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

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.

EVI1 protein interaction dynamics: Targetable for therapeutic intervention?

“…also by targeting the translocated enhancer binding to specific transcriptional regulators. ( 21,22,85) . Nevertheless, better understanding of EVI1 and the other MECOM proteins with respect to posttranslational modifications and protein interactions might also offer targeted therapeutic exploitation.…”

Cracking chromatin with proteomics: From chromatome to histone modifications

“…The second enrichment with streptavidin beads allows for harsh washing conditions and selection of functional chromatin-mediated interactors identified by LCMS. First applied in mESCs to characterize the interactome dynamics of TFs involved in pluripotency [62], it has been more recently employed on other classes of chromatin-binding proteins (nuclear receptors, TFs) for the identification of their on-chromatin interactome [63][64][65].…”

TET2lesions enhance the aggressiveness ofCEBPA-mutant AML by rebalancingGATA2expression

“…In further support of a role of CEBPA, the G2DHE is highly active in CEBPA DM AML, with both elevated eRNA expression and levels of H3K27ac 51 . An equally important role for CEBPA is observed in the context of inv(3) and t(3;3) AML in which inversions, translocations, and rearrangements involving the EVI1 gene at the MECOM locus, lead to hijacking of the G2DHE to promote EVII expression at the expense of GATA2 expression thus resulting in GATA2 haploinsufficiency [53][54][55][56] . Here, EVI1 expression was found to be downregulated following knockdown of CEBPA in inv(3) AML cells, and mutation of the CEBPA binding site in the hijacked enhancer reduced enhancer activity 57 .…”

“…An equally important role for CEBPA is observed in the context of inv(3) and t(3;3) AML in which inversions, translocations, and rearrangements involving the EVI1 gene at the MECOM locus, lead to hijacking of the G2DHE to promote EVII expression at the expense of GATA2 expression thus resulting in GATA2 haploinsufficiency [53][54][55][56] . Here, EVI1 expression was found to be downregulated following knockdown of CEBPA in inv(3) AML cells, and mutation of the CEBPA binding site in the hijacked enhancer reduced enhancer activity 57 . In this context, CEBPA MUT would not be favorable, and these lesions are indeed underrepresented in inv(3) and t(3;3) AML [58][59][60] .…”