DOT1L inhibits SIRT1-mediated epigenetic silencing to maintain leukemic gene expression in MLL-rearranged leukemia

Abstract

Rearrangements of MLL (encoding lysine-specific methyltransferase 2A and officially known as KMT2A; herein referred to as MLL to denote the gene associated with mixed-lineage leukemia) generate MLL fusion proteins that bind DNA and drive leukemogenic gene expression. This gene expression program is dependent on the disruptor of telomeric silencing 1–like histone 3 lysine 79 (H3K79) methyltransferase DOT1L, and small-molecule DOT1L inhibitors show promise as therapeutics for these leukemias. However, the mechanisms underlying this dependency are unclear. We conducted a genome-scale RNAi screen and found that the histone deacetylase SIRT1 is required for the establishment of a heterochromatin-like state around MLL fusion target genes after DOT1L inhibition. DOT1L inhibits chromatin localization of a repressive complex composed of SIRT1 and the H3K9 methyltransferase SUV39H1, thereby maintaining an open chromatin state with elevated H3K9 acetylation and minimal H3K9 methylation at MLL fusion target genes. Furthermore, the combination of SIRT1 activators and DOT1L inhibitors shows enhanced antiproliferative activity against MLL-rearranged leukemia cells. These results indicate that the dynamic interplay between chromatin regulators controlling the activation and repression of gene expression could provide novel opportunities for combination therapy.

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Figure 1: Genome-scale RNAi screen for antagonists of DOT1L in MLL-AF9 leukemia.
Figure 2: SIRT1 mediates the response of MLL-AF9 leukemia cells to the DOT1L inhibitor EPZ4777.
Figure 3: SIRT1 localizes to active genes and mediates deacetylation of H3K9 in response to DOT1L inhibition.
Figure 4: Unique H3K9 epigenomic signature at MLL-AF9–bound gene loci in MLL-fusion leukemia.
Figure 5: Methylation of H3K9 by SUV39H1 is involved in SIRT1-mediated silencing of the MLL-AF9 leukemic program upon suppression of DOT1L.
Figure 6: The SIRT1 activator SRT1720 sensitizes MLL-r leukemia to the DOT1L inhibitor EPZ4777.

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Acknowledgements

We would like to thank J. Bradner for providing EPZ4777, and J. Brady and Z. Feng for administrative assistance. This work was supported by the Leukemia and Lymphoma Society, by Gabrielle's Angel Research Foundation and by US National Institutes of Health grant nos. CA66996, CA140575 and CA176745 (to S.A.A.).

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C.-W.C. and S.A.A. conceived the study and wrote the paper; R.P.K. and A.U.S. conducted genome-wide data analyses; A.J.D. and N.Z. performed ChIP-seq experiments; R.E., S.H.C., H.X., X.W. and C.D. performed molecular biology, cell culture and animal experiments; J.G.D., D.E.R. and W.C.H. processed shRNA library screens; K.M.B. generated the Dot1l mouse model and conceived experiments; J.Q. and J.E.B. synthesized and supplied EPZ4777 and provided conceptual input.

Corresponding author

Correspondence to Scott A Armstrong.

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S.A.A. is a consultant for Epizyme, Inc. The remaining authors report no competing financial interests.

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Chen, C., Koche, R., Sinha, A. et al. DOT1L inhibits SIRT1-mediated epigenetic silencing to maintain leukemic gene expression in MLL-rearranged leukemia. Nat Med 21, 335–343 (2015). https://doi.org/10.1038/nm.3832

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