Page 59 - Molecular features of low-grade developmental brain tumours

DISTINCT DNA METHYLATION PATTERNS IN SEGA IN TSC
Introduction
Tuberous sclerosis complex (TSC) is a multisystem monogenetic disorder caused by mutations in either TSC1 or TSC2 and is characterized by hamartoma development in several organs, including the brain, kidneys, lungs, heart, eyes, and skin 1. Patients with TSC often have neurological manifestations including neurodevelopmental disorders (such as autism) and severe epilepsy 2. The majority of patients with TSC have seizure onset before the age of two 3. The hallmark brain lesions in TSC include cortical/subcortical tubers, subependymal nodules (SENs) and subependymal giant cell astrocytomas (SEGAs) 4,5. SEGAs are benign, slow growing tumours classified as WHO grade I making up for 1-2% of all paediatric brain tumours 6,7. Usually, SEGAs develop during the first 2 decades of life of patients with TSC, with a mean age at presentation below 18 years 6,8. They are typically located near the foramen of Monro where extended growth of the tumour can result in blockage of the cerebral fluid circulation and subsequent obstructive hydrocephalus 9. SEGAs are thought to arise from subependymal nodules (SEN) along the ependymal lining of the lateral ventricles 10-12. Histologically, they are characterized by spindle cells, gemistocytic-like cells and giant cells and demonstrate an immature neuroglial phenotype.
Tumour suppressors hamartin (TSC1) and tuberin (TSC2) can form an intracellular complex with TBC1 Domain Family Member 7 (TBC1D7) that exerts GTPase-activating protein (GAP) activity towards the small GTPase Ras homolog enriched in brain 1 (RHEB1) 13,14. Inhibition of RHEB1 is important in regulating the mechanistic target of rapamycin complex (mTOR) pathway, which can affect cell growth and proliferation. Pathogenic loss of function mutations in TSC1 or TSC2 result in constitutive activation of the mTOR pathway and uncontrolled cell cycle progression 15. Besides the mTOR pathway, the immune system, the Mitogen-activated protein kinase (MAPK) pathway and extracellular matrix (ECM) organization have been suggested to play a role in SEGA development based on gene expression studies 16-18. However, the precise mechanisms behind these gene expression changes in SEGA are still largely unknown.
Gene expression can be controlled through regulation of the epigenome, via epigenetic mechanisms 19. DNA methylation is one of most recognized epigenetic markers and is generally associated with silencing of gene expression, and its role in tumourigenesis has become a topic of interest 20. It is characterized by the addition of a methyl or hydroxymethyl by DNA methyltransferases (DNMTs) to cytosine residues in CG (CpG sites), CXG and CXX DNA sequences (where X corresponds to A, T, or C). Changes in DNA methylation have been well studied in cancer including central nervous system (CNS) tumours 21,22 and profound changes of methylation profiles have also been seen in neuro-psychiatric diseases such as autism spectrum disorders, epilepsy and TSC 17,23,24. Furthermore, DNA methylation profiling is highly robust and reproducible and has therefore been successfully used to distinguish subtypes in CNS tumours and focal cortical dysplasia 25-28. These DNA methylation-based classifications of CNS tumours have proven helpful for better diagnostics especially in cases with ambiguous histology or contradictory molecular profiles. Although, SEGAs have been included in previous methylation based studies, none of these studies have gone into depth
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