MLL-fusion-driven leukemia requires SETD2 to safeguard genomic integrity

Anna Skucha,Balázs Győrffy,Johannes Schmöllerl,André C Müller,Adrián César-Razquin,Julian Jude,Jessica Ebner,Sarah Vittori,Giulio Superti‐Furga ,Alexey Stukalov,Peter Valent,Martin Aichinger,Mareike Roth,Matthias Muhar,Thomas Eder,Johannes Zuber,Christopher R Vakoc,Keiryn L Bennett,Bin Lü ,Florian Grebien

doi:10.1038/s41467-018-04329-y

Abstract

MLL-fusions represent a large group of leukemia drivers, whose diversity originates from the vast molecular heterogeneity of C-terminal fusion partners of MLL. While studies of selected MLL-fusions have revealed critical molecular pathways, unifying mechanisms across all MLL-fusions remain poorly understood. We present the first comprehensive survey of protein–protein interactions of seven distantly related MLL-fusion proteins. Functional investigation of 128 conserved MLL-fusion-interactors identifies a specific role for the lysine methyltransferase SETD2 in MLL-leukemia. SETD2 loss causes growth arrest and differentiation of AML cells, and leads to increased DNA damage. In addition to its role in H3K36 tri-methylation, SETD2 is required to maintain high H3K79 di-methylation and MLL-AF9-binding to critical target genes, such as Hoxa9. SETD2 loss synergizes with pharmacologic inhibition of the H3K79 methyltransferase DOT1L to induce DNA damage, growth arrest, differentiation, and apoptosis. These results uncover a dependency for SETD2 during MLL-leukemogenesis, revealing a novel actionable vulnerability in this disease.

Highlights

MLL-fusions represent a large group of leukemia drivers, whose diversity originates from the vast molecular heterogeneity of C-terminal fusion partners of MLL
Pioneering biochemical experiments have shown that several fusion partners of MLL, such as AF4, AF9, and ENL are members of the DOT1L complex (DotCom) and the superelongation complex (SEC)[10,11,12,13], which are both involved in transcriptional control
We identify the methyltransferase SETD2 as an interactor of all MLL-fusion proteins. shRNA-mediated and CRISPR/Cas9-mediated loss of SETD2 leads to growth arrest and differentiation of MLL-fusionexpressing cells in vitro and in vivo

Summary

Introduction

MLL-fusions represent a large group of leukemia drivers, whose diversity originates from the vast molecular heterogeneity of C-terminal fusion partners of MLL. SETD2 loss synergizes with pharmacologic inhibition of the H3K79 methyltransferase DOT1L to induce DNA damage, growth arrest, differentiation, and apoptosis. These results uncover a dependency for SETD2 during MLL-leukemogenesis, revealing a novel actionable vulnerability in this disease. The MLL N-terminus takes part in >120 different translocations, resulting in the generation of MLL-fusion proteins encompassing more than 75 different partner genes[5]. It has been proposed that the oncogenic activity of MLLfusion proteins depends on chromatin targeting functions exerted by the MLL N-terminus in combination with other functional properties encoded by the fusion partners[6]. As the SEC can regulate the transcriptional activity of RNA polymerase II, it was hypothesized that these MLL-fusions induce aberrant regulation of transcriptional elongation on MLL-target genes[14]

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Conclusion