Fig. 6: GSK-J4 induces a transcriptome that mimics CDK4/6 inhibition, and vice versa.

a Genes downregulated by KDM6B knockdown were compared with gene profiles induced with chemical compounds from Library of Integrated Network-Based Cellular Signatures (LINCS)¹⁰⁸. The top chemical signature hits, which are basically overrepresented by palbociclib, are highlighted in pink dots. The y-axis indicates the combined score. The x-axis indicates adjusted p value. n = 18,947 for gene signatures. p Value is calculated from one-sided Fisher exact test. Combined score is computed by taking the log of p-value from the Fisher exact test and multiplying that by the z-score of the deviation from the expected rank. b Same analysis performed as in (a) for GSK-J4 treatment. n = 22231 for gene signatures. c The 89-gene signature derived from palbociclib treatment of 4 neuroblastoma cell lines was included in gene sets for GSEA analysis of KDM6B knockdown. p Value calculated by one-sided Fisher’s exact test. The FDR is calculated by comparing the distribution of normalized enrichment scores from many different genesets. d The 89-gene signature derived from palbociclib treatment was included in gene sets for GSEA analysis of GSK-J4. p Value calculated by one-sided Fisher’s exact test. The FDR is calculated by comparing the distribution of normalized enrichment scores from many different genesets. e BE2C cells were seeded with low numbers in six-well plate and treated with different concentrations of GSK-J4 or/and palbociclib for 10 days. The cell colonies were stained with crystal violet. f Bliss index for the combination of GSK-J4 and palbociclib. Positive scores indicate synergy, negative scores indicate antagonism. g Western blot to assess the expression of CDK4 and CDK6 that were transduced into BE2C cells. The blots are representative of three independent experiments. h The BE2C parental and CDK4/6 overexpressing cells were seeded with low numbers in six-well plate and treated with different concentrations of GSK-J4 or palbociclib for 8 days. The cell colonies were stained with crystal violet. i, j BE2C and CDK4 or CDK6 overexpressing BE2C cells (BE2C-CDK4-OE, BE2C-CDK6-OE) were treated with different concentrations of palbociclib (i) or GSK-J4 (j). EC50 was calculated using Prestoblue assay. n = 4 for each dose. Data are represented as mean ± SD. k Western blot to assess the expression of pRB after inducible knockout in BE2C cells. The blots are representative of three independent experiments. l Photos taken under microscope (10×) show Rb1 knockout leads to resistance to palbociclib. Scale bar = 100 μM. The photos are representative of three independent experiments. m The BE2C wildtype and Rb1 knockout cells were seeded with low numbers in six-well plate and treated with different concentrations of GSK-J4 or/and palbociclib for 8 days. The cell colonies were stained with crystal violet. Source data are provided as a “Source data” file.