LKB1, Salt-Inducible Kinases, and MEF2C Are Linked Dependencies in Acute Myeloid Leukemia

Tarumoto, Yusuke; Lü, Bin; Somerville, Tim D.D.; Huang, Yuhan; Milazzo, Joseph P.; Wu, Xiaoli; Klingbeil, Olaf; Demerdash, Osama E.; Shi, Junwei; Vakoc, Christopher R.

doi:10.1016/j.molcel.2018.02.011

Cited by 135 publications

(186 citation statements)

References 61 publications

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“…This included suppression of HOXA9 , MEIS1 , or MEF2C following ZFP64 or MLL knockout in each context (Figure 1D–F). We did not observe this same correlation when comparing the knockout of ZFP64 with knockout of SIK3 or RUNX1 , which are also essential in MOLM-13 cells (Tarumoto et al, 2018) (Figure S1H). Targeting of ZFP64 or MLL in MOLM-13 cells also resulted in myeloid differentiation (Figure S1I).…”

Section: Resultsmentioning

confidence: 84%

A Transcription Factor Addiction in Leukemia Imposed by the MLL Promoter Sequence

et al. 2018

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Summary The Mixed Lineage Leukemia gene (MLL) is altered in leukemia by chromosomal translocations to produce oncoproteins comprised of the MLL N-terminus fused to the C-terminus of a partner protein. Here, we used domain-focused CRISPR screening to identify ZFP64 as an essential transcription factor in MLL-rearranged leukemia. We show that the critical function of ZFP64 in leukemia is to maintain MLL expression via binding to the MLL promoter, which is the most enriched location of ZFP64 occupancy in the human genome. The specificity of ZFP64 for MLL is accounted for by an exceptional density of ZFP64 motifs embedded within the MLL promoter. These findings demonstrate how a sequence anomaly of an oncogene promoter can impose a transcriptional addiction in cancer.

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Section: Resultsmentioning

confidence: 84%

A Transcription Factor Addiction in Leukemia Imposed by the MLL Promoter Sequence

et al. 2018

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“…We have previously demonstrated that prior to the application of drug, there is a rare subpopulation of cells (pre-resistant cells) that express high levels of a number of markers, and that these "primed" cells are far more likely to become resistant than other cells 14 . In order to identify modulators of the fluctuations that lead to the formation of this subpopulation of primed cells, we designed a large scale loss-of-function pooled CRISPR genetic screen (which we dubbed the "priming screen") comprised of ~13,000 single guide RNAs (sgRNAs) targeting functionally relevant domains of ~2,000 proteins, with roughly six distinct single guide RNAs per domain (1402 transcription factor targets, 481 kinase targets, 176 epigenetic targets; each single guide RNA targets an important functional domain, see Supplemental Tables 1-3) [27][28][29] .…”

Section: Crispr/cas9 Genetic Screens Identify Factors That Affect Primentioning

confidence: 99%

“…Approximately 6 independent single guide RNAs were designed against individual DNA binding domains (Supplementary tables 1-3). [27][28][29] The design principle of single guide RNA was based on previous reports and the single guide RNAs with the predicted high off-target effect were excluded (Hsu et al 2013) . For the initial pooled CRISPR screens, all of the single guide RNAs oligos including positive and negative control single guide RNAs were synthesized in a pooled format (Twist Bioscience) and then amplified by PCR.…”

Section: Construction Of Domain-focused Single Guide Rna Pooled Librarymentioning

confidence: 99%

Genetic screening for single-cell variability modulators driving therapy resistance

Torre

Arai

Bayatpour

et al. 2019

Preprint

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Cellular plasticity describes the ability of cells to transition from one set of phenotypes to another. In the context of cancer therapeutics, plasticity refers to transient fluctuations in the molecular state of tumor cells, driving the formation of rare cells primed to survive drug treatment and ultimately reprogram into a stably resistant fate. However, the biological processes governing this cellular plasticity remain unknown. We used CRISPR/Cas9 genetic screens to reveal genes that affect cell fate decisions by altering cellular plasticity across a range of functional categories. We found that cellular plasticity and cell fate decision making can be decoupled in that factors can affect cell fate decisions in both plasticity-dependent and independent manners. We discovered a novel mode of altering resistance based on cellular plasticity that, contrary to known mechanisms, pushes cells towards a more differentiated state. We further confirmed our prediction that manipulating cellular plasticity before the addition of the main therapy would result in changes in therapy resistance more than concurrent administration. Together, our results indicate that identifying pathways modulating cellular plasticity has the potential to alter cell fate decisions and may provide a new avenue for treating drug resistance.

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“…In this disease, MLL fusion oncoproteins induce an active chromatin state and transcriptional hyper-activation at the MEF2C locus 9,15,16 . This results in overexpression of MEF2C, which promotes enhancer-mediated gene activation to promote self-renewal, tissue invasion, and chemotherapy resistance 15,16,20,22 . Importantly, it has been shown that MLL fusion AML cells are addicted to continuous MEF2C expression for their growth and viability 15,22 .…”

Section: Introductionmentioning

confidence: 99%

“…This results in overexpression of MEF2C, which promotes enhancer-mediated gene activation to promote self-renewal, tissue invasion, and chemotherapy resistance 15,16,20,22 . Importantly, it has been shown that MLL fusion AML cells are addicted to continuous MEF2C expression for their growth and viability 15,22 . The powerful nature of MEF2C addiction in MLL-rearranged AML has been most convincingly demonstrated in the hypomorphic Mef2c S222A/S222A mouse strain, which lacks any detectable developmental abnormalities, but is entirely resistant to leukemic transformation by the MLL-AF9 oncoprotein 21 .…”

Section: Introductionmentioning

confidence: 99%

The Salt-Inducible Kinase inhibitor YKL-05-099 suppresses MEF2C function and acute myeloid leukemia progressionin vivo

Tarumoto

Lin

Wang

et al. 2019

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Running title: SIK3 inhibition in AML Category: Myeloid Neoplasia Key PointsAML cells are uniquely sensitive to genetic or chemical inhibition of Salt-Inducible Kinase 3 in vitro and in vivo.A SIK inhibitor YKL-05-099 suppresses MEF2C function and AML in vivo. AbstractLineage-defining transcription factors (TFs) are compelling targets for leukemia therapy, yet they are among the most challenging proteins to modulate directly with small molecules. We previously used CRISPR screening to identify a Salt-Inducible Kinase 3 (SIK3) requirement for the growth of acute myeloid leukemia (AML) cell lines that overexpress the lineage TF MEF2C. In this context, SIK3 maintains MEF2C function by directly phosphorylating histone deacetylase 4 (HDAC4), a repressive cofactor of MEF2C. Here, we evaluated whether inhibition of SIK3 with the tool compound YKL-05-099 can suppress MEF2C function and attenuate disease progression in animal models of AML. Genetic targeting of SIK3 or MEF2C selectively suppressed the growth of transformed hematopoietic cells under in vitro and in vivo conditions. Similar phenotypes were obtained when exposing cells to YKL-05-099, which caused cell cycle arrest and apoptosis in MEF2C-expressing AML cell lines. An epigenomic analysis revealed that YKL-05-099 rapidly suppressed MEF2C function by altering the phosphorylation state and nuclear localization of HDAC4. Using a gatekeeper allele of SIK3, we found that the antiproliferative effects of YKL-05-099 occurred through on-target inhibition of SIK3 kinase activity. Based on these findings, we treated two different mouse models of MLL-AF9 AML with YKL-05-099, which attenuated disease progression in vivo and extended animal survival at well-tolerated doses. These findings validate SIK3 as a therapeutic target in MEF2C-positive AML and provide a rationale for developing drug-like inhibitors of SIK3 for definitive pre-clinical investigation and for studies in human patients with leukemia.

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LKB1, Salt-Inducible Kinases, and MEF2C Are Linked Dependencies in Acute Myeloid Leukemia

Cited by 135 publications

References 61 publications

A Transcription Factor Addiction in Leukemia Imposed by the MLL Promoter Sequence

A Transcription Factor Addiction in Leukemia Imposed by the MLL Promoter Sequence

Genetic screening for single-cell variability modulators driving therapy resistance

The Salt-Inducible Kinase inhibitor YKL-05-099 suppresses MEF2C function and acute myeloid leukemia progressionin vivo

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