Role of RNA-Exosome in PRC2- and NF1-Mutant Malignant Peripheral Nerve Sheath Tumors
Abstract
Malignant peripheral nerve sheath tumors (MPNSTs) are heterogeneous soft tissue sarcomas that have significant propensity for local recurrence and metastatic spread and a 5-year survival rate of less than 25%. The major obstacle faced when treating these highly chemo- and radio-resistant tumors is the lack of effective systemic therapies. Surgical resection is often impossible owing to tumor location or metastasis. About 50% of the MPNSTs occur in neurofibromatosis type 1 (NF1) patients. In addition, 70-90% of MPNSTs have mutations and copy number loss of genes - SUZ12 and/or EED - that are core components a major repressor complex, polycomb repressor complex 2 (PRC2). This complex has enzymatic activity that deposits H3K27me3 (Histone H3 Lysine 27 Trimethyl) mark on its cognate promoters/genomic loci, creating a repressive environment. To identify new targets for therapy in this disease, we performed a functional genomic “drop-out” screen using genome wide gRNA library (~76,000 gRNAs for ~18,000 genes) in a PRC2- and NF1-mutant tumor-derived MPNST cell line. We identified multiple components of RNA-exosome complex as hits in this screen. The nuclear RNA-exosome complex is involved in 3 processing of various stable RNA species and is crucial for RNA quality control in the nucleus. It also degrades many types of cryptic transcripts that are generated as a result of pervasive transcription and removes aberrant RNA molecules that failed to mature. Importantly, RNA-exosome regulated control of long non-coding RNA transcription controls super-enhancer activity. In support of this, our epigenome profiles showed higher levels of enhancer transcription in a NF1- and PRC2-mutant cell line. Furthermore, we observed increased expression of ERVs (Endogenous Retroviral Elements), which have been previously demonstrated to be dependent on PRC2 complex for its silencing. RNA-DNA hybrids, formed as part of transcription, are aberrantly increased upon loss of activity of RNA-exosomes. This may lead to accumulation of DNA damage in cells and eventual cell death. Finally, we observed increased RNA-DNA hybrids in NF1 mutant cells. Our model is that, in PRC2- and NF1-mutant MPNSTs, loss of H3K27me3 de-represses general RNA transcription from enhancer and other viral RNAs, which needs to be resolved by enhanced activity of RNA-exosomes. Depletion of RNA-exosomes leads to accumulation of these toxic RNAs and DNA damage signaling, eventually causing cell death. Our hypothesis is that PRC2-mutant and NF1-mutant MPNSTs harbor a targetable dependency on RNA-exosome components that could be potentially used for novel targeted therapy in this disease. We posit that loss of H3K27me3-based silencing in PRC2-mutant MPNST tissues leads to increased RNA synthesis from generally repressed regions, which needs to be resolved with enhanced activity of RNA-exosome components. In the first aim, we will characterize the dependence of NF-1- and PRC2-mutant MPNST cells on the RNA-exosome complex by functional experiments in human and murine cells. In the second aim, we will identify the various RNA species that may be accumulated in NF1- and PRC2- mutant MPNST cells due to lack of repression and may serve as targets for RNA-exosome. We will specifically focus on two species: enhancer RNAs and endogenous retroviral elements. In the third aim, we will study how accumulation of the RNA-DNA hybrid structures may lead to induction of DNA damage signaling and cell death in the absence of RNA surveillance by RNA-exosomes. Our work will be one of the first to link NF1 and PRC2 mutations with RNA surveillance machinery in the context of MPNSTs. We will examine how RNA-exosomes, a key component of the surveillance machinery in the cell, take care of the accumulation of various RNA-species due to a defect in the major epigenetic repressor complex. We will examine the therapeutic potential of these findings as well. Overall, our proposed studie
Document Details
- Document Type
- DoD Grant Award
- Publication Date
- Mar 10, 2021
- Source ID
- W81XWH2010646
Entities
People
- Kunal Rai
Organizations
- The University of Texas MD Anderson Cancer Center
- United States Army