Fig. 3: PRDM9 activity is required for survival of drug-tolerant persisters.

a, b Nuclear-ID red stain images (pseudo-coloured yellow) and quantification of drug-tolerant persister (DTP) cells surviving CMPD1 (25 µM, 14 days) treatment combined with UNC1999 (3 μM), KDOBA-67a (5 µM), GSK-J4 (5 µM) and MRK-740 (3 µM). Data are mean ± SD (n = 3 biological replicates). One sample t-test between co-treatment vs CMPD1: * indicates p (two tailed) = 0.0234. Scale bar = 100 µm. c, d DAPI stain images and quantification of DTP cells surviving CMPD1 (25 µM, 14 days) treatment combined with BAY-6035 (3 μM) or EPZ-719 (1 µM). Data are mean ± SD (n = 4 biological replicates for CMPD1 + BAY-6035 in FPW1; n = 3 for all other treatments). One sample t-test between co-treatment vs CMPD1: * indicates p (two tailed) = 0.0163, ** indicates p (two tailed) = 0.0024. Scale bar = 100 µm. e, f DAPI stain images and quantification of DTP cells surviving CMPD1 (25 µM, 14 days) treatment combined with CTSL1i (3 μM). Data are mean (n = 2 biological replicates) for FPW1 cells; and mean ± SD (n = 3 biological replicates) for RKI1 cells. Scale bar = 100 µm. g, h Representative images and quantification of glioblastoma colonies treated with CMPD1 (25 µM, 7 days) ± MRK-740 (3 µM) or MRK-740-NC (3 µM), followed by drug holiday. Data are mean ± SD (n = 3 biological replicates). One sample t-test between co-treatment vs CMPD1: * indicates p (two tailed) = 0.0136, p (two tailed) = 0.0139 for HW1 and SB2b cells, respectively; ** indicates p (two tailed) = 0.0078 for MMK1 cells; *** indicates p (two tailed) = 0.0007 for RKI1 cells. i Representative immunoblots of H3K4 methylation in RKI1 cells treated with CMPD1 (10 µM, 3 days) ± MRK-740 (3 µM) ± MRK-740-NC (3 µM). Quantification of n = 3 biological replicates is provided in the Supplementary Fig. 3h. j Combined intensity (RPGC) of H3K4me3 peaks aligning with a PRDM9 motif in RKI1 cells treated with CMPD1 (10 µM, 3 days) ± MRK-740 (3 µM). k Individual genome track of H3K4me3 intensity (RPGC) at intergenic regions aligning with PRDM9 motif (blue bar) in RKI1 cells treated with CMPD1 (10 µM, 3 days) ± MRK-740 (3 µM). Source data are provided as a Source Data file.