Super-enhancer Driven Core Regulatory Circuitry in MYCN-amplified Neuroblastoma [array]

Transcriptional dysregulation plays a major role in the development and progression of human tumors such as pediatric neuroblastoma. Therefore, we sought to elucidate the relationship between genes required for neuroblastoma cell growth and survival and the transcriptional core regulatory circuitry (CRC) that controls the gene expression program. A genome-scale CRISPR-Cas9 screen for oncogenic dependencies revealed that 143 genes are essential for cell survival and growth in neuroblastoma relative to other cancers, including many super-enhancer (SE) regulated transcription factors. Genome-wide occupancy analysis of transcription factor binding demonstrated that at least six of these transcription factors were both dependency genes and components of the CRC in MYCN-amplified neuroblastoma including: HAND2, ISL1, PHOX2B, GATA3, TBX2, and MEIS2. Binding sites for these transcription factors were clustered within a few hundred base pairs in their own enhancers and the enhancers of downstream target genes, which surprisingly included 40% of the independently determined neuroblastoma dependency genes. This profound level of transcriptional control of oncogenesis through self-reinforcing transcriptional circuits led us to test combinatorial pharmacological inhibition of transcriptional initiation and elongation, which synergistically induced tumor cell death, supporting drugging transcription as a means to advance the treatment of high risk neuroblastoma. Array-based expression profiling of neuroblastoma cells treated with JQ1 and 125nM THZ1 for up to 12hrs.

转录失调在儿童神经母细胞瘤等人类肿瘤的发生与进展中发挥关键作用。因此，本研究旨在阐明神经母细胞瘤细胞生长与存活所必需的基因，与调控基因表达程序的转录核心调控环路（transcriptional core regulatory circuitry, CRC）之间的关联。通过针对致癌依赖基因的全基因组CRISPR-Cas9筛选，本研究发现相较于其他癌症类型，共有143个基因对神经母细胞瘤的细胞存活与生长至关重要，其中包含众多受超级增强子（super-enhancer, SE）调控的转录因子。对转录因子结合位点的全基因组占据分析显示，在MYCN扩增型神经母细胞瘤中，至少有6个此类转录因子同时属于致癌依赖基因与CRC组分，分别为HAND2、ISL1、PHOX2B、GATA3、TBX2及MEIS2。这些转录因子的结合位点聚集在自身增强子及下游靶基因增强子的数百碱基对范围内，令人意外的是，该区域涵盖了40%经独立鉴定的神经母细胞瘤致癌依赖基因。这种通过自我强化转录环路对肿瘤发生进行的深度转录调控，促使我们测试转录起始与延伸的联合药理学抑制策略，该策略可协同诱导肿瘤细胞死亡，证实了以转录过程为靶点可作为优化高危神经母细胞瘤治疗方案的可行途径。本数据集包含经JQ1与125nM THZ1处理长达12小时的神经母细胞瘤细胞的基于芯片的表达谱数据。