Direct therapeutic targeting of SWI/SNF induces epigenetic reprogramming and durable tumor regression in rhabdoid tumor

Abstract

PurposeRhabdoid tumor is a pediatric cancer characterized by the biallelic inactivation of SMARCB1, a subunit of the SWI/SNF chromatin remodeling complex. SMARCB1 inactivation leads to SWI/SNF redistribution to favor a proliferative dedifferentiated cellular state. Although this deletion is the known oncogenic driver, SWI/SNF therapeutic targeting remains a challenge. Experimental DesignWe define a novel epigenetic mechanism for mithramycin using biochemical fractionation, chromatin immunoprecipitation sequencing (ChIP-seq), and a dual spike-in assay for transposase accessible chromatin sequencing (ATAC-seq). We correlate epigenetic reprogramming with changes with chromatin A/B compartments and promoter accessibility with chromHMM models and RNA-seq. Finally, we demonstrate durable, marked tumor response in an intramuscular rhabdoid tumor xenograft model. ResultsHere we show mithramycin and a second-generation analogue EC8042 evict mutated SWI/SNF from chromatin and are effective in rhabdoid tumor. SWI/SNF blockade triggers chromatin compartment remodeling and promoter reprogramming leading to differentiation and amplification of H3K27me3, the catalytic mark of PRC2. Treatment of rhabdoid rumor xenografts with EC8042 leads to marked, durable tumor regression and differentiation of the tumor tissue into benign mesenchymal tissue, including de novo bone formation. ConclusionOverall, this study identifies a novel therapeutic candidate for rhabdoid tumor and an approach that may be applicable to the 20% of cancers characterized by mutated SWI/SNF. STATEMENT OF TRANSLATIONAL RELEVANCEThere is a tremendous need for novel therapeutic approaches for rhabdoid tumor and the more than 20% of human cancers characterized by dysregulation of the SWI/SNF chromatin remodeling complex. While approaches to target associated complexes, such as PRC2, known to be influenced by dysregulated SWI/SNF are currently being evaluated in the clinic, the direct therapeutic targeting of SWI/SNF has not been explored. Here we identify an inhibitor of SWI/SNF and thoroughly explore the therapeutic development of this compound from a mechanistic and translational perspective thus providing insight into the targeting of this complex as well as a dose, schedule, and biomarker of target inhibition that is immediately clinically translatable.