Fig. 4

Inhibition of mTOR corrects translational but not transcriptional dysfunction. a Number of upregulated (gray) or downregulated (black) genes at the level of translation or transcription in cells treated with rapamycin or AZD-8055 as compared to vehicle-treated cells. b Venn diagrams for genes that change in gene expression in opposite directions by TSC2 loss (red) and by compound treatments (green, blue), respectively. Overlap highlights how many genes deregulated in TSC2 depleted cells (upregulated on left, downregulated on right) can be reset to control levels by inhibitor treatment. Thresholds of differentially expressed gene calling: abs(logFC) >= 0.5, counts per million no less than 1, and FDR < 0.05. c Heat map of translational efficiency for transcripts of ribosomal proteins in control cells and TSC2-deficient cell line (n = 2) after six weeks of differentiation. Vehicle (DMSO)-treated samples reveal the induced TE in TSC2 depleted cell lines that is largely reversed after treatment with either rapamycin or AZD-8055. d Box plots displaying fold changes in transcription, translation, and total protein output for genes associated with proteins synthesis, angiogenesis, and inflammation in control and TSC2-deficient cell lines. While different levels of translation of protein synthesis factors between vehicle-treated control and mutant cells are balanced out by mTOR inhibitor treatment, the different transcriptional and protein output for angiogenesis and inflammation genes remains unchanged. Values are log2-transformed and normalized to controls. Statistical significance was determined by a two-tailed paired t-test, ***p < 1×10⁻⁶. e Western blot analysis for STAT3 or its phosphorylated form (p-STAT3) from neural cultures after six weeks of differentiation; cultured in the presence (+) or absence (−) of growth factors or rapamycin for the last 12 h before harvest. Elevated phosphorylation even in the presence of rapamycin indicates continued increased pathway activity. f Molecular mechanisms of the neuropathology of TSC and new treatment options to be considered