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Non-canonical H3K79me2-dependent pathways promote the survival of MLL-rearranged leukemia
William F Richter1, Rohan N Shah1,2, Alexander J Ruthenburg1,3
1Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, United States.
Abstract:
MLL-rearranged leukemia depends on H3K79 methylation. Depletion of this transcriptionally activating mark by DOT1L deletion or high concentrations of the inhibitor pinometostat downregulates HOXA9 and MEIS1, and consequently reduces leukemia survival. Yet, some MLL-rearranged leukemias are inexplicably susceptible to low-dose pinometostat, far below concentrations that downregulate this canonical proliferation pathway. In this context, we define alternative proliferation pathways that more directly derive from H3K79me2 loss. By ICeChIP-seq, H3K79me2 is markedly depleted at pinometostat-downregulated and MLL-fusion targets, with paradoxical increases of H3K4me3 and loss of H3K27me3. Although downregulation of polycomb components accounts for some of the proliferation defect, transcriptional downregulation of FLT3 is the major pathway. Loss-of-FLT3-function recapitulates the cytotoxicity and gene expression consequences of low-dose pinometostat, whereas overexpression of constitutively active STAT5A, a target of FLT3-ITD-signaling, largely rescues these defects. This pathway also depends on MLL1, indicating combinations of DOT1L, MLL1 and FLT3 inhibitors should be explored for treating FLT3-mutant leukemia.
Insights
Low-dose pinometostat targets alternative pathways in MLL-rearranged leukemia by downregulating FLT3, not just H3K79 methylation. This suggests combining DOT1L, MLL1, and FLT3 inhibitors for improved leukemia treatment.
Area of Science:
- Oncology
- Molecular Biology
- Epigenetics
Background:
- MLL-rearranged leukemia relies on H3K79 methylation for survival.
- DOT1L inhibition or deletion downregulates HOXA9 and MEIS1, impacting leukemia growth.
- Some leukemias respond to low-dose pinometostat via unknown mechanisms.
Purpose of the Study:
- To identify alternative proliferation pathways affected by H3K79me2 loss in MLL-rearranged leukemia.
- To investigate the role of FLT3 signaling in low-dose pinometostat sensitivity.
- To explore therapeutic strategies combining DOT1L, MLL1, and FLT3 inhibition.
Main Methods:
- Chromatin immunoprecipitation sequencing (ICeChIP-seq) to analyze histone modifications.
- Gene expression analysis to identify affected pathways.
- Functional assays using gene manipulation (loss-of-function, overexpression).
Main Results:
- H3K79me2 is depleted at MLL-fusion targets, with altered H3K4me3 and H3K27me3 levels.
- Transcriptional downregulation of FLT3 is a major driver of low-dose pinometostat cytotoxicity.
- Loss of FLT3 function mimics pinometostat effects, and STAT5A activation rescues these defects.
- This pathway is dependent on MLL1, suggesting a role in MLL-rearranged leukemia.
Conclusions:
- Low-dose pinometostat induces cytotoxicity through FLT3 downregulation, independent of canonical HOXA9/MEIS1 repression.
- FLT3 signaling is a critical alternative pathway in MLL-rearranged leukemia.
- Combination therapy targeting DOT1L, MLL1, and FLT3 warrants investigation for FLT3-mutant leukemia.
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