Fig. 6. SALL4-HDAC2 targets that are upregulated after SALL4 depletion or HDAC inhibition enrich in invasion-related processes.

a Significantly upregulated genes after SALL4 knockdown (Fig. 4a, b) were overlaid with the C&R data of direct SALL4-HDAC2 targets (Fig. 5b, c), which resulted in 184 direct SALL4-HDAC2 targets significantly upregulated after SALL4 knockdown. b MetaCore™ Process Network enrichment of the 184 direct targets from a. The top 12 most significant processes are given with the specific genes of each process listed in red. Genes that were validated for DE  in other cell lines are highlighted in bold. c Log2 fold change heatmap of qRT-PCR-based gene expression (normalized to PPIA and set relative to vehicle (DMSO)-treated samples) after 48 h cell treatment with the HDAC inhibitors Mocetinostat (0.6 µM) and Panobinostat (7 nM). t-tests were performed for significance between HDACi and vehicle-treated groups with N = 3 and p values ≥ 0.05 = not significant (n.s.). d Images of DAPI-stained nuclei in invasion assays as in Fig. 3 i–k. Cells were seeded into the invasion chamber, which was supplemented with vehicle or 600 nM Mocetinostat or 7 nM Panobinostat in both the starvation as well as the FCS high medium. After 24 h, the invaded cells were analyzed by counting DAPI-stained nuclei of invaded cells at the bottom of the membrane (inverted and set to black and white (B/W)). Scale bars 200 µm. e Quantification of invaded cells in d set relative to control cells. Moce: mocetinostat, Pano: panobinostat. Error bars represent mean ± SD in e. For significance, two-sided t-tests were performed with N = 3 (c) and N = 4 (e) and p values ≥0.05 = n.s.; <0.05 = *; <0.01 = **; and <0.001 = *** with Moce in e (top panel) P = 0.0218; Moce in e (middle panel) P = 0.0051; Pano in e (middle panel) P = 0.0463; Moce in e (lower panel) P = 0.0332; Pano in e (lower panel) P = 0.0051. Source data for c and e are provided as a Source Data file.