Fig. 3

Loss of CCDC9B is associated with higher abundance of the MYC-regulator IVNS1ABP and sensitivity to bromodomain inhibitors. (A) MS and MS/MS spectra corresponding to the peptide LYIVGGSDPYGQK (IVNS1ABP protein) derived from the protein interactome experiments. At left, extracted Ion chromatogram showing the peptide isotopic distribution found in the CCDC9B-FLAG transfected HEP3B2-1-7 cells, and its absence in EV-transfected cells (middle). The identification of the peptide is shown at right (MS/MS spectrum). The b- and y-ions are depicted in blue and red, respectively. (B) IVNS1ABP protein levels in NSUN7 WT and KO HEP3B2-1-7 cells analyzed by western blot. (C) JQ1 bromodomain inhibitor IC50 values in Sanger cell lines according to NSUN7-promoter methylation status shows enhanced sensitivity to JQ1-mediated growth inhibition in epigenetically-silenced cells. The units in the “Y” axis are the natural logarithm (Ln) of the IC50 micromolar values. Mann–Whitney–Wilcoxon test, ****p-value < 0.0001. (D) IC50 determination for three bromodomain inhibitors using the SRB assay in NSUN7 WT HEP3B2-1-7 cells compared to NSUN7 KO HEP3B2-1-7 cells. (E) IC50 values for the three bromodomain inhibitors in NSUN7-transfected SNU-423 cells in comparison with EV-transfected cells. Data shown represent IC50 values obtained in biological triplicates, and p-values were calculated by a Student’s T test. *p-value < 0.05, **p-value < 0.01, ***p-value < 0.001, ****p-value < 0.0001