Fig. 4
Specific transcriptional reprogramming of microglial cells upon TPFPD chronic-type inflammatory activation. A Principal component analysis (PCA) of gene expression data based on the first two PCs shows, on the one hand, a clear distinction between nonstimulated (NSC) and activated cells (LPS and TPFPD) and, on the other hand, strong differences between M1-type (LPS) and chronic-type (TPFPD) inflammatory activation. B Hierarchical clustering and heatmap of differentially expressed genes (DEGs; n = 413) in TPFPD-activated microglia versus nonstimulated (NSC) and LPS-treated cells. The scaled expression value (Z-score transformed) is shown in a blue-red color scheme with red indicating higher expression, and blue lower expression. Biological replicates are indicated in brackets. C PCA analysis of pathway-related data generated by the Pathifier method [55] demonstrates clear clustering and separation of stimulated and nonstimulated (NSC) cells and of M1-type (LPS) and chronic-type (TPFPD) inflammatory activation. D Bubble chart showing the enrichment of the KEGG Pathway in TPFPD-treated microglial cells (adjusted p < 0.05). The bubble size indicates the number of genes annotated in the indicated KEGG pathway. The colors represent pathway enrichment (% of overlapping genes) in TPFPD-exposed cells. E Volcano plot depicting individual DEGs (|log2 Fold Change| > 2) in TPFPD-treated microglia versus M1-type (LPS) activated cells. The red and blue dots show upregulated and downregulated genes in TPFPD-treated cells, respectively. Individual genes of interest are indicated. F Fold change in individual gene expression level (qPCR) of LPS-activated and TPFPD-exposed microglial cells relative to nonstimulated cells (NSC). The data are represented as the means ± SEM (n = 5 biological replicates from independent experiment). *p < 0.05 vs TPFPD (Student’s t test)