Limitations of current in vitro models for testing the clinical potential of epigenetic inhibitors for treatment of pediatric ependymoma

Abstract

BackgroundEpigenetic modifications have been shown to play an important role in the classification and pathogenesis of the pediatric brain tumor ependymoma, suggesting they are a potential therapeutic target.ResultsAgents targeting epigenetic modifications inhibited the growth and induced the death of ependymoma cells with variable efficiency. However, this was often not at clinically achievable doses. Additionally, DNA methylation profiling revealed a lack of similarity to primary ependymomas suggesting alterations were induced during culture. Toxicity to fetal neural stem cells was also seen at similar drug concentrationsConclusionsAgents targeting epigenetic modifications were able to inhibit the growth and induced the death of ependymoma cells grown in vitro. However, many agents were only active at high doses, outside clinical ranges, and also resulted in toxicity to normal brain cells. The lack of similarity in DNA methylation profiles between cultured cells and primary ependymomas questions the validity of using in vitro cultured cells for pre-clinical analysis of agents targeting epigenetic mechanisms and suggests further investigation using models that are more appropriate should be undertaken before agents are taken forward for clinical testing.Materials and MethodsThe effects of agents targeting epigenetic modifications on the growth and death of a panel of ependymoma cell lines was investigated, as well as toxicity to normal fetal neural stem cells. The ependymoma cell lines were characterized using DNA methylation profiling.

De novo DNA methyltransferase activity in colorectal cancer is directed towards H3K36me3 marked CpG islands

“…A further potential limitation of the use of cell lines is that DNA methylation patterns are altered by cell culture 56 . Little correspondence is reported between global methylation patterns in clinical ependymomas and cultured cell lines 57 . However, we have previously shown that aberrantly methylated CGIs identified in breast cancer cell lines are also identified in clinical tumours 5 and here we have focused on CGIs whose methylation is observed in vivo.…”

Cell-of-Origin and Genetic, Epigenetic, and Microenvironmental Factors Contribute to the Intra-Tumoral Heterogeneity of Pediatric Intracranial Ependymoma

“…The establishment of appropriate preclinical models, which mirror the distinct EPN subgroups and even the distinct EPN subpopulations, is critical for drug testing and identification of drug response biomarkers [ 226 ]. Although there are many preclinical studies in EPN models [ 74 , 199 , 227 , 228 ], few studies have hitherto compared drug sensitivities in heterogeneous subpopulations of EPN cell lines [ 78 , 79 , 216 ].…”

CN133, a Novel Brain-Penetrating Histone Deacetylase Inhibitor, Hampers Tumor Growth in Patient-Derived Pediatric Posterior Fossa Ependymoma Models

“…EPP and EPV patient-derived cells were always cultured in 3D conditions using Neurocult medium supplemented with NeuroCult NS-A Proliferation Supplement Human (Stem Cell Technologies, Vancouver, BC, Canada), Epidermal Growth Factor (EGF; 20 ng/mL; Stem Cell Technologies), and basic Fibroblast Growth Factor (bFGF; 10 ng/mL; Stem Cell Technologies) and maintained at 37 °C and in a 5% CO 2 saturated atmosphere. DNA-methylation profiled was performed, but as expected for the majority of cultured EPN cell lines [ 40 ], results were not conclusive.…”