Abstract
Rhabdomyosarcoma (RMS) is a pediatric malignancy of skeletal muscle lineage. The aggressive alveolar subtype is characterized by t(2;13) or t(1;13) translocations encoding for PAX3- or PAX7-FOXO1 chimeric transcription factors, respectively, and are referred to as fusion positive RMS (FP-RMS). The fusion gene alters the myogenic program and maintains the proliferative state while blocking terminal differentiation. Here, we investigated the contributions of chromatin regulatory complexes to FP-RMS tumor maintenance. We define the mSWI/SNF functional repertoire in FP-RMS. We find that SMARCA4 (encoding BRG1) is overexpressed in this malignancy compared to skeletal muscle and is essential for cell proliferation. Proteomic studies suggest proximity between PAX3-FOXO1 and BAF complexes, which is further supported by genome-wide binding profiles revealing enhancer colocalization of BAF with core regulatory transcription factors. Further, mSWI/SNF complexes localize to sites of de novo histone acetylation. Phenotypically, interference with mSWI/SNF complex function induces transcriptional activation of the skeletal muscle differentiation program associated with MYCN enhancer invasion at myogenic target genes, which is recapitulated by BRG1 targeting compounds. We conclude that inhibition of BRG1 overcomes the differentiation blockade of FP-RMS cells and may provide a therapeutic strategy for this lethal childhood tumor.
Highlights
Rhabdomyosarcoma (RMS) is a pediatric malignancy of skeletal muscle lineage
We found that the canonical BAF subunit ARID1A was overexpressed in fusion negative (FN)-RMS and fusion positive RMS (FP-RMS) tissue compared to differentiated muscle, while its mutually exclusive homologous BAF subunit ARID1B was downregulated in RMS tissue compared to muscle (Fig. S1a)
We found that FN- and FP-RMS cells rank among the most highly BRG1-dependent cancer cell lines based on the DepMap data repository (Fig. 1a), while RMS cell lines did not show strong dependence on BRM relative to other cell lines (Fig. S1b)
Summary
Rhabdomyosarcoma (RMS) is a pediatric malignancy of skeletal muscle lineage. The aggressive alveolar subtype is characterized by t(2;13) or t(1;13) translocations encoding for PAX3- or PAX7-FOXO1 chimeric transcription factors, respectively, and are referred to as fusion positive RMS (FP-RMS). Interference with mSWI/SNF complex function induces transcriptional activation of the skeletal muscle differentiation program associated with MYCN enhancer invasion at myogenic target genes, which is recapitulated by BRG1 targeting compounds. Despite the expression of core regulatory myogenic transcription factors, RMS tumor cells are unable to terminally differentiate[9,10]. PAX3-FOXO1 mediated epigenetic changes maintain the proliferative state in FP-RMS, while preventing terminal muscle differentiation through direct transcriptional targets of the fusion protein and its capability to induce altered enhancer architecture[22,23,24,25,26,27]. We determine which chromatin regulatory complexes contribute to RMS tumor maintenance and demonstrate that BRG1-containing mSWI/SNF complexes are essential in both major RMS subtypes. Our study is consistent with previous reports suggesting targeting of ACTL6A (encoding BAF53a) as potential differentiation therapy in RMS28, while our findings reveal that the BRG1 ATPase plays a key role in differentiation block and oncogenesis in FP-RMS
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