Fig. 5: MALNC knockout alters the expression of genes associated with differentiation and retinoic acid signaling and impairs cell viability.

A Relative expression (determined by RT-qPCR) of MALNC in NB4 WT and KO clones (three clones each) used for RNA-sequencing. Data are shown as means ± SEM from three biological experiments relative to MALNC^WT#3 clone expression and normalized towards endogenous control TBP. B MA-plot showing the shrunken log2 fold changes (LFC) of differentially expressed genes (DEGs) between (top) MALNC^KOA and MALNC^WT and (bottom) MALNC^KOB and MALNC^WT. C Venn diagram showing the overlap of DEGs between MALNC^KOA vs MALNC^WT and MALNC^KOB vs MALNC^WT (n = 25). Lists indicate which of those identified differentially expressed genes are shared up-regulated (n = 14) and shared down-regulated (n = 11) in MALNC^KOA vs MALNC^WT and MALNC^KOB vs MALNC^WT. A hypergeometric test was performed to assess the overlap between DEGs in MALNC KOA and KOB. D Cell viability in HL60-MALNC^KO (n = 3), MALNC^WT (n = 3) cells. Cell viability in percent of control (4 h) was measured by WST-8 reagent up to 72 h. Data is shown as means ± SEM from three biological experiments. E Relative colony formation between MALNC^KO and MALNC^WT cells in both HL60 and NB4 cells. Data is shown as means ± SEM from three biological experiments using three KO clones and three WT clones, respectively. The percentage of colony formation is relative to WT. P-values were determined by Student’s t-test: ns, not significant, * < 0.05, ** < 0.01, *** < 0.001.