Histone methyltransferase PRDM9 promotes survival of drug-tolerant persister cells in glioblastoma [ChIP-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 screen, 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 demonstrate a previously unknown role of PRDM9 in promoting metabolic reprogramming that enables the survival of drug-tolerant persister cells. Drug Treated glioblastoma stem cell line RKI1, followed by ChIP-seq. Treatment with tubulin inhibitor CMPD1 (10uM) +/- PRDM9 inhibitor MRK-740 (3uM) for 72 hours.

化疗通常可杀灭大部分癌细胞，但会残留少量耐药持久细胞（drug-tolerant persister cells）。此类持久细胞通过可逆的非遗传机制躲过药物治疗，并在治疗停止后引发肿瘤复发。本研究报道了一种由生殖细胞特异性H3K4甲基转移酶PRDM9调控的耐药机制。通过组蛋白蛋白质组学、转录组学、脂质组学及染色质免疫沉淀测序（ChIP-sequencing）研究，结合CRISPR基因敲除与表型药物筛选，我们发现化疗诱导的PRDM9上调可促进胶质母细胞瘤干细胞的代谢重编程，进而介导化疗耐药。机制层面，PRDM9依赖的胆固醇生物合成基因位点H3K4me3修饰可增强胆固醇合成能力，而持久细胞依赖该过程在化疗诱导的氧化应激与脂质过氧化状态下维持细胞稳态。PRDM9抑制剂联合化疗在临床前胶质母细胞瘤模型中展现出强劲的抗癌活性，通过清除持久细胞显著增强了抗肿瘤应答的强度与持续时间。本研究揭示了PRDM9此前未被发现的功能：其可通过促进代谢重编程，使耐药持久细胞得以存活。本数据集的样本为经药物处理的胶质母细胞瘤干细胞系RKI1，后续进行了ChIP-seq检测。实验设置为：以微管蛋白抑制剂CMPD1（10μM）单独或联合PRDM9抑制剂MRK-740（3μM）处理细胞72小时。