Page 21 - Molecular features of low-grade developmental brain tumours

GENERAL INTRODUCTION & OUTLINE OF THE THESIS
Interestingly, one of the groups, containing LEATs enriched for astrocytic differentiation, BRAF mutation and activation of MAPK/FGFR/EGFR pathways was at higher risk of tumour recurrence than the other three groups. This highlights how RNA-seq can provide novel insights that can be translated to the clinic. Furthermore, in TSC, RNA-seq has identified novel pathways and small RNAs that might play a role in TSC pathogenesis of cortical tubers 114,201. With the constant development of novel RNA-seq methods we are just at the beginning of fully understanding the transcriptome and the molecular features of such neurological diseases and tumours.
microRNAs
Amongst all small RNA species, microRNAs (miRNAs) have received the most interest as a molecule for study. These short RNAs are crucial post-transcriptional regulators of gene expression/ miRNAs work in concert with the RNA-inducing silencing complex (RISC) to direct post-transcriptional repression of target mature mRNA transcripts by binding to complementary 3’ untranslated regions (UTR) 203. Furthermore, each miRNA can regulate the expression of multiple target genes, and each transcript can be targeted by multiple miRNAs 204. Thus, miRNAs can potentially regulate entire pathways or networks of genes and as such are immensely important regulators of the transcriptome; so far miRNAs appear to play pivotal roles in regulation of cellular proliferation, differentiation and apoptosis 205. Interestingly, approximately 70% of all known miRNAs are expressed in the brain and the role of miRNAs in various neurodevelopmental processes, such as neurogenesis, cell fate determination, migration and synapse development has been shown 206,207.
In TSC, dysregulation of miRNAs has been shown, identifying the mir34 family among the most significantly overexpressed miRNAs 202. Alterations in the expression of numerous miRNAs have also been described in pLGGs, including PA and GGs 208-213. Moreover, a decision tree has been proposed based on the expression of miRNAs for pediatric neuronal and mixed neuronal-glial tumours suggesting that miRNAs can be useful for classifying tumours that are difficult to distinguish by classical histopathological examination 214.
Methylation profiling of low grade gliomas
Epigenetics refers to the process by which specific epigenetic marks can influence gene regulation and transposon activity without altering the actual sequence of the DNA. The most studied epigenetic marker is DNA-methylation, which is characterized by the addition of a methyl or hydroxymethyl by DNA methyltransferases (DNMTs) to cytosine residues in CG, CXG and CXX DNA sequences (CpG-sites; where X corresponds to A, T, or C), producing 5-methylcytosines (5-mC). When located in a gene promoter region it is generally associated with silencing of gene expression 215. DNA-methylation is thought to play a role in several key processes including genomic imprinting, X-chromosome inactivation, repression of transposable elements, aging and carcinogenesis. One of the most widely utilized methylation analysis method utilizes specialized microarrays developed by Illumina known as the Infinium 450k microarray or the more recently developed Infinium 850k microarray 216. First, DNA is bisulfite-treated and the specific CpG sites are detected through hybridization
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