Fig. 4: PRDM9 is a chemotherapy-induced vulnerability.
From: Histone methyltransferase PRDM9 promotes survival of drug-tolerant persister cells in glioblastoma
a KMT2 family mRNA in CMPD1 (25 μM, 14 days) derived drug-tolerant persister (DTP) cells compared to parent cells. Data are mean ± SD (n = 3 biological replicates). b PRDM9 mRNA in RKI1 cells treated with CMPD1 (25 μM). Data are mean ± SD (n = 3 biological replicates). One sample t-test between CMPD1 vs Parent: * indicates p (two tailed) = 0.0382, p (two tailed) = 0.0386 for 3 and 14 days, respectively. c PRDM9 mRNA in glioblastoma stem cell lines treated with CMPD1 (25 μM, 3 days). Data are mean ± SD (n = 3 biological replicates). One sample t-test between CMPD1 vs Parent: * indicates p (two tailed) = 0.0351, p (two tailed) = 0.0205, p (two tailed) = 0.0406 for RKI1, JK2 and MMK1 cells, respectively; ** indicates p (two tailed) = 0.0045 for FPW1 cells. d Cell cycle distribution of RKI1 cells treated with Ro-3306 (10 μM) or CMPD1 (25 µM, 3 days). Data are mean ± SD (n = 4 biological replicates). ER: endoreduplication (DNA content > 4 N). e PRDM9 mRNA in cells treated with Ro-3306 (10 μM, 3 days). Data are mean ± SD (n = 3 biological replicates). One sample t-test between Ro-3306 vs parent: * indicates p (two tailed) = 0.0359. f, g DAPI stained images and quantification of DTP cells surviving CMPD1 (25 µM, 14 days) treatment combined simultaneously with MRK-740 (3 μM) or added 3 days before or after CMPD1. Data are mean ± SD (n = 3 biological replicates). One sample t-test between co-treatment vs CMPD1: ** indicates p (two tailed) = 0.0058; *** indicates p (two tailed) = 0.0007. Scale bar = 100 µm. h Chronos scores for SETD1A, SETD1B, and PRDM9 knockout in 1095 cancer cell lines (23Q2 + Score dataset, DepMap). Box plots display the mean as the centre line, the box representing the 25th–75th percentiles, and the whiskers extending to 1.5x the interquartile range (IQR) beyond the box limits. Outliers are shown as individual data points. i Representative immunoblots of RKI1 cells transduced with non-targeted control (NTC) sgRNA and orthogonal SETD1B sgRNAs (n = 2 biological replicates). j Representative immunoblots of RKI1 cells transduced with non-targeted control (NTC) sgRNA and orthogonal PRDM9 sgRNAs (n = 3 biological replicates). k, l DAPI stained images and quantification of RKI1 cells following SETD1B and PRDM9 knock-out (KO) and treated with CMPD1 (25 µM, 14 days). Data are mean ± SD (n = 3 biological replicates for SETD1B KO lines; n = 6 biological replicates for parent, non-targeted control (NTC) and PRDM9 KO lines). Unpaired t-test between KO lines vs NTC: ** indicates p (two tailed) = 0.0065. Scale bar = 100 µm. Source data are provided as a Source Data file.
