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. 2019 Dec 27;7(2):e656. doi: 10.1212/NXI.0000000000000656

Figure 2. Differential gene expression in MS NAGM vs control case cortical gray matter.

Figure 2

(A) Volcano plot of the differential gene expression analysis between MS NAGM and control gray matter (GM) revealed HLA-DRB1 as the most significant differentially regulated gene (FC = 4.62, adj. p value = 0.013, marked in red). Differentially expressed genes with an adjusted p value between 0.05 and 0.1 are marked in black. This was the case for ITGB1BP1 (FC = 1.67, adj. p value = 0.065), PRKAR1A (FC = 1.93, adj. p value = 0.065), LINC00115 (FC = 1.5, adj. p value = 0.065), MAP3K7 (FC = 1.34, adj. p value = 0.067), and SRGAP2 (FC = 1.5, adj. p value = 0.067). Boxplots show the log2 gene expression of HLA-DRB1 (B), HLA-DRB5 (C), and HLA-DQA1 (D) and HLA-DQB1 (E) between MS NAGM and GM. HLA-DRB1 is significantly differentially expressed between MS NAGM and GM (B). Both, HLA-DRB1 (B) and HLA-DRB5 (C) show a bimodal expression pattern in MS and control tissue, whereas the expression of HLA-DQA1 (D) was normally distributed within the sample groups, and HLA-DQB1 (E) was at the lower detection limit. (F) Boxplots show log2 of the HLA-DRB1 gene expression in all tissue samples and in all cases used for the microarray analysis. All cases with the HLA-DRB1*15:01 genotype show a high HLA-DRB1 expression (red dots). (G) HLA-DRB1 expression between samples from cases carrying the HLA-DRB1*15:01 or other HLA-DRB1 alleles. Boxplot shows that all HLA-DRB1*15:01 tissue samples belong to the HLA-DRB1 high expresser group. (H) HLA-DRB3, 4, and 5 expression of all samples. (I) Comparison of hetero- and homozygote carriers of the HLA-DRB1*15:01 allele. (J) Correlation of HLA-DRB1 with HLA-DRA within the HLA-DRB1*15:01 positive samples. (H and I) p Values are derived from a 2-sided Welch t test. (J) p Value is derived from a linear model.