Abstract
MIR139 is a tumor suppressor and is commonly silenced in acute myeloid leukemia (AML). However, the tumor-suppressing activities of miR-139 and molecular mechanisms of MIR139-silencing remain largely unknown. Here, we studied the poorly prognostic MLL-AF9 fusion protein-expressing AML. We show that MLL-AF9 expression in hematopoietic precursors caused epigenetic silencing of MIR139, whereas overexpression of MIR139 inhibited in vitro and in vivo AML outgrowth. We identified novel miR-139 targets that mediate the tumor-suppressing activities of miR-139 in MLL-AF9 AML. We revealed that two enhancer regions control MIR139 expression and found that the polycomb repressive complex 2 (PRC2) downstream of MLL-AF9 epigenetically silenced MIR139 in AML. Finally, a genome-wide CRISPR-Cas9 knockout screen revealed RNA Polymerase 2 Subunit M (POLR2M) as a novel MIR139-regulatory factor. Our findings elucidate the molecular control of tumor suppressor MIR139 and reveal a role for POLR2M in the MIR139-silencing mechanism, downstream of MLL-AF9 and PRC2 in AML. In addition, we confirmed these findings in human AML cell lines with different oncogenic aberrations, suggesting that this is a more common oncogenic mechanism in AML. Our results may pave the way for new targeted therapy in AML.
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Introduction
Mixed-lineage leukemia (MLL) or Lysine Methyltransferase 2A (KMT2A) rearrangements occur in 10% of adult acute leukemias and in 35% of pediatric cases [1, 2]. MLL rearrangements cause in-frame fusions with >60 different genes of which AF4, AF9, AF10, ENL, and ELL are most common [3, 4]. MLL-fusion proteins cause heterogeneous leukemia of lymphoid or myeloid origin and are associated with therapy resistance and poor prognosis [3, 5]. MLL-fusion proteins retain the DNA-binding domain of MLL and deregulate target genes that are normally controlled by MLL [26]. The use of human MLL-AF9 patient samples was approved by the Erasmus MC Medical Ethics Committee (METC 2016-606). Human MLL-AF9 AML cell lines THP-1, Molm-13, and other AML cell lines MV4-11, HL-60, HEL, and U937 were cultured in Roswell Park Memorial Institute-1640 supplemented with Pen-Strep (100 U/mL), fetal bovine serum (FBS) (10%), and l-Glut (2 mM). AML cell line Kasumi-1 was cultured as above with 20% FBS and AML cell line TF-1 was cultured as above supplemented with human granulocyte-macrophage colony-stimulating factor (5 ng/mL, 300-03-B, Peprotech) and sodium pyruvate (1%). The MLL-AF9 patient samples were cultured in Iscove’s Modified Dulbecco’s Medium, supplemented with FBS (20%), Pen-Strep (100 U/mL), IL-3 (10 ng/mL, 200-03, Peprotech), IL-6 (10 ng/mL, 200-06, Peprotech), TPO (50 ng/mL, 300-18, Peprotech), FLT-3L (50 ng/mL, 300-09, Peprotech), and SCF (50 ng/mL, 300-07, Peprotech).
Statistical analyses
Data are presented as mean ± SEM, unless otherwise specified in the figure legends. Data were compared with the two-tailed independent samples Student’s t test, unless otherwise specified in the figure legends.
Results
MLL-AF9 downregulates Mir139 expression
We generated a murine MLL-AF9 model by transduction of bone marrow (BM) HSPCs with MLL-AF9-expressing retrovirus. MLL-AF9 leukemia cells were positive for c-Kit, GR-1, CD16/CD32, and CD11b and negative for CD3 expression, suggesting a myeloid progenitor origin of the leukemia cells (Fig. 1A). As expected from previous studies [27], DOT1L-inhibitors diminished cell survival of MLL-AF9 cells (Supplementary Fig. 1A). To validate our model, we performed proteomics and observed differential protein expression in MLL-AF9 cells (Supplementary Fig. 1B, Supplementary Table 2). The most upregulated protein was 15-hydroxyprostaglandin dehydrogenase (HPGD), suggesting a role for the HPGD pathway in MLL-AF9 leukemogenesis (Supplementary Fig. 1B). We performed Ingenuity Pathway Analysis of differentially expressed proteins and found that pathways involved in Cell Death and Survival (P < 2.74e−3), Hematological System Development and Function (P < 2.60e−3), and Hematological Diseases (P < 2.60e−3) were deregulated (Supplementary Fig. 1C). Transcriptomics and Gene Set Enrichment Analyses showed enrichment of MLL-AF9 targets [28] in the upregulated fraction of genes in MLL-AF9 cells compared to WT HSPCs (Supplementary Fig. 1D). In contrast, myeloid differentiation factors such as C/ebpa, Csf1r, Csf3r, and Id2 were downregulated (Supplementary Fig. 1E). In concordance with previous studies [22, 29], we found enrichment of PRC1 and PRC2 targets, class-I (EZH2-controlled) and class-II (EZH2-independent) PcG target genes in the set of downregulated genes in MLL-AF9 cells compared to WT HSPCs (Supplementary Fig. 1F).
MIR139 is downregulated in AML patients including cases with MLL rearrangements and in THP-1 cells that express MLL-AF9 compared with normal HSPCs and myeloid cells including monocytes, macrophages, and neutrophils [13]. We therefore asked whether genomic Mir139 deletion collaborates with MLL-AF9 in AML outgrowth. Mir139KO mice developed normally and had expected HSPC counts and hematopoietic cell types in peripheral blood and BM [25]. Next, we asked whether Mir139 influences genes that have potential effects on pathways other than those that are critical for hematopoiesis. We found that WT and Mir139KO HSPCs were indistinguishable at the transcriptome and proteome level, including Pde2a host gene expression (Fig. 1B, Supplementary Fig. 2A, Supplementary Table 3). These data suggest that MIR139 is expressed at too low levels in normal HSPCs to sufficiently downregulate its targets to detectable levels. In contrast, genomic deletion of Mir139 enhanced primary and secondary colony-forming capacity (more colonies) and proliferation (larger colonies) of MLL-AF9 cells (Fig. 1C). Strikingly, we observed a >60% reduction of miR-139-3p and miR-139-5p expression in MLL-AF9 cells, suggesting that MLL-AF9 silences Mir139 (Fig. 1D). Pde2a expression in MLL-AF9 was unchanged, indicating that Mir139 and the host gene are not co-regulated (Fig. 1E). Together, these results indicate that Mir139 is a target of MLL-AF9.
MiR-139 upregulation and repression of miR-139 targets eliminate MLL-AF9 AML
To determine effects of miR-139 expression on MLL-AF9 cell survival, we generated (DOX)-inducible miR-139-expressing MLL-AF9 clones (MLL-AF9-i139). DOX-treatment of MLL-AF9-i139 cells induced miR-139-5p (up to 130 Fold) and miR-139-3p (up to 100 Fold) expression (Fig. 2A). DOX-treated MLL-AF9-i139 cells lost their colony-forming capacity, whereas DOX-inducible eGFP expressing MLL-AF9 control cells (MLL-AF9-ieGFP) expanded as expected (Fig. 2B). DOX-mediated induction of miR-139 expression caused cell death and apoptosis of MLL-AF9-i139 cells as indicated by Annexin-V positivity and loss of replating capacity (Fig. 2C, D). In addition, induction of miR-139 expression in MLL-AF9-i139 cells cultured in expansion medium without GM-CSF, stimulating mainly leukemia stem cell (LSC) expansion, completely blocked colony outgrowth (Fig. 2D). Similarly, MLL-AF9-i139 cells generated from hematopoietic stem cells (Lin−Sca-1+c-Kit+, LSK)(LSK-MLL-AF9-i139) showed loss of cells upon miR-139 induction (Supplementary Fig. 2B). Together, our results suggest that miR-139 expression also eliminates LSCs.
Next, we asked whether miR-139 expression inhibits MLL-AF9 leukemia development in mice. Mice transplanted with MLL-AF9-i139 cells developed AML with a short latency of 3 weeks. However, DOX-mediated miR-139 induction significantly delayed leukemia development of transplanted mice (Fig. 2E). Mice had malignant MLL-AF9-i139 cells in BM (Supplementary Fig. 2C), blood, and spleen (data not shown). Leukemia cells from mice that were treated with DOX showed an average miR-139-5p and miR-139-3p overexpression induction of eightfold and sevenfold, respectively (Fig. 2F), which suggests that this level of upregulation in esca** MLL-AF9-i139 cells is not sufficient to eliminate MLL-AF9 cells in mice. In full agreement, secondary transplantation experiments with these AML cells show no difference in latency between DOX-treated and non-treated controls (data not shown). These data indicate the tumor-suppressing activities of miR-139 in MLL-AF9 AML.
To gain mechanistic insight, we performed mRNA sequencing of DOX-treated MLL-AF9-i139 and untreated clones and found that a subset of genes were differentially expressed between these populations (Supplementary Fig. 2D, Supplementary Table 4). We established that genes that inhibit cell cycle progressions, such as Btg2, Cdkn1a, and Cdkn2d, and pro-apoptotic genes such as Bmf, Dusp1, Rnasel, Trp53inp1, Ypel3, and Zc3h12a were upregulated in DOX-treated MLL-AF9-i139 cells (Supplementary Table 4, Supplementary Fig. 2F). Furthermore, we noted that predicted miR-139 targets such as Eif4g2, Ptprt and Hpgd were downregulated in miR-139 expressing MLL-AF9 cells (Fig. 2G, Supplementary Table 4).
Next we wanted to validate miR-139 targets that mediate its tumor suppressor activity in MLL-AF9 cells. We performed a genome-wide CRISPR-KO screen to identify genes critical for MLL-AF9 survival or proliferation (Supplementary Fig. 2E). After 14 days, cells with sgRNAs that target such genes will be lost. Confirming the effectivity of our sgRNA screen, we found that sgRNAs targeting Men1 (six sgRNAs), a crucial co-factor for MLL-AF9 [30], the PRC2 subunits Eed (three out of six sgRNAs) and Rbbp4 (five out of six sgRNAs), Dot1l (five out of six sgRNAs) and Mllt3 (four out of six sgRNAs) were lost (Fig. 2H, Supplementary Table 5). We found that MLL-AF9 cells with sgRNAs targeting Ptprt (three out of six) Hpgd (five out of six) and Eif4g2 (five out of six) were also lost, suggesting that expression of our identified miR-139-targets is essential for cell survival (Fig. 2H, Supplementary Table 5). Validation experiments with single sgRNAs targeting Hpgd, Eif4g2, and Ptprt in colony-forming unit assays confirmed these results and showed that the depletion of these miR-139 target genes could, at least in part, phenocopy miR-139 expression in MLL-AF9 cells (Supplementary Fig. 2G). Furthermore, luciferase-based miRNA target validation assays confirmed that Hpgd and, Eif4g2 and Ptprt are direct targets of miR-139 (Supplementary Fig. 2H). Taken together, these data show that miR-139 expression and the downregulation of miR-139 targets inhibit MLL-AF9 leukemia.
Mir139 is epigenetically silenced by PRC2 in MLL-AF9 cells
We next investigated how MIR139 expression is regulated. MIR139 is epigenetically silenced in AML, including the THP-1 cell line that expresses MLL-AF9 [13]. We hypothesized that Mir139 silencing by histone modifications is critical for MLL-AF9 AML. To test this, we treated MLL-AF9 and MLL-AF9-Mir139KO cells with Trichostatin-A (TSA) or valporic acid (VPA), which are inhibitors of class-I and II histone deacetylases. We found that MLL-AF9 cells treated with either TSA or VPA, were significantly reduced in their colony-forming capacity compared with MLL-AF9-Mir139KO cells (Supplementary Fig. 3A). These results suggest a role for MIR139 epigenetic silencing in MLL-AF9 AML expansion and survival.
Next, we investigated the epigenetic landscape of Mir139 by reanalyzing publicly available ChIP-seq data sets from mouse MLL-AF9 cells and WT HSPCs [29, 31, 32]. Mir139 is located in intron-1 of the Pde2a host gene with the same orientation, downstream of the highly conserved putative Pde2a promoter (P). As expected, H3K4me3 peaks overlapped with P and H3K27Ac peaks overlapped with enhancer region-1 (E1) and E2 (Fig. 3A). In these genomic regions we noted two POL-II peaks: one located at the first exon of Pde2a and one on E2, in intron-1 of Pde2a (Fig. 3A). We found H3K27me3 levels, which are associated with epigenetic silencing, at P, E1, and E2 in MLL-AF9 cells (Fig. 3A). MLL-AF9 cells treated with UNC1999, a specific inhibitor of the methyltransferases EZH1 and EZH2 [29], showed decreased H3K27me3 and increased H3K27Ac levels compared to UNC2400 control inhibitor-treated cells. In addition, ChIP-seq data revealed SUZ12 binding to P, E1, and E2, which was decreased in cells treated with UNC1999 (Fig. 3A).
Aberrant enhancer DNA methylation is acquired during malignant transformation [33]. PRC2, a chromatin-modifying enzyme that catalyzes histone-H3 lysine 27 trimethylation, is known to have a critical role in MLL-AF9 pathogenesis [22, 23] and prefers binding to methylated DNA via AEBP2 [34]. To address the role of PRC2 in context of MIR139, we determined the CpG methylation status of human MLL-AF9 cell lines Molm-13 and THP-1. We observed that a small percentage of CpGs present in the MIR139 promoter region of Molm-13 (22.73%) and THP-1 (6.36%) are methylated (Fig. 3B). Although there is a lower density of CpGs in the enhancer regions close to MIR139, we detected an increased percentage of methylated CpGs in E1 (67% and 79%) and E2 (60% and 87%) in Molm-13 cells and THP-1 cells, respectively (Fig. 3B).
To experimentally validate the relevance of PRC2-mediated silencing of Mir139, we treated MLL-AF9 cells with UNC1999 and determined cell survival compared with MLL-AF9-Mir139KO cells. UNC1999 activity was confirmed by reduced H3K27me3 levels at the P, E1, and E2 (Fig. 3C). We observed a decreased viability of MLL-AF9 cells compared with MLL-AF9-Mir139KO cells, strongly suggesting that UNC1999 treatment activates miR-139 expression (Fig. 3D). Indeed, loss of cell viability coincided with up to 25-fold increased levels of miR-139-5p and up to 20-fold increased miR-139-3p expression (Fig. 3E). Notably, treatment of MLL-AF9 cells with UNC2400 did not upregulate miR-139 and sustained cell viability (Supplementary Fig. 3B, C). Expression of miR-139-5p was not induced when WT HSPCs were treated with UNC1999 (Supplementary Fig. 3D). Cdkn2a is a known target of PRC2 in MLL-AF9 AML [22, 23]. In agreement, we observed a three to sixfold upregulation of Cdkn2a (Supplementary Fig. 3E). The expression of Pde2a was unaffected by UNC1999 (Supplementary Fig. 3F). This mechanism is conserved between mouse and human, because comparable results were obtained with Molm-13 (Fig. 3F, G), THP-1 (Supplementary Fig. 3G, H) and primary MLL-AF9 patient samples (Fig. 3H, I). In addition, UNC1999 treatment of a panel of AML cell lines caused decreased cell viability and increased miR-139 expression (Supplementary Fig. 3I, J). This suggests that PRC2-mediated MIR139 silencing may not be exclusive for MLL-AF9 AML. Taken together, these data indicate that MLL-AF9 silences MIR139 by a PRC2-mediated mechanism.
E1 and E2 control the expression of Mir139
To further investigate the role of the P, E1, and E2 in Mir139 expression, we deleted these genomic regions in mice (Fig. 4A). We were unable to generate mice with genomic deletion of the Pde2a promoter, which overlaps with exon-1, suggesting that a Pde2a KO is embryonically lethal. In contrast, E1 and E2 deletion mutant mice were viable and developed normally. Under physiological conditions, deletion of either E1 or E2 caused a >60% reduction of miR-139-5p expression, a 40–50% reduction of miR-139-3p expression in WT HSPCs and a 70–80% reduction of Pde2a expression (Fig. 4B, C). Next, we investigated whether E1 and E2 are involved in Mir139 silencing in MLL-AF9 cells. Therefore, we generated MLL-AF9-E1KO and MLL-AF9-E2KO cells. Similar to MLL-AF9 cells, these cells were positive for GR-1, CD11b, CD16/32, c-Kit, and negative for CD3 (Fig. 4D). Next, we treated these cells with UNC1999 and noted reduced cell death of MLL-AF9-E1KO and MLL-AF9-E2KO cells compared to MLL-AF9 cells, suggesting that the miR-139 induction is affected (Fig. 4E). Indeed, we found that upon UNC1999 treatment, miR-139-5p and miR-139-3p were not upregulated in MLL-AF9-E1KO cells (Fig. 4F). Notably, Pde2a expression was not affected in UNC1999-treated MLL-AF9-E1KO cells (Fig. 4G). MLL-AF9-E2KO cells showed a significantly reduced miR-139-5p and miR-139-3p induction, which coincided with slightly reduced Pde2a levels with 5 µM UNC1999 (Fig. 4F, G). Together, these data indicate that both E1 and E2 regions control Mir139 expression in AML.
POLR2M silences MIR139 in MLL-AF9 cells
To identify novel factors that are involved in transcriptional silencing of Mir139 in MLL-AF9 cells, we performed a genome-wide CRISPR-KO screen [35]. We used MLL-AF9-Mir139KO cells as a reference, which allowed for screening of factors that specifically silence Mir139 transcription. We expected that inactivation of genes encoding for factors responsible for Mir139 silencing would upregulate miR-139 expression and induce apoptosis in MLL-AF9 cells, but not in MLL-AF9-Mir139KO cells (Fig. 5A). We selected all sgRNAs with 10 or more reads in MLL-AF9 cells and MLL-AF9-Mir139KO cells (MLL-AF9-WT + MLL-AF9-Mir139KO ≥ 10) after 14 days of incubation (Fig. 5B). We reasoned that a higher number of sgRNAs lost per gene will increase the chance that these genes are relevant for Mir139 regulation. According to our analysis of control sgRNAs, the chance that a loss of five sgRNAs or more per gene is an artifact is >0.0016%. Out of the genes shown in Fig. 5B, we identified only 16 genes targeted by 5–6 sgRNAs that were significantly reduced by ≥ 10 fold in MLL-AF9 cells compared with MLL-AF9-Mir139KO cells (Supplementary Fig. 4A, Supplementary Table 6). Among these 16 genes, RNA Polymerase 2 Subunit M (Polr2m), involved in stable transcriptional pausing of POL-II [36,37,38], was the only negative transcriptional regulator and was selected for further validation (Fig. 5C). CRISPR-Cas9-mediated KO of Polr2m reduced colony outgrowth and cell viability of MLL-AF9 cells compared with MLL-AF9-139-KO cells (Fig. 5D). In agreement, POLR2M depletion reduced the viability of Molm-13 cells and primary MLL-AF9 cells from patients (Fig. 5E). Furthermore, sgRNA-mediated targeting of POLR2M caused an increase of pri-miR-139 and mature miR-139 expression in Molm-13 cells and in primary MLL-AF9 patient samples compared with control sgRNA treated cells (Fig. 5F, Supplementary Fig. 4B, C). In these experiments, Pde2a expression was not affected by Polr2m depletion (Supplementary Fig. 4D). These results were confirmed in various human AML cell lines with different oncogenic aberrations (Fig. 5G, Supplementary Fig. 4D). Collectively, these data suggest that POLR2M is a silencing factor of MIR139 downstream of PRC2, an oncogenic mechanism that may not be exclusive for MLL-AF9 AML.
POLR2M binds to E1, E2, and the transcriptional start site of MIR139
Because POLR2M binds to POL-II to mediate stable transcriptional pausing [36,37,38], we hypothesized that POLR2M is bound at the POL-II interaction sites within the MIR139 locus. We used publicly available data sets to determine enrichment of H3K4me3, H3K27Ac, H3K4me1, and POL-II binding on E1, E2, and P regions (Supplementary Fig. 5). In our analysis, we included a previously identified MIR139 transcriptional start site (TSS) [13]. Third, inhibition of methyltransferases EZH1 and EZH2 by UNC1999 greatly induced miR-139 expression in MLL-AF9 AML patient samples and other subtypes of AML, demonstrating direct silencing of Mir139 by PRC2 in AML, which is in agreement with previous findings in solid cancers [44, 45]. This suggests that the PRC2-mediated MIR139 silencing is a general mechanism in cancer and may be a key event in oncogenesis. Fourth, we identified Eif4g2, Ptprt, and Hpgd as miR-139 targets, which are involved in MLL-AF9 cell survival. Deregulation of these three genes by mutation, disruption of miRNA-mediated regulation or genomic aberrations are frequently found in different types of cancer [13, 46,47,48,49,64]. A recent study showed that DROSHA and DGCR8 interact with super-enhancer regions and boost miRNA production [65]. In agreement with these studies, our data suggest a mechanism in which the RNA-processing machinery is directly coupled to enhancer-mediated transcription of MIR139. This interaction may occur under cellular stress conditions resulting in increased miR-139 expression and cell death to prevent oncogenic transformation.
POL-II is the key factor responsible for the transcription of miRNAs [66]. Although stable paused transcription seems a logical downstream consequence of PcG-mediated gene silencing [67], the factors involved in the molecular mechanism of PRC2-mediated transcriptional pausing remained unknown. We found that POLR2M is recruited in a PRC2-dependent fashion to E1 and E2 to silence MIR139 expression. POLR2M interacts with the POL-II complex to pause transcription [38, 68, 69]. Promoter-proximal pausing of POL-II at TSSs has been correlated with H3K27me3 and PcG-silenced genes [70,71,72]. Paused POL-II complexes have also been found at enhancer regions [73]. Together, our study indicates that POLR2M interacts with E1 and E2 and silences MIR139 expression in MLL-AF9.
Our data demonstrate in different ways that POLR2M is a direct silencer of MIR139 in AML. First, POLR2M depletion in MLL-AF9 patient samples and human AML cell lines induced the expression of pri-miR-139. Although the levels of the mature miR-139-5p and miR-139-3p are low compared with experiments with UNC1999-mediated repression of PRC2, this could be explained by the fact that the CRISPR-Cas9-mediated depletion of POLR2M by lentiviral transduction is an asynchronous process. This causes a heterogeneous induction of MIR139 expression and subsequent cell death, thereby underestimating miR-139 levels. Second, POLR2M-depleted MLL-AF9 cells were lost in our CRISPR-Cas9 screen and validation experiments, whereas POLR2M-depleted MLL-AF9-Mir139KO cells survived, indicating that POLR2M-controlled survival is specifically mediated by the silencing of MIR139. Third, we showed that POLR2M is bound to the E1 and E2 regions and TSS of MIR139. Depletion of POLR2M at these loci was observed as a result of UNC1999-mediated inhibition of PRC2 and coincides with induction of miR-139 expression and cell death.
In conclusion, we have identified key molecular mechanisms that control tumor suppressor MIR139 in MLL-AF9 leukemia and report functionally relevant targets of miR-139-mediated cell death of MLL-AF9 cells. Furthermore, our findings reveal a PRC2-dependent POLR2M-mediated silencing mechanism of the MIR139 tumor suppressor in MLL-AF9 leukemia. The specific interaction of POLR2M with the POL-II complex is essential for transcriptional inhibition [74]. Therefore, POLR2M would be interesting for therapeutic targeting, for instance by molecularly interfering with the interaction with POL-II, thereby activating MIR139 expression and eliminating AML. Together, our findings highlight the importance of POLR2M-mediated silencing of MIR139 in MLL-AF9 AML.
Data availability
The NGS data generated in this paper is available from the GEO database with the following identifiers. GSE160404: RNA-seq of WT HSPCs, Mir139KO HSPCs and MLL-AF9 cells GSE160405: RNA-seq of MLL-AF9-i139 cells treated with and without DOX GSE160403: DNA-seq of MLL-AF9 WT and MLL-AF9 Mir139KO cells transduced with LentiCRISPRv2 GeCKOv2 sgRNA library. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the identifier PXD022488.
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Acknowledgements
For this work, C.J.S. and I.V.Z. were supported by the Dutch Cancer Foundation (KWF), grant no.: 10948. Furthermore, the Dutch Research Council (NWO) Medium Investment Grant 91116004 (partly financed by ZonMw) to P.A.v.V. also supported the work. Furthermore, we would like to thank Yvette Caljouw, Fabiënne van Opstal, Bernard Stikker and Stijn van den Broek for their technical assistance and Dr. G. Dal Collo and Dr. C. Kiernan for critically reviewing the manuscript. In addition, we would like to acknowledge Dr. R. Delwel and Dr. R. Avelino for their experimental and technical advice.
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C.J.S., P.D.K., and S.J.E. wrote the manuscript. S.J.E. designed the project. C.J.S., I.V.Z., A.Ö., and A.V.H.B. performed most of the experiments. G.M.C.J. and P.A.V.V. performed the proteomic analysis. E.B. performed next-generation sequencing (NGS). L.G.L. performed the bioinformatics analysis of the RNA-sequence data. C.J.S., C.S., and J.S.A.V. performed CRISPR-KO screens. R.W.W.B. and W.F.J. performed CRISPR library sequencing and bioinformatic analysis. A.M. generated the E1KO and E2KO mouse models. V.H.J.vd V. wrote the METC protocol and collected human MLL-AF9 patient samples. E.K., M.B., and M.A.J. performed the mouse leukemia and MLL-AF9 stem cell experiments.
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Stavast, C.J., van Zuijen, I., Karkoulia, E. et al. The tumor suppressor MIR139 is silenced by POLR2M to promote AML oncogenesis. Leukemia 36, 687–700 (2022). https://doi.org/10.1038/s41375-021-01461-5
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DOI: https://doi.org/10.1038/s41375-021-01461-5
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