The genetic complexity, heterogeneity and plasticity of human cancers pose a daunting challenge for the development of effective targeted therapeutics. RNA interference (RNAi) provides a unique tool to systematically identify cancer-specific vulnerabilities and functionally evaluate candidate target genes prior to drug development. However, negative selection RNAi studies and high-throughput screens remain technically challenging and have yet to reach their full potential. In an effort to improve the utility of RNAi for probing candidate therapeutic targets, we recently have implemented a series of technological advances, including (1) improved shRNA design and cloning strategies for the rapid generation of customized shRNA libraries, (2) an “RNAi Sensor assay” for high-throughput shRNA knockdown validation, (3) optimized Tet-on shRNA expression vectors enabling inducible and reversible target gene suppression in established tumors in vivo; and (4) methodology for multiplexed shRNA screening in vitro and in vivo.
In a first study, we have applied these new tools to systematically probe chromatin-associated dependencies in acute myeloid leukemia (AML). To this end, we constructed a chromatin-focused shRNA library targeting 243 chromatin regulators (4-5 shRNAs/gene) and screened it in an MLL-AF9;NrasG12D-driven AML mouse model. Among several interesting dependencies, our screen identified the histone-acetyl reader Brd4 as top sensitivity, which led to the testing of JQ1, a small-molecule BET bromodomain inhibitor, in AML. Strikingly, JQ1 precisely copied the potent anti-leukemic effects of Brd4 shRNAs in vitro and in vivo, demonstrating the ability of our RNAi system to accurately predict drug action. These effects are, at least in part, due to a role of BRD4 in sustaining expression of the MYC oncogene, which implicates BET inhibitors as the first pharmacologic approach to suppress MYC in cancer. Together, our results identify BRD4 as a promising therapeutic target in AML, and unambiguously highlight the utility of advanced RNAi technologies for the discovery of cancer-specific vulnerabilities and the development of targeted therapeutics.