BAF complex maintains glioma stem cells in pediatric H3K27M-glioma [ATAC-seq]

Diffuse midline gliomas (DMGs) are uniformly fatal pediatric central nervous system cancers, refractory to standard of care therapeutic modalities. The primary genetic drivers are a set of recurrent amino acid substitutions in genes encoding histone H3 (H3.3 and H3.1, K27M), which are currently undruggable. These H3K27M oncohistones perturb normal chromatin architecture, resulting in an aberrant epigenetic landscape, which we interrogated here for epigenetic dependencies using a CRISPR screen in patient-derived H3K27M-glioma neurospheres. We show that H3K27M-glioma cells are dependent on core components of the mammalian SWI/SNF (BAF) chromatin remodeling complex for maintaining glioma stem cells in a cycling, oligodendrocyte precursor cell (OPC)-like state. Genetic perturbation of the BAF catalytic subunit SMARCA4 (BRG1), as well as pharmacological suppression opposes proliferation, promotes differentiation, and improves overall survival of patient-derived xenograft (PDX) models. In summary, we demonstrate that therapeutic inhibition of BAF complex has translational potential for children with H3K27M-gliomas. DNA accessibility assessed by ATACseq of BT869 cells upon SMARCA4 knockout or treatment with BRG1 antagonists.

弥漫性中线胶质瘤（Diffuse midline gliomas, DMGs）是一类致死性儿童中枢神经系统恶性肿瘤，对标准治疗方案均耐药。其核心遗传驱动因素为编码组蛋白H3（H3.3和H3.1，K27M位点）的一组复发性氨基酸替换突变，目前此类突变仍不可成药。这类H3K27M致癌组蛋白（oncohistones）会扰乱正常染色质结构，进而形成异常的表观遗传景观。本研究通过在患者来源的H3K27M胶质瘤神经球中开展CRISPR筛选（CRISPR screen），探究该肿瘤的表观遗传依赖特征。研究结果显示，H3K27M胶质瘤细胞依赖哺乳动物SWI/SNF（BAF）染色质重塑复合物的核心组分，以维持胶质瘤干细胞（glioma stem cells）处于增殖性少突胶质前体细胞（oligodendrocyte precursor cell, OPC）样状态。对BAF催化亚基SMARCA4（BRG1）进行遗传扰动，或采用药物手段进行抑制，均可抑制肿瘤细胞增殖、促进细胞分化，并可改善患者来源异种移植（patient-derived xenograft, PDX）模型的整体生存期。综上，本研究证实靶向抑制BAF复合物的治疗策略对H3K27M胶质瘤患儿具有临床转化潜力。本研究同时通过ATAC测序（ATACseq）检测了BT869细胞在SMARCA4敲除或使用BRG1拮抗剂处理后的DNA可及性。