Page 71 - Molecular features of low-grade developmental brain tumours

DISTINCT DNA METHYLATION PATTERNS IN SEGA IN TSC
Figure 2. Methylation of the mTOR pathway in SEGAs. a. Volcano plot showing the differentially methylated CpGs on the promoter region (adjusted p-value<0.01 and a β-value difference of >0.2) between TSC1 mutated SEGAs and control tissue (TSC1-control). A total of 4008 CpGs were hypomethylated and 2111 were hypermethylated in TSC1-control. b. Volcano plot showing the differentially methylated CpGs on the promoter region (adjusted p-value<0.01 and a β-value difference of >0.2) between TSC2 mutated SEGAs and control tissue(TSC2-control). A total of 4008 CpGs were hypomethylated and 2111 were hypermethylated in TSC2-control. c. Venn diagram showing the overlap of CpGs between TSC1-control and TSC2-control. 5293 CpGs were overlapping, whereas 1773 CpGs were only found differentially methylated in TSC1-control and 826 CpGs in TSC2-control. d. Pie chart showing the distribution of differentially methylated and not differentially methylated mTOR pathway related genes (based on Reactome). A total of 18 CpGs located on 6 mTOR pathway related genes were differentially methylated, whereas 441 CpGs located on 29 mTOR pathway related genes were not differentially methylated.
hypomethylated and 2345 hypermethylated CpGs in TSC2-control (Figure 2b) and no CpGs differentially methylated in TSC1-TSC2 (adjusted p-value 0.01, β-value difference of >0.2, promoter region). Furthermore, the majority of the differentially methylated CpGs in TSC1- control and TSC2-control were overlapping (5293 CpGs), whereas 1773 CpGs were only found differentially methylated in TSC1-control and 826 CpGs in TSC2-control (Figure 2c).
We further evaluated the methylation of mTOR pathway related genes by extracting CpGs that were located on genes from the Reactome based mTOR pathway or mTORC1 signaling pathway. A total of 459 CpGs were located on 35 mTOR pathway related genes of which 18 CpGs located on 6 genes (2/17 CpGs on AKT2, 1/17 on EEF2K, 4/21 on EIF4E, 4/33 on EIF4G1, 1/19 on MTOR and 6/43 on PRKAG2) were differentially methylated (Figure 2d). The majority of these CpGs were hypomethylated (15/18), whereas 3 CpGs located on PRKAG2 were hypermethylated.
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