Phase separation of YAP fusion proteins drives supratentorial ependymoma (methyl-seq)

HIPPO-YAP/TAZ signaling has been implicated in supratentorial ependymoma formation from neural progenitor cells (NPC) in the brain, however, the underlying mechanisms to trigger the neural progenitor cell transformation remains elusive. Here, we uncover that patient-derived tumorigenic YAP-fusion proteins (YAP-MAMLD1 and C11ORF95-YAP) promote ependymoma tumorigenesis through forming liquid-liquid phase-separated condensates. Intrinsically disordered regions (IDR) in the fusion proteins promote oligomerization of YAP-transcriptional co-activators and self-assembly of nuclear puncta-like membrane-less organelles. Phase separation of YAP-fusion proteins further facilitates the compartmentalization of transcriptional coactivators, BRD4 and MED1, resulting in pervasive enhancer landscape changes and exclusion of transcriptional repressors such as PRC2 complexes. YAP-fusion proteins-induced nuclear puncta recruit RNA polymerase II to promote transcriptional bursting of multiple oncogenic pathways. Moreover, we show that IDR-mediated phase separation is necessary for YAP-fusion protein-induced tumor formation. Distinct YAP fusion-proteins identified in other human tumors also encompass IDR features. Together, our data suggest that IDR-mediated phase separation is an integral component of YAP-fusion protein-induced tumorigenesis and might serve as a therapeutic target in supratentorial ependymoma. Overall design: methyl-Seq, 6 samples

Hippo-YAP/TAZ信号通路（HIPPO-YAP/TAZ signaling）已被证实与脑内神经前体细胞（neural progenitor cells，简称NPC）来源的幕上室管膜瘤发生相关，但引发神经前体细胞转化的潜在分子机制仍有待阐明。本研究发现，患者来源的致瘤性YAP融合蛋白（YAP-MAMLD1与C11ORF95-YAP）可通过形成液-液相分离凝聚体，促进室管膜瘤的肿瘤发生过程。融合蛋白所含的内在无序区域（IDR）可促进YAP转录共激活因子的寡聚化，并介导核斑点样无膜细胞器的自组装。YAP融合蛋白的相分离进一步促成转录共激活因子BRD4与MED1的区室化，引发广泛的增强子图谱改变，并排斥PRC2复合物等转录抑制因子。YAP融合蛋白诱导形成的核斑点可招募RNA聚合酶II，以激活多条致癌通路的转录爆发。此外，本研究证实，IDR介导的相分离是YAP融合蛋白诱导肿瘤形成的必要条件。在其他人类肿瘤中鉴定出的不同YAP融合蛋白同样具备IDR结构特征。综上，本研究数据表明，IDR介导的相分离是YAP融合蛋白诱导肿瘤发生的核心组成部分，或可作为幕上室管膜瘤的潜在治疗靶点。实验整体设计：甲基化测序（methyl-Seq），共6个样本。