Genome-wide CRISPR screens reveal synthetic lethal interaction between CREBBP and EP300 in diffuse large B-cell lymphoma

Man Nie,Julia Joung,Kui Wu,Likun Du,Dongbing Liu,Xiaofei Ye,Qiang Pan-Hammarström,Feng Zhang,Sibel Ciftci,Xi Shi,Weicheng Ren

doi:10.1038/s41419-021-03695-8

Abstract

Diffuse large B-cell lymphoma (DLBCL) is the most common type of aggressive lymphoid malignancy and a highly heterogeneous disease. In this study, we performed whole-genome and transcriptome sequencing, and a genome-wide CRISPR-Cas9-knockout screen to study an activated B-cell-like DLBCL cell line (RC-K8). We identified a distinct pattern of genetic essentialities in RC-K8, including a dependency on CREBBP and MDM2. The dependency on CREBBP is associated with a balanced translocation involving EP300, which results in a truncated form of the protein that lacks the critical histone acetyltransferase (HAT) domain. The synthetic lethal interaction between CREBBP and EP300 genes, two frequently mutated epigenetic modulators in B-cell lymphoma, was further validated in the previously published CRISPR-Cas9 screens and inhibitor assays. Our study suggests that integration of the unbiased functional screen results with genomic and transcriptomic data can identify both common and unique druggable vulnerabilities in DLBCL and histone acetyltransferases inhibition could be a therapeutic option for CREBBP or EP300 mutated cases.

Highlights

Introduction Diffuse largeB-cell lymphoma (DLBCL) is one of the most common types of aggressive lymphoid malignancy
We further identified 384 genes with nonsynonymous mutations (n = 436), including genes involved in DNA damage response and repair (RAD21, TP63, TP73, and XRCC6), B-cell receptor (BCR)/nuclear factor-κB (NF-κB) signalling (TNFAIP3 and NFKBIA), and transcription factors important for B-cell development (IKZF1 and IKZF3) (Supplementary Table S2)
Through whole-genome sequencing (WGS), we identified and mapped structural variants to base pair resolution including translocations involving IGH and BCL6, as well as a balanced translocation between chromosomes 22 and 6 in RC-K8 (Fig. 1B), which resulted in a C-terminal truncation of EP300 that has been previously reported as EP300ΔC104723,29

Summary

Introduction

Introduction Diffuse largeB-cell lymphoma (DLBCL) is one of the most common types of aggressive lymphoid malignancy. With the current standard immunochemotherapy, ~30–40% of DLBCL patients still suffer from refractory disease or relapse[1,2]. Two major subtypes of DLBCL have been defined: germinal centre B-cell like (GCB) and activated B-cell like (ABC)[1]. Large-scale genome sequencing has further enabled the identification of several molecular subtypes of DLBCL based on genetic alterations affecting the proto-oncogenes. We have shown that hepatitis B virus (HBV)-related DLBCLs are associated with unique genetic and clinical features, as well as shorter overall patient survival, and may be considered a distinct subtype[7]. DLBCL is a highly heterogeneous disease and identification of genetic vulnerabilities that are specific to a subtype or subgroup of patients will aid in the development of novel targeted therapeutic strategies and improve clinical outcome

Methods

Results

Conclusion