PU.1 and MYC transcriptional network defines synergistic drug responses to KIT and LSD1 inhibition in acute myeloid leukemia

et al. 2021

Preprint

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Colony stimulating factor 3 receptor (CSF3R) mutations lead to JAK pathway activation and are the molecular hallmark of chronic neutrophilic leukemia (CNL). Approximately half of CNL patients also have mutations in SET binding protein 1 (SETBP1). In this study, we developed models of SETBP1-mutant leukemia to understand the role that SETBP1 plays in CNL. SETBP1 mutations promote self-renewal of CSF3R-mutant hematopoietic progenitors in vitro and prevent cells from undergoing terminal differentiation. In vivo, SETBP1 mutations accelerate leukemia progression, leading to the rapid development of hepatosplenomegaly and granulocytosis. Through transcriptomic and epigenomic profiling, we found that SETBP1 enhances progenitor-associated programs—most strongly upregulating Myc and Myc target genes. This upregulation of Myc can be reversed by epigenetic modulatory drugs. In summary, we find that SETBP1 mutations promote aggressive hematopoietic cell expansion when expressed with mutant CSF3R through the upregulation of Myc-associated gene expression programs.Statement of SignificanceSETBP1 is frequently mutated in chronic neutrophilic leukemia, but its role in the biology of this disease is unclear. We find that mutant SETBP1 enhances transcription of Myc and Myc target genes to promote aggressive disease biology, and that these oncogenic transcriptional programs can be reversed by epigenetic modulatory drugs.

Section: Discussionsupporting

confidence: 93%

Mutant-SETBP1 activates transcription of Myc programs to accelerate CSF3R-driven myeloproliferative neoplasms

Carratt

Kong

et al. 2021

Preprint

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“…However, the MYC BENC is bound by many other transcription factors, indicating that drug combination efficacy may be dependent on interruption of other MYC BENC-bound factors. Prior studies have shown that LSD1 inhibitor monotherapy decreases MYC expression (20)(21)(22). A critical component of LSD1-inhibitor efficacy is the disruption of LSD1 scaffolding of GFI1 from the CoREST transcription repressor complex (25).…”

Section: Lsd1 Inhibition Represses the Expression Of Myc And Its Targ...mentioning

confidence: 99%

“…Prior work from our lab and others suggest that the combination of kinase and LSD1 inhibition may be an effective therapeutic strategy in AML (20)(21)(22)(23). To establish whether this approach is effective for FLT3-ITD AML, we treated FLT3-ITD-positive (MOLM13 and MV4-11) and FLT3-ITD-negative (K562) cell lines with multiple FLT3/LSD1 inhibitors.…”

Section: Combined Flt3/lsd1 Inhibition Synergistically Represses Myc ...mentioning

confidence: 99%

“…Inhibitors of LSD1 have been shown to decrease MYC in AML cell lines and primary samples (20)(21)(22). Our prior work and that of other groups shows that LSD1 inhibition augments the efficacy of kinase inhibitors in AML (21)(22)(23). However, the extent to which synergy exists between LSD1 and FLT3 inhibition and the underlying mechanism of drug synergy has not been investigated.…”

Section: Introductionmentioning

confidence: 97%

“…LSD1 regulates gene expression by the removal of activating methylation marks on lysine 4 of histone 3 (H3K4) and repressive methylation marks on lysine 9 of histone 3 (H3K9) or by the recruitment of repressive complexes to gene promoters (18,19). Inhibitors of LSD1 have been shown to decrease MYC in AML cell lines and primary samples (20–22). Our prior work and that of other groups shows that LSD1 inhibition augments the efficacy of kinase inhibitors in AML (21–23).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Disruption of the MYC Super-Enhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia

Yashar

Coleman

et al. 2022

Preprint

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Clinical responses to kinase inhibitor therapy in acute myeloid leukemia (AML) are limited by the inevitable development of resistance. A major contributor to resistance is early epigenetic adaptation, leading to persistence of a small number of leukemia cells. Here we show that inhibition of the epigenetic regulator lysine-specific demethylase 1 (LSD1) augments the response to inhibitors of the FLT3 kinase in AML. We demonstrate that combined FLT3 and LSD1 inhibition results in synergistic cell death of FLT3-mutant AML cells. The drug combination activates a pro-differentiative epigenetic and transcriptional program while simultaneously suppressing the activity of MYC target genes. High-resolution, multi-modal epigenetic analyses revealed that combined FLT3 and LSD1 inhibition results in the suppression of MYC-bound promoters and the activation of PU.1-bound enhancers. Regulon enrichment analysis in primary AML samples nominated STAT5 as a putative regulator of MYC gene expression. Inhibition of FLT3 results in a loss of STAT5 binding at the MYC blood super-enhancer and a loss of super-enhancer activation. In contrast, LSD1 inhibition prevents the removal of repressive H3K9me1 marks at MYC target genes, resulting in suppression of MYC expression. We validated these findings in 66 primary AML samples including 17 FLT3-ITD-positive AML samples, with the majority demonstrating improved responses with the drug combination. High MYC regulon activity was a predictor of response to the drug combination and RNA-seq on drug-treated AML samples revealed suppression of MYC target genes. Finally, single cell ATAC-seq on primary AML blasts treated ex vivo with the FLT3 and LSD1 inhibitor combination results in a shift from MYC super-enhancer-high to a MYC super-enhancer-low cell state. Collectively, these studies provide preclinical rationale for the investigation of dual FLT3 and LSD1 inhibition in a clinical trial.

Disruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia

Yashar

Molecular Cancer Research

Coleman

et al. 2023

Mutations in Fms-like tyrosine kinase 3 (FLT3) are common drivers in acute myeloid leukemia (AML) yet FLT3 inhibitors only provide modest clinical benefit. Prior work has shown that inhibitors of lysine-specific demethylase 1 (LSD1) enhance kinase inhibitor activity in AML. Here we show that combined LSD1 and FLT3 inhibition induces synergistic cell death in FLT3-mutant AML. Multi-omic profiling revealed that the drug combination disrupts STAT5, LSD1, and GFI1 binding at the MYC blood superenhancer, suppressing superenhancer accessibility as well as MYC expression and activity. The drug combination simultaneously results in the accumulation of repressive H3K9me1 methylation, an LSD1 substrate, at MYC target genes. We validated these findings in 72 primary AML samples with the nearly every sample demonstrating synergistic responses to the drug combination. Collectively, these studies reveal how epigenetic therapies augment the activity of kinase inhibitors in FLT3-ITD (internal tandem duplication) AML. Implications: This work establishes the synergistic efficacy of combined FLT3 and LSD1 inhibition in FLT3-ITD AML by disrupting STAT5 and GFI1 binding at the MYC blood-specific superenhancer complex.