Page 78 - Molecular features of low-grade developmental brain tumours

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CHAPTER 3
skeletal system development
phagocytosis
regulation of neuron projection development
peptidyl-tyrosine modification
regulation of inflammatory response
Discussion
GO: 5,41576 0001501 E-08
GO: 7,04139 0006909 E-08
GO: 9,70394 0010975 E-08
GO: 1,23872 0018212 E-07
GO: 1,39894 0050727 E-07
2,65467 1,98178 127 32 82 13 E-06 E-06
3,36302 2,51057 73 13 56 4 E-06 E-06
4,48146 3,34552 108 40 59 9 E-06 E-06
5,49362 4,10112 99 18 76 5 E-06 E-06
6,10724 4,55921 85 12 68 5 E-06 E-06
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In this study we performed DNA methylation profiling of SEGAs from TSC patients and showed that the differential methylation profile between SEGAs and control tissue is enriched for GO terms including the adaptive immune system, T cell activation, leukocyte mediated immunity, extracellular structure organization and the ERK1 & ERK2 cascade. Histological markers for T cells, microglia reactivity, mTOR activation and neurons were higher expressed, whereas the glial marker GFAP was lower expressed in SEGA compared to periventricular control tissue. Furthermore, we identified two robust subgroups in the DNA methylation of SEGA, with a distinct methylation profile of genes related to the adaptive immune response and the MAPK pathway. Moreover, we found differences in positivity of the T cell marker CD3 between the two largest subgroups.
Figure 5. Unique methylation of genes related to the adaptive immune response and the MAPK pathway between the two SEGA subgroups. 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 one subgroup of SEGAs and control tissue (SEGA1-control). A total of 4377 CpGs were hypomethylated and 1411 were hypermethylated in SEGA1-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 the other subgroup of SEGAs and control tissue (SEGA2-control). A total of 4883 CpGs were hypomethylated and 3132 were hypermethylated in SEGA2-control. c. 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 the two subgroups of SEGA (SEGA1-SEGA2). A total of 321 CpGs were hypomethylated and 70 were hypermethylated in SEGA1-SEGA2. d. Venn diagram showing the overlap of genes corresponding to the differentially methylated CpGs between SEGA1-control, SEGA2-control and SEGA1-SEGA2. Genes overlapping between SEGA1-control and SEGA1-SEGA2 but not with SEGA2-control were considered unique for SEGA1. Genes overlapping between SEGA2-control and SEGA1-SEGA2 but not with SEGA1- control were considered unique for SEGA2 (70 genes SEGA1 unique and 58 genes SEGA2 unique). e. Bar chart showing the GO terms enriched for the SEGA1 and SEGA 2 unique genes. Each GO term is listed on the y-axis, the log10(1/adjusted p-value) on the x-axis and the n is equal to the number of differentially methylated genes in each GO term. f. Heatmap with Z-score hierarchical clustering for the RNA expression data of 12 SEGAs. Each row indicates one of unique SEGA1 or SEGA2 genes based on the methylation data that was expressed on RNA level in SEGA. The color scale means the gene expression standard deviations from the mean, with green for low expression and red for the high expression levels.