Fig. 3
RNA-seq analysis revealed that treatment with the monoclonal AQP4 antibody E5145A and human complement induces the expression of inflammatory and reactive genes in U-87MG cells expressing AQP4. (A) Volcano plot of differentially expressed genes between U-87MG-AQP4-ECFP cells treated with E5145+AC compared to E5145+IC; green indicates upregulated genes and red indicates downregulated genes. Groups (n=3) were compared using DSeq2 analysis, and changes with an adjusted p-value <0.001 and a two-fold change were considered statistically significant. (B) Pie chart of the results shown in (A) summarizing the upregulated, downregulated, and unchanged genes. (C) Pairwise comparisons using DSeq2 analysis of E5145+AC-treated U-87MG-AQP4-ECFP cells with U-87MG-AQP4-ECFP and U-87MG-ECFP cells after other treatments indicated 59 specifically changed genes. (D) A heat map (created with GraphPad Prism 10.4.) showing the mean standardized expression (z-scores, according to decreasing principal component 1 scores) of these 59 differential genes. Each row shows the relative expression level for a single sample, and each column shows the expression level of single genes. (E) A bubble plot (created with GraphPad Prism 10.4) showing the functional annotation by DAVID of the 59 specifically changed genes, showing the most significant associations indicated three functional clusters. P-values are visualized by a heatmap and different sizes. AC, active complement; AQP4, aquaporin-4; ECFP, enhanced cyan fluorescent protein; EmGFP, emerald green fluorescent protein; IC, inactive complement.
