METB-10. GENOME-WIDE DNA METHYLATION PROFILING OF PRIMARY CELLS FROM PEDIATRIC BRAIN TUMORS IS AN INFORMATIVE TOOL TO ASSESS CELL CULTURE RELIABILITY AND IN VITRO SELECTION

Abstract

Abstract BACKGROUND Recent genomic and epigenomic profiling analyses have provided remarkable insights into biology of pediatric brain tumors (pBTs). Nonetheless, pBTs represent the deadliest childhood cancer worldwide and are associated with high morbidity. In vitro models of pBT are instrumental for better understanding the mechanisms contributing to oncogenesis and testing new therapies; thus, ideally, they should recapitulate the original tumor. METHODS We applied DNA methylation (DNAm) and copy number variation (CNV) profiling to characterize 241 pBT samples from medulloblastomas, high-grade gliomas, low-grade gliomas, ependymoma, and meningiomas. The cohort included 155 tumors and 86 pBT-derived cell cultures. For the analysis of pBT-derived cell cultures, we have considered the most significant variables: i) cultured medium (serum vs serum-free), ii) passages (late vs early), and iii) dimensionality (2D vs 3D cultures). As a complementary approach, the global relationships between the 241 samples based on the DNAm information were visualized using fast interpolation-based t-distributed stochastic neighbour embedding (t-SNE) and differentially methylated regions in tumors compared to cell models were identified. RESULTS Our findings showed that cell cultures cultured under stem-like cells enriching conditions (serum-free, 3D) and maintained in culture early passages are characterized by a higher degree of faithfulness to the parental tumors, in terms of methylation class and CNV profile, than the counterparts maintained in 2D cultures, in presence of serum, and maintained for extended passages. All divergent cells clustered together acquiring a common deregulated epigenetic signature suggesting a shared selective pressure. We identified a set of hypomethylated genes shared among unfaithful cells converging on response to growth factors and migration pathways, such as signaling cascade activation, tissue organization, and cellular migration. CONCLUSIONS DNAm and CNV are informative tools that should be used to assess the recapitulation of pBT-cells from parental tumors.