Reduced chromatin binding of MYC is a key effect of HDAC inhibition in MYC amplified meduloblastoma [ChIP-seq]. Reduced chromatin binding of MYC is a key effect of HDAC inhibition in MYC amplified meduloblastoma [ChIP-seq]

MYC is a driver oncogene in many cancers. Inhibition of MYC promises high therapeutic potential, but specific MYC inhibitors remain unavailable for clinical use. Previous studies suggest that MYC amplified Medulloblastoma cells are vulnerable to HDAC inhibition. Using co-immunoprecipitation, mass spectrometry and ChIP-sequencing we show that HDAC2 is a cofactor of MYC in MYC amplified primary medulloblastoma and cell lines. The MYC-HDAC2 complex is bound to genes defining the MYC-dependent transcriptional profile. Class I HDAC inhibition leads to stabilization and reduced DNA binding of MYC protein inducing a down-regulation of MYC activated genes (MAGs) and up-regulation of MYC repressed genes (MRGs). MAGs and MRGs are characterized by opposing biological functions and distinct E-box distribution. We conclude that MYC and HDAC2 (class I) are localized in a complex in MYC amplified medulloblastoma and drive a MYC-specific transcriptional program, which is reversed by the class I HDAC inhibitor entinostat. Thus, the development of HDAC inhibitors for treatment of MYC amplified medulloblastoma should include HDAC2 in its profile in order to directly target MYC´s trans-activating and trans-repressing function. Overall design: In this specific experimental design, ChIP-sequencing data of MYC, HDAC2, H3K27ac and RNApolII was generated from three primary MYC amplified Group 3 medulloblastoma tumors. In addition to primary tumors, in order to assess the effect of HDAC inhibition, we generated MYC, HDAC2, H3K27ac and RNApolII ChIP-seq data from HDMB03 cells before and after subjecting to treatment with 5μM entinostat (MS275) for 6 hours. **RAW data were deposited at EGA with id - EGAS00001003855**

MYC是多种癌症中的驱动癌基因（driver oncogene）。靶向MYC的治疗潜力极高，但目前尚无特异性MYC抑制剂可应用于临床。既往研究表明，MYC扩增型髓母细胞瘤（Medulloblastoma）细胞对组蛋白去乙酰化酶（HDAC）抑制具有敏感性。
本研究通过免疫共沉淀（co-immunoprecipitation）、质谱（mass spectrometry）及染色质免疫共沉淀测序（ChIP-sequencing）技术，证实HDAC2（组蛋白去乙酰化酶2）是MYC扩增型原发性髓母细胞瘤及细胞系中MYC的辅因子。
MYC-HDAC2复合物结合于定义MYC依赖型转录谱的基因区域。I类HDAC抑制可导致MYC蛋白稳定化并降低其DNA结合能力，进而诱导MYC激活基因（MYC activated genes，简称MAGs）的下调及MYC抑制基因（MYC repressed genes，简称MRGs）的上调。MAGs与MRGs具有相反的生物学功能及截然不同的E盒（E-box）分布特征。
综上，MYC与HDAC2（I类HDAC）在MYC扩增型髓母细胞瘤中以复合物形式存在，并驱动MYC特异性转录程序，而该程序可被I类HDAC抑制剂恩替司他（entinostat）逆转。因此，开发用于治疗MYC扩增型髓母细胞瘤的HDAC抑制剂时，应将HDAC2纳入评估指标，以直接靶向MYC的反式激活与反式抑制功能。

**整体实验设计**：本实验设计中，我们从3例原发性MYC扩增型第3组髓母细胞瘤样本中获取了MYC、HDAC2、H3K27ac及RNA聚合酶II（RNApolII）的染色质免疫共沉淀测序数据。除原发性肿瘤样本外，为评估HDAC抑制的效应，我们还分别在经5μM恩替司他（MS275）处理6小时前后的HDMB03细胞中，获取了MYC、HDAC2、H3K27ac及RNApolII的ChIP-seq数据。**原始数据已提交至欧洲基因组学档案（EGA），编号为EGAS00001003855**