Page 193 - Molecular features of low-grade developmental brain tumours

Summary
Although it is not unusual for brain tumours to clinically manifest with seizures, especially slowly growing low grade tumours tend to be highly epileptogenic. In particular, glioneuronal tumours (GNTs) such as gangliogliomas (GGs) and dysembryoplastic neuroepithelial tumours (DNTs) are known as low-grade epilepsy-associated tumours (LEATs). LEATs are characterized by a history of 2 or more years of drug-resistant chronic epilepsy with a mean age of onset at 16.5 years and often arise in younger age groups. Paediatric low grade gliomas (pLGGs) are a heterogeneous group of neoplasms that account for approximately 30% of brain tumours in children. In contrast to most adult low grade gliomas, pLGGs can also have a hereditary component. SEGAs are low grade brain tumours that account for ~2% of pLGGs and occur almost exclusively in patients with tuberous sclerosis complex (TSC), a monogenetic disease caused by a germline mutation in either the TSC1 or TSC2 gene, which results in constitutive activation of the mechanistic target of rapamycin complex (mTOR) pathway. SEGAs are not a direct cause of epilepsy in children and adolescents with TSC, but can effect seizure burden. The aim was to investigate the molecular mechanisms involved in SEGA development and growth on a (epi)genomic, transcriptomic and proteomic level and to investigate molecular features of several GNTs.
In chapter 2, we assessed the prevalence of the BRAFV600E mutation in a large cohort of TSC related SEGAs and found no evidence of either BRAFV600E or other mutations in BRAF. Additionally, massively parallel sequencing of TSC1/TSC2 was performed confirming that the majority of the SEGA samples had evidence of loss of heterozygosity, indicating an additional mutation in the same gene in which the germline mutation was identified, consistent with TSC1/TSC2 molecular findings seen in other TSC-related tumours.
In chapter 3, we investigated the methylation profile of SEGAs using the Illumina Infinium HumanMethylation450 BeadChip. The SEGA methylation profile was enriched for the adaptive immune system, T cell activation, leukocyte mediated immunity, extracellular structure organization and the ERK1 & ERK2 cascade. Furthermore, we identified two major subgroups in the SEGA methylation data and show that the differentially expressed genes between the two subgroups are related to the mitogen-activated protein kinase (MAPK)/ extracellular signal-regulated kinase (ERK) cascade and adaptive immune response and could potentially hold predictive information on target treatment response. However, the clinical relevance of the two subgroups remains elusive and needs further investigation in retrospective studies.
In chapter 4, we analysed the coding and non-coding transcriptome of SEGAs and show that the SEGA transcriptome profile was enriched for the MAPK/ERK pathway, a major regulator of cell proliferation and survival. Analysis at the protein level confirmed MAPK/ ERK activation in SEGAs. Subsequently, the inhibition of ERK independently of mTORC1 blockade decreased efficiently the proliferation of primary patient-derived SEGA cultures. This suggests that MAPK/ERK pathway could be used as a target for treatment of SEGAs. Furthermore, we found that LAMTOR1, LAMTOR2, LAMTOR3, LAMTOR4 and LAMTOR5 were over-expressed on both gene and protein level in SEGA compared to control tissue. Taken
SUMMARY
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