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Acute Myeloid Leukemia
SETDB1 mediated histone H3 lysine 9 methylation suppresses MLL-fusion target expression and leukemic transformation
Ferrata Storti Foundation
Haematologica 2020 Volume 105(9):2273-2285
James Ropa,1,2 Nirmalya Saha,1* Hsiangyu Hu,1* Luke F. Peterson,3 Moshe Talpaz3 and Andrew G. Muntean1
1Department of Pathology, University of Michigan Medical School; 2Department of Computational Medicine and Bioinformatics, University of Michigan Medical School and 3Department of Internal Medicine/Division of Hematology/Oncology, University of Michigan School of Medicine and Comprehensive Cancer Center, Ann Abor, MI, USA
*NS and HH contributed equally as co-second authors.
ABSTRACT
Epigenetic regulators play a critical role in normal and malignant hematopoiesis. Deregulation, including epigenetic deregulation, of the HOXA gene cluster drives transformation of about 50% of acute myeloid leukemia (AML). We recently showed that the histone 3 lysine 9 methyltransferase SETDB1 negatively regulates the expression of the pro- leukemic genes Hoxa9 and its cofactor Meis1 through deposition of promot- er H3K9 trimethylation in MLL-AF9 leukemia cells. Here, we investigated the biological impact of altered SETDB1 expression and changes in H3K9 methylation on AML. We demonstrate that SETDB1 expression is correlat- ed to disease status and overall survival in AML patients. We recapitulated these findings in mice, where high expression of SETDB1 delayed MLL-AF9 mediated disease progression by promoting differentiation of leukemia cells. We also explored the biological impact of treating normal and malig- nant hematopoietic cells with an H3K9 methyltransferase inhibitor, UNC0638. While myeloid leukemia cells demonstrate cytotoxicity to UNC0638 treatment, normal bone marrow cells exhibit an expansion of cKit+ hematopoietic stem and progenitor cells. Consistent with these data, we show that bone marrow treated with UNC0638 is more amenable to transformation by MLL-AF9. Next generation sequencing of leukemia cells shows that high expression of SETDB1 induces repressive changes to the promoter epigenome and downregulation of genes linked with AML, including Dock1 and the MLL-AF9 target genes Hoxa9, Six1, and others. These data reveal novel targets of SETDB1 in leukemia that point to a role for SETDB1 in negatively regulating pro-leukemic target genes and sup- pressing AML.
Introduction
Epigenetic deregulation has emerged as an important contributor to oncogenesis and disease progression in a variety of malignancies, including leukemia.1 Deep sequencing has revealed that genes encoding epigenetic modifying proteins are mutated in over 70% of acute myeloid leukemia (AML) patients.2 H3K9me2/3 marks large regions of condensed transcriptionally inactive chromatin, such as peri- centric heterochromatin.3 H3K9me2/3 also plays a functional role in the dynamic repression of genes in euchromatic regions of the genome.4 Two families of pro- teins are associated with deposition of H3K9 methylation: the SUV39 family and PRDM family. The SUV39 family of H3K9 methyltransferases consists of SUV39H1/2, EHMT1/2, and SETDB1/2.4 Our lab and others have previously demonstrated that members of the SUV39 family of H3K9 methyltransferases bind to the polymerase associated factor complex (PAF1c).5,6 SETDB1, G9a (EHMT2), and GLP (EHMT1), were identified in a proteomics study exploring the interactome of the PAF1c in AML.5 The PAF1c is an epigenetic regulator complex that physically
Correspondence:
ANDREW G. MUNTEAN
andrewmu@umich.edu
Received: April 4, 2019.
Accepted: September 25, 2019. Pre-published: September 26, 2019.
doi:10.3324/haematol.2019.223883
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