Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia

Sandra Kiehlmeier,Gianluca Sigismondo,Jeroen Krijgsveld,Peter Schmezer,Mahmoud-Reza Rafiee,Sabrina Kruse,Stefan Gröschel,Judith Müller,Ali Bakr,Sabrina Schweiggert,Jagoda Mika,Carl Herrmann

doi:10.1038/s41375-021-01235-z

Abstract

Deregulation of the EVI1 proto-oncogene by the GATA2 distal hematopoietic enhancer (G2DHE) is a key event in high-risk acute myeloid leukemia carrying 3q21q26 aberrations (3q-AML). Upon chromosomal rearrangement, G2DHE acquires characteristics of a super-enhancer and causes overexpression of EVI1 at 3q26.2. However, the transcription factor (TF) complex of G2DHE remains poorly characterized. The aim of this study was to unravel key components of G2DHE-bound TFs involved in the deregulation of EVI1. We have identified several CEBPA and RUNX1 binding sites to be enriched and critical for G2DHE function in 3q-AML cells. Using ChIP-SICAP (ChIP followed by selective isolation of chromatin-associated proteins), a panel of chromatin interactors of RUNX1 and CEBPA were detected in 3q-AML, including PARP1 and IKZF1. PARP1 inhibition (PARPi) caused a reduction of EVI1 expression and a decrease in EVI1–G2DHE interaction frequency, highlighting the involvement of PARP1 in oncogenic super-enhancer formation. Furthermore, 3q-AML cells were highly sensitive to PARPi and displayed morphological changes with higher rates of differentiation and apoptosis as well as depletion of CD34 + cells. In summary, integrative analysis of the 3q-AML super-enhancer complex identified CEBPA and RUNX1 associated proteins and nominated PARP1 as a potential new therapeutic target in EVI1 + 3q-AML.

Highlights

Aberrant expression of the zinc finger transcription factor (TF) Ecotropic Viral Integration Site 1 (EVI1) is a potent oncogenic event involved in the pathogenesis of high-risk hematopoietic neoplasms [1, 2]
TF binding sites (TFBS) prediction analyses showed predominant enrichment of MYB, RUNX1, and CEBPA motifs in the left part, while other prominent myeloid TFs, such as PU.1, GATA2, TAL1, and Ikaros family zinc finger 1 (IKZF1) motifs clustered in the right region
For validation of candidate TFs used in further proteomic studies, we chose RUNX1 and CEBPA, since (i) both TFs are pioneer TFs and key myeloid transcriptional regulators expressed at sufficiently high levels in inv(3)/t(3;3) acute myeloid leukemia (AML) allowing for subsequent protein capture experiments (Fig. S2a, b); (ii) RUNX1 has been implicated in the regulation of EVI1 previously [29]; and (iii) CEBPA mutations are mutually exclusive with inv(3)/t(3;3) in AML [1, 30]

Summary

Introduction

Aberrant expression of the zinc finger transcription factor (TF) Ecotropic Viral Integration Site 1 (EVI1) is a potent oncogenic event involved in the pathogenesis of high-risk hematopoietic neoplasms [1, 2]. EVI1 and its isoforms are part of the PRDI-BF1 (positive regulatory domain I-binding factor 1) and RIZ1 (retinoblastoma protein-interacting zinc finger gene 1) homology domain (PRDM) family of epigenetic remodelers, with EVI1 being known as PRDM3 [5, 6]. Imbalanced expression of MECOM-transcribed isoforms is often the consequence of (i) chromosomal rearrangements leading either to EVI1 gene fusions (e.g., AML1-EVI1) [12]; (ii) MECOM locus amplifications as found with high frequency in high-grade serous ovarian cancer [13]; (iii) aberrant promoter activation [14]; or (iv) displacement of regulatory DNA elements into the EVI1 locus, the latter being a hallmark of 3q26.2/MECOM rearranged acute myeloid leukemia (AML) [15, 16]

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