Histone methyltransferase PRDM9 promotes survival of drug-tolerant persister cells in glioblastoma [RNA-seq]

Chemotherapy often kills a large fraction of cancer cells but leaves behind a small population of drug-tolerant persister cells. These persister cells survive drug treatments through reversible, non-genetic mechanisms and cause tumour recurrence upon cessation of therapy. Here, we report a drug tolerance mechanism regulated by the germ-cell-specific H3K4 methyltransferase PRDM9. Through histone proteomic, transcriptomic, lipidomic, and ChIP-sequencing studies combined with CRISPR knockout and phenotypic drug screens, we identified that chemotherapy-induced PRDM9 upregulation promotes metabolic rewiring in glioblastoma stem cells, leading to chemotherapy tolerance. Mechanistically, PRDM9-dependent H3K4me3 at cholesterol biosynthesis genes enhances cholesterol biosynthesis, which persister cells rely on to maintain homeostasis under chemotherapy-induced oxidative stress and lipid peroxidation. PRDM9 inhibition, combined with chemotherapy, resulted in strong anti-cancer efficacy in preclinical glioblastoma models, significantly enhancing the magnitude and duration of the antitumor response by eliminating persisters. These findings reveal a previously unknown role of PRDM9 in promoting metabolic reprogramming that enables the survival of drug-tolerant persister cells. PRDM9 Knock-out RKI1 glioblastoma stem cell line was treated with +/- 10µM CMPD1 for 72 hours. The KO cell line was compared to Non-Targetted Control (NTC) RKI1 glioblastoma stem cell line, also treated with +/- 10µM CMPD1 for 72 hours, of the same transduction batch and passage number within each biological replicate. There are three biological repeats. We excluded RKI1 n=2 NTC CMPD1 (Sample006) from downstream analysis due to the sample not clustering with the other two NTC CMPD1 repeats.