Primary effusion lymphoma enhancer connectome links super-enhancers to dependency factors

Chong Wang,Shijun Li,Liangru Ke,Weiyue Ding,Bo Zhao,Jun Liang,Eva Gottwein,Sizun Jiang,Mingxiang Teng,Yohei Narita,Kenneth M Kaye,Difei Li,Luyao Zhang,Haipeng Xiao,Isabella Hou

doi:10.1038/s41467-020-20136-w

Abstract

Primary effusion lymphoma (PEL) has a very poor prognosis. To evaluate the contributions of enhancers/promoters interactions to PEL cell growth and survival, here we produce H3K27ac HiChIP datasets in PEL cells. This allows us to generate the PEL enhancer connectome, which links enhancers and promoters in PEL genome-wide. We identify more than 8000 genomic interactions in each PEL cell line. By incorporating HiChIP data with H3K27ac ChIP-seq data, we identify interactions between enhancers/enhancers, enhancers/promoters, and promoters/promoters. HiChIP further links PEL super-enhancers to PEL dependency factors MYC, IRF4, MCL1, CCND2, MDM2, and CFLAR. CRISPR knock out of MEF2C and IRF4 significantly reduces MYC and IRF4 super-enhancer H3K27ac signal. Knock out also reduces MYC and IRF4 expression. CRISPRi perturbation of these super-enhancers by tethering transcription repressors to enhancers significantly reduces target gene expression and reduces PEL cell growth. These data provide insights into PEL molecular pathogenesis.

Highlights

Primary effusion lymphoma (PEL) has a very poor prognosis
The expression of KSHV genes is important for PEL growth and survival2–5. vFLIP (KSHV) and LMP1 (EBV), each activate NFkB6,7
Analysis of PEL cell genomes revealed that coinfection with Epstein-Barr virus (EBV) is associated with fewer host genomic alterations compared to PELs that are only KSHV infected[11]

Summary

Introduction

To evaluate the contributions of enhancers/promoters interactions to PEL cell growth and survival, here we produce H3K27ac HiChIP datasets in PEL cells. CRISPRi perturbation of these super-enhancers by tethering transcription repressors to enhancers significantly reduces target gene expression and reduces PEL cell growth. PEL cells depend on a group of genes for their continuous proliferation, identified by genome-wide CRISPR screens[13]. These genes include MYC, IRF4, CCND2, MCL1, and CFLAR, which are important for transcription, cell cycle progression, and survival[13]. The expression of these oncogenes is controlled by enhancers and promoters. The recently developed HiCHIP method can achieve the same goal with much higher efficiency and much less input DNA16

Methods

Results

Conclusion