<i>PVT1</i> interacts with polycomb repressive complex 2 to suppress genomic regions with pro-apoptotic and tumour suppressor functions in multiple myeloma

Abstract

Multiple myeloma is a heterogeneous haematological disease that originates from the bone marrow and is characterized by the monoclonal expansion of malignant plasma cells. Despite novel therapies, multiple myeloma remains clinically challenging. A common feature among patients with poor prognosis is the increased activity of the epigenetic silencer EZH2, which is the catalytic subunit of the PRC2. Interestingly, the recruitment of PRC2 lacks sequence specificity and, to date, the molecular mechanisms that define which genomic locations are destined to PRC2-mediated silencing remain unknown. The presence of a lncRNA-binding pocket on EZH2 suggests that lncRNAs could potentially mediate PRC2 recruitment to specific genomic regions. Here, we coupled RIP-seq, RNA-Seq and ChIP-seq analysis of human multiple myeloma primary cells and cell lines to identify potential lncRNA partners to EZH2. We found that the lncRNA plasmacytoma variant translocation 1 (PVT1) directly interacts with EZH2 and is overexpressed in patients with a poor prognosis. Moreover, genes predicted to be targets of PVT1 exhibited H3K27me3 enrichment and were associated with pro-apoptotic and tumour suppressor functions. In fact, PVT1 inhibition independently promotes the expression of the PRC2 target genes ZBTB7C, RNF144A and CCDC136. Altogether, our work suggests that PVT1 is an interacting partner in PRC2-mediated silencing of tumour suppressor and pro-apoptotic genes in multiple myeloma, making it a highly interesting potential therapeutic target.

The complex nature of lncRNA-mediated chromatin dynamics in multiple myeloma

“…We and others have shown the importance of lncRNAs in chromatin remodelling and the impact they have on MM patient outcome ( 6 , 15 – 17 ). In fact, aberrant lncRNA expression has been demonstrated to have an oncogenic role in MM pathogenesis and progression ( 35 , 36 ).…”

“…Moreover, lncRNAs can modulate PRC2 activity by acting as a complex recruiter to target genomic locations. For instance, the lncRNA PVT1 was recently described to be overexpressed in primary MM patient samples and associated with poor prognosis, a seemingly independent feature from patients’ cytogenetic background ( 6 ). Moreover, PVT1 was shown to interact directly with EZH2, facilitating recruitment of PRC2 to target genomic loci and transcriptional repression of genes associated with pro-apoptotic and tumour suppressor functions ( 6 ) ( Table 1 ).…”

“…For instance, the lncRNA PVT1 was recently described to be overexpressed in primary MM patient samples and associated with poor prognosis, a seemingly independent feature from patients’ cytogenetic background ( 6 ). Moreover, PVT1 was shown to interact directly with EZH2, facilitating recruitment of PRC2 to target genomic loci and transcriptional repression of genes associated with pro-apoptotic and tumour suppressor functions ( 6 ) ( Table 1 ). Similarly to the function of PVT1 , the lncRNA ANRIL , was described to exert a guiding function for PRC1 and PRC2 DNA binding in MM and was demonstrated to promote resistance to conventional therapies such as bortezomib by guiding PRC2 to promote gene silencing of the tumour suppressor gene PTEN.…”

“…Thus, treatment of MM is clinically challenging and new therapeutic interventions are required. Prior studies, by us and others, have suggested that the epigenetic machinery plays a crucial role in MM pathogenesis, including aberrant DNA methylation and abnormal histone modification patterns (6)(7)(8)(9)(10)(11)(12)(13)(14). Furthermore, more recently, dysregulation of long non-protein coding RNAs (lncRNAs) has been suggested to contribute to MM pathogenesis, patient outcome and drug resistance (15)(16)(17).…”

“…as, N6-methyladenosine (m6A), N1-methyladenosine (m1A), 5methylcytosine (m5C), and 7-methylguanosine (m7G), play a crucial role in regulating various aspects of lncRNA function, structure, stability, localization, and lncRNA-mediated interactions (26-34) (Figure 2). We and others have shown the importance of lncRNAs in chromatin remodelling and the impact they have on MM patient outcome (6,(15)(16)(17). In fact, aberrant lncRNA expression has been demonstrated to have an oncogenic role in MM pathogenesis and progression (35,36).…”