Research Projects

Cancer cells often harbor specific genomic or functional alterations that help them tolerate excessive genomic instability or adapt to a changing microenvironment. Such alterations could introduce particular vulnerabilities that could be exploited for cancer therapy. Repetitive elements, especially retrotransposons (RTEs) that comprise about 50% of the human genome, are epigenetically silenced by DNA methylation in somatic cells. Genome-wide loss of DNA methylation is a characteristic feature of cancer cells, which may lead to widespread activation of RTEs, causing genomic instability, activation of interferon responses and, eventually, cell death. However, cancer cells suppress the widespread activation of RTEs by other epigenetic silencing mechanisms, such as repressive histone modifications. Identifying such mechanisms could lead to the development of novel therapeutic approaches to treat breast cancer. We have identified breast cancer cells are dependent on PRMT5, a protein arginine methyltransferase (PRMT) and RBBP4 (Retinoblastoma binding protein 4), a histone chaperone which is a subunit of repressive chromatin remodeling complexes. PRMT5 deposits the repressive histone H4 arginine 3 symmetric dimethylation (H4R3me2s) mark, whereas RBBP4 is part of the NuRD and PRC2 complexes that deposit repressive histone modifications H3K9me3 and H3K27me3 respectively. Inhibition or deletion of PRMT5 or RBBP4 leads to reduced proliferation of breast cancer cells as per genome-wide CRISPR screen datasets. Moreover, we also identified a synthetic lethal interaction between PRMT5 and RBBP4, indicating a common function. However, the mechanisms underlying the epigenetic vulnerability of breast cancer cells to PRMT5 and RBBP4 depletion are not studied. Our overarching hypothesis is that PRMT5 and RBBP4 repress RTEs through arginine methylation and histone methylation, respectively, in cancer cells that lack DNA methylation. Inhibition or depletion of both could lead to massive activation of RTEs and cell death. We will use multiple approaches such as shRNA mediated knockdown, CRISPR-Cas9 mediated knockout, AID-degron mediated depletion or small molecule mediated inhibition to deplete PRMT5 and RBBP4 levels or function in breast cancer cells. We will perform transcriptome profiling (RNA-seq) to determine the genes and RTEs upregulated upon ablation of PRMT5 and RBBP4. We will assess whether viral mimicry induction occurs in response to inhibition/depletion of PRMT5 or RBBP4 and when co-depleted. We will perform epigenome profiling (CUT&RUN) to understand underlying mechanisms, specifically, whether these proteins directly repress RTEs. We will profile chromatin accessibility (ATAC-seq) after depletion of PRMT5 or RBBP4 and co-depletion to test whether there is an increase in open chromatin at RTEs. The proposed study will identify novel epigenetic vulnerabilities in breast cancer cells, which could be used to improve the response to immunotherapy approaches.