Delineating the Cytogenomic and Epigenomic Landscapes of Glioma Stem Cell Lines

Abstract

Glioblastoma multiforme (GBM), the most common and malignant type of glioma, is characterized by a poor prognosis and the lack of an effective treatment, which are due to a small sub-population of cells with stem-like properties, termed glioma stem cells (GSCs). The term “multiforme” describes the histological features of this tumor, that is, the cellular and morphological heterogeneity. At the molecular level multiple layers of alterations may reflect this heterogeneity providing together the driving force for tumor initiation and development. In order to decipher the common “signature” of the ancestral GSC population, we examined six already characterized GSC lines evaluating their cytogenomic and epigenomic profiles through a multilevel approach (conventional cytogenetic, FISH, aCGH, MeDIP-Chip and functional bioinformatic analysis). We found several canonical cytogenetic alterations associated with GBM and a common minimal deleted region (MDR) at 1p36.31, including CAMTA1 gene, a putative tumor suppressor gene, specific for the GSC population. Therefore, on one hand our data confirm a role of driver mutations for copy number alterations (CNAs) included in the GBM genomic-signature (gain of chromosome 7- EGFR gene, loss of chromosome 13- RB1 gene, loss of chromosome 10-PTEN gene); on the other, it is not obvious that the new identified CNAs are passenger mutations, as they may be necessary for tumor progression specific for the individual patient. Through our approach, we were able to demonstrate that not only individual genes into a pathway can be perturbed through multiple mechanisms and at different levels, but also that different combinations of perturbed genes can incapacitate functional modules within a cellular networks. Therefore, beyond the differences that can create apparent heterogeneity of alterations among GSC lines, there’s a sort of selective force acting on them in order to converge towards the impairment of cell development and differentiation processes. This new overview could have a huge importance in therapy.

Chromosomal Instability Affects the Tumorigenicity of Glioblastoma Tumor-Initiating Cells

“…Further studies have analyzed different types of genetic diversity within TICs and showed that glioblastoma TICs and non-TICs had abnormal karyotypes but reported that these karyotypes were clonal and that single cell clones were genetically homogeneous (12,14,36–38). In contrast, we demonstrate that glioblastoma TICs have extensive sub-clonal karyotype heterogeneity and that single cell clones do not maintain a homogenous karyotype.…”

The role of glioma stem cells in chemotherapy resistance and glioblastoma multiforme recurrence

“…GBM is heterogeneous in many ways, including appearance, genetic composition and the variety of mechanisms by which it evades therapy [21]. Extensive study of GBM has borne out the concept that within tumors, cells exist both in differentiated and undifferentiated, progenitor-like states [20].…”

Epigenetic targeting of glioma stem cells: Short-term and long-term treatments with valproic acid modulate DNA methylation and differentiation behavior, but not temozolomide sensitivity

“…The seven GSC lines used in this study (GBM2, GBM7, GBM04, G144, G166, G179 and GliNS2) were isolated from patients affected by GBM (22,23) and, in 2013, our research group characterized their cytogenomic and epigenomic profiles (24). Cells were cultured in neural stem cell-specific medium, and their stem-like properties were periodically monitored, as previously described (22)(23)(24).…”

“…The seven GSC lines used in this study (GBM2, GBM7, GBM04, G144, G166, G179 and GliNS2) were isolated from patients affected by GBM (22,23) and, in 2013, our research group characterized their cytogenomic and epigenomic profiles (24). Cells were cultured in neural stem cell-specific medium, and their stem-like properties were periodically monitored, as previously described (22)(23)(24). Cells were cultured in an adherent culture condition using 10 µg/ml laminin (Invitrogen) in a proliferation permissive medium composed of Dulbecco's modified Eagle's medium (DMEM)/F-12 and Neurobasal 1:1 (Invitrogen), B-27 supplement without vitamin A (Invitrogen), 2 mM L-glutamine, 10 ng/ml recombinant human bFGF and 20 ng/ml recombinant human EGF (Miltenyi Biotec), 20 uI/ ml penicillin and 20 µg/ml streptomycin (Euroclone).…”