Fig. 5

The TGFB1 transcriptional regulator is differentially activated by RA and MYCN overexpression and interacts with MYCN’s protein–protein interaction network. a Activation/inhibition score of the TGB1 ITR in neuroblastoma cells across a range of conditions: group 1, upon MYCN overexpression (SY5Y-MYCN cells); group 2, in amplified MYCN cell lines (KCN, Kelly, IMR32 and KCNR) compared with MYCN single copy cells (SY5Y); group 3, IMR32 cells induced to undergo apoptosis by 24-h 28-mM LiCl treatment compared with control IMR32 cells. Values for each group are relative to the TGFB1 activity levels of the relevant control cells, SY5Y-MYCN un-induced, SY5Y cells and untreated IMR32 cells, respectively. These values were generated, using IPA, from RNA-seq data from both the present study and two of our previous publications [42, 45]. b Levels of absolute gene expression of TGFB1 mRNA in each of the SY5Y-MYCN RNA-seq treatments. Expression is in read counts per million adjusted by gene length in kilobases (CPMkb), with error bars denoting the standard deviation between replicates. P values above each bar are from t-test comparisons of TGFB1 expression in that condition with RA-treated cells. c Levels of absolute gene expression of TGFB1 mRNA across a panel of neuroblastoma cell lines. IMR32, Kelly, KCN and KCNR are lines with amplified MYCN, while SY5Y is a single copy MYCN cell line. Cell line data were mined from paired-end RNA-seq [42]. Expression is in read counts per million adjusted by gene length in kilobases (CPMkb), with error bars denoting the standard deviation between replicates. P values above each bar are from t-test comparisons of TGFB1 expression in that cell line with SY5Y cells. d Protein–protein interaction map of known TGFB1 targets (regulated proteins) which were found to bind to MYCN protein in the SY5Y-MYCN interaction proteomic dataset. The protein interaction map of previously known connections between these proteins was generated with the String database. e TGFB1 target proteins which showed differential binding (SY5Y-MYCN interaction proteomics) to MYCN protein when the RA-only treatment and the RA and Dox (MYCN overexpression) combination treatment were compared