Epstein-Barr Virus Oncoprotein Super-enhancers Control B Cell Growth

Abstract

Summary Super-enhancers are clusters of gene-regulatory sites bound by multiple transcription factors that govern cell transcription, development, phenotype, and oncogenesis. By examining Epstein-Barr virus (EBV) transformed lymphoblastoid cell lines (LCLs), we identified four EBV oncoproteins and five EBV-activated NF-κB subunits co-occupying ~1800 enhancer sites. Of these, 187 had markedly higher and broader histone H3K27ac signals characteristic of super-enhancers, and were designated “EBV super-enhancers”. EBV super-enhancer-associated genes included the MYC and BCL2 oncogenes, enabling LCL proliferation and survival. EBV super-enhancers were enriched for B cell transcription factor motifs and had a high co-occupancy of the transcription factors STAT5 and NFAT. EBV super-enhancer-associated genes were more highly expressed than other LCL genes. Disrupting EBV super-enhancers by the bromodomain inhibitor, JQ1 or conditionally inactivating an EBV oncoprotein or NF-κB decreased MYC or BCL2 expression and arrested LCL growth. These findings provide insight into mechanisms of EBV-induced lymphoproliferation and identify potential therapeutic interventions.

Epstein–Barr virus super-enhancer eRNAs are essential for MYC oncogene expression and lymphoblast proliferation

“…Genome-wide analyses found most EBNAs and NF-κB components bound to enhancer sites. Although each EBNA and NF-κB subunit is independent and functionally nonredundant, EBNA2, EBNALP, EBNA3A, EBNA3C, and the five LMP1-activated NF-κB subunits converge at 187 EBV super-enhancer (ESE) sites that have extraordinary broad and high H3K27ac ChIP-seq signals, characteristic of super-enhancers (26). ESEs are linked to key oncogenes including MYC and MIR155.…”

“…ESEs are also linked to genes critical for B-cell functions, including IKZF3, RUNX3, and OCA-B. ESEs are co-occupied by many cell TFs, including EBF, SPI-1, PAX5, ETS1, IRF4, and BATF (26). However, only EBNA2, RBPJ, NFATc, STAT5, RNA polymerase II (Pol II), and H3K27ac ChIP-seq signals differentiate ESEs from typical enhancers.…”

“…EBV typical enhancers (ETE), with all associated EBV transcription factors or NF-κB subunits, have significantly less H3K27ac and Pol II signals. Their associated genes are expressed at lower levels (26).…”

“…ESEs have high signals for TFs associated with high-level transcription, such as EBNA2, which has a strong transactivation domain and active histone modifications, including H3K27ac, H3k4me1, and H3K4me3. ESEs also have high signals for p300, BRD4, and Pol II (26). RNA Pol II is frequently paused without active transcription elongation.…”

“…The small molecule inhibitor, JQ1, blocks BRD4 association with H3K27ac to suppress transcription. LCLs treated with JQ1 have much reduced MYC expression resulting in cell growth arrest (26).…”