Epigenetic and clinical impact of SMARCB1 loss in cancer

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The SMARCB1 (hSNF5/INI-1) gene encodes the INI-1 protein, a component of the SWI/SNF chromatin remodeling complex. While the SWI/SNF complex is known to play an important role in transcriptional regulation, how it does so is largely unknown. Rhabdoid Tumors (RT) are rare, highly malignant sarcomas of infancy that demonstrate mutation and/or deletion of SMARCB1. We recently reported the global gene expression pattern of RT, and provided evidence that RTs arise within very early progenitor cells during a critical developmental window during which loss of SMARCB1 directly results in striking repression of differentiation and loss of cyclin dependent kinase inhibition. We provide additional evidence that these changes are largely mediated by changes in histone methylation. In this proposal we test our hypothesis that loss of SMARCB1 in early progenitor cells results in a global failure to release the polycomb group mediated repressive H3K27me3 on bivalent genes, resulting in arrested development and abnormal proliferation. Aim 1: To knock-down SMARCB1 within hESC and to measure changes in cell proliferation, differentiation, gene expression and DNA methylation compared with three RT cell lines. We will utilize RNA interference to knock-down SMARCB1 in two hESC and measure changes in proliferation, EZH2 expression, differentiation, and RNA and DNA methylation changes. These will be compared to those features in three RT cell lines. Global RNA and DNA methylation analysis in these studies will be compared with histone modifications in RT detected by global ChIP-SEQ being performed outside of this proposal. Aim 2: To investigate the direct and indirect impact of pharmacologic inhibition of EZH2 on cell proliferation in SMARCB1-deficient cells in vitro and in vivo. EZH2 represents the most important polycomb group protein in humans, and has been shown to be upregulated in a large number of tumors. It is therefore an attractive therapeutic target. We have established an agreement with GlaxoSmithKline for the study of a promising EZH2 inhibitor that is ready for preclinical development. We will perform in vitro cytotoxic assays on the three RT cell lines, and in vivo studies on xenografts created from the same cell lines. Both the in vitro and in vivo studies that are proposed are required prior to our ability to develop early clinical trials. Relevance: With an overall survival rate of 23%, new therapeutic options are urgently needed for RT. If our hypothesis is correct, it may result in novel therapeutic targets for RTs and the many other tumors that show histone modification or EZH2 overexpression. In addition, it will introduce a unique and important model of epigenetic control of both early embryonic differentiation and tumor development. Long-term, these studies will help to identify the underlying mechanisms by which histone modifications interact with other epigenetic mechanisms. This would then enable the investigation of epigenetic regulation more broadly in different patient populations, developmental stages, and diseases.