High-throughput small molecule screen identifies inhibitors of aberrant chromatin accessibility
High-throughput small molecule screen identifies inhibitors of aberrant chromatin accessibility
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DOI：
10.1073/pnas.1521827113
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发表时间：
2016-03-15
影响因子：
11.1
通讯作者：
Davis, Ian J.
中科院分区：
文献类型：
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作者：
Pattenden, Samantha G.;Simon, Jeremy M.;Davis, Ian J.
染色质修饰蛋白和转录因子的突变通常与多种癌症有关。通过功能的获得或丧失，这些突变可能导致可获得的染色质的特征性变化，这表明全基因组调控元件的格局发生了变化。识别逆转特定染色质特征的化合物可能导致化学探针或潜在的治疗方法。为了探索染色质的可及性是否可以作为小分子筛选的平台，我们采用了甲醛辅助的调节元件分离(FIRE)作为一种高通量、自动化的分析方法，这是一种对核小体缺失基因组区域进行浓缩的化学方法。在证明了这种方法的有效性和稳健性之后，我们应用这种方法通过评估EWSR1-FLI1介导的异常核小体缺失区域来筛选表观遗传学靶向的小分子文库。EWSR1-FLI1是骨和软组织肿瘤尤文肉瘤的关键嵌合转录因子。作为一类，组蛋白脱乙酰酶抑制剂在活性化合物中被大量使用。这些化合物通过干扰EWSR1-FLI1的转录，导致靶点的可及性降低。利用染色质可及性的精确差异为药物发现工作提供了显著的优势，因为它不依赖于单个分子靶标的先验选择，并可能发现新的生物相关途径。
Mutations in chromatin-modifying proteins and transcription factors are commonly associated with a wide variety of cancers. Through gain-or loss-of-function, these mutations may result in characteristic alterations of accessible chromatin, indicative of shifts in the landscape of regulatory elements genome-wide. The identification of compounds that reverse a specific chromatin signature could lead to chemical probes or potential therapies. To explore whether chromatin accessibility could serve as a platform for small molecule screening, we adapted formaldehyde-assisted isolation of regulatory elements (FAIRE), a chemical method to enrich for nucleosome-depleted genomic regions, as a high-throughput, automated assay. After demonstrating the validity and robustness of this approach, we applied this method to screen an epigenetically targeted small molecule library by evaluating regions of aberrant nucleosome depletion mediated by EWSR1-FLI1, the chimeric transcription factor critical for the bone and soft tissue tumor Ewing sarcoma. As a class, histone deacetylase inhibitors were greatly overrepresented among active compounds. These compounds resulted in diminished accessibility at targeted sites by disrupting transcription of EWSR1-FLI1. Capitalizing on precise differences in chromatin accessibility for drug discovery efforts offers significant advantages because it does not depend on the a priori selection of a single molecular target and may detect novel biologically relevant pathways.