Background
Untreatable gliomas, such as anaplastic astrocytoma, progress rapidly and responds poorly to treatment with a higher chance of relapse leading to very low survival rates. Epigenetic changes such as DNA methylation affecting major molecular markers such as BRAF and HDAC have been shown to facilitate tumor progression. However, our complete knowledge of all such epigenetic changes is yet to be characterised. This study investigates the differential methylation of molecular markers in pediatric astrocytoma samples at diagnosis and relapse stages to identify genes undergoing epigenetic alterations.
Methods
Methylation datasets were downloaded from NCBI and was analysed using an R- based differential methylation analysis tool, RnBeads. The datasets were normalised using BMIQ method and principal component analysis was performed. Differential methylation of CpG islands, CpG sites, promotors and genes were computed.
Results
Differential methylation analysis (DMA) of CpG sites showed significant hyper-methylation at 211674 sites and significant hypo-methylation at 153807 sites. DMA of CpG islands showed significant hyper-methylation at 3980 sites and significant hypo-methylation at 16595 sites. DMA of promotors showed significant hyper-methylation at 13146 sites and significant hypo-methylation at 13690 sites. DMA of genes showed significant hyper-methylation at 6580 sites and significant hypo-methylation at 4187 sites (Samples having mean b value > 0.8, combined p < value 0.01 were considered hypermethylated and those having mean b value < 0.2, combined p value < 0.01 were considered hypo methylated).
Conclusion
This study has identified significantly different hyper and hypo methylated regions within the genome of patients with high grade anaplastic astrocytoma at diagnosis and relapse stages which is crucial in devising prognostic criteria for characterising different molecular subtypes of pediatric astrocytoma and in studying the effects of epigenetic alterations in promoting tumor progression. Further studies will be done to understand metastases and invasion in 3D and monolayer cultures.