mutations typical of gliomas and initiate authentic tumors followingorthotopic xenotransplantation. here, we analyzed gns and ns cell transcriptomes to identify gene expressionalterations underlying the disease phenotype. methods: sensitive measurements of gene expression were obtained by high-throughput sequencing of transcript tags (tag-seq) on adherent gns cell lines from three glioblastoma cases and two normal ns cell lines. validation by quantitative real-time pcr was performed on 82 differentially expressed genes across a panel of 16 gns and 6 ns cell lines. the molecular basis and prognostic relevance of expression differences were investigated by genetic characterization of gns cells and comparison with public data for 867 glioma biopsies. results: transcriptome analysis revealed major differences correlated with glioma histological grade, and identifiedmisregulated genes of known significance in glioblastoma as well as novel candidates, including genes associatedwith other malignancies or glioma-related pathways. this analysis further detected several long non-coding rnaswith expression profiles similar to neighboring genes implicated in cancer. quantitative pcr validation showedexcellent agreement with tag-seq data (median pearson r = 0.91) and discerned a gene set robustly distinguishinggns from ns cells across the 22 lines. these expression alterations include oncogene and tumor suppressorchanges not detected by microarray profiling of tumor tissue samples, and facilitated the identification of a gnsexpression signature strongly associated with patient survival (p = 1e-6, cox model).

conclusions: these results support the utility of gns cell cultures as a model system for studying the molecularprocesses driving glioblastoma and the use of ns cells as reference controls.theassociation between a gns expression signature and survival is consistent with the hypothesis that a cancer stem cell component drives tumorgrowth. we anticipate that analysis of normal and malignant stem cells will be an important complement to largescaleprofiling of primary tumors.