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Mixed-lineage leukemia fusion proteins activate their target genes predominantly by stimulating transcriptional elongation. A core component necessary for this activity is cyclin-dependent kinase 9. Here we explored the effectiveness of small molecules targeting this enzyme as potential therapeutics. A screen of seven compounds with anti-CDK9 activity applied to a panel of leukemia cell lines identified flavopiridol and the experimental inhibitor PC585 as superior in efficacy with inhibitory concentrations in the submicromolar range. Both substances induced rapid dephosphorylation of the RNA polymerase II C-terminal domain, accompanied by downregulation of CDK9-dependent transcripts for MYC and HOXA9. Global gene expression analysis indicated the induction of a general stress response program, culminating in widespread apoptosis. Importantly, colony-forming activity in leukemia lines and primary patient samples could be completely inhibited under conditions that did not affect native precursors from bone marrow. In vivo application in a mouse transplant model significantly delayed disease with PC585 showing also oral activity. These results suggest CDK9 inhibition as novel treatment option for mixed-lineage leukemia.

Mixed lineage leukemia (MLL) fusion proteins are derived from translocations at 11q23 that occur in aggressive subtypes of leukemia. As a consequence, MLL is joined to different unrelated proteins to form oncogenic transcription factors. Here we demonstrate a direct interaction between several nuclear MLL fusion partners and present evidence for a role of these proteins in histone binding. In two-hybrid studies, ENL interacted with AF4 and AF5q31 as well as with a fragment of AF10. A structure-function analysis revealed that the AF4/AF5q31/AF10 binding domain in ENL coincided with the C-terminus that is essential for transformation by MLL-ENL. The ENL/AF4 association was corroborated by GST-pulldown experiments and by mutual coprecipitation. Both proteins colocalized in vivo in a nuclear speckled pattern. Moreover, AF4 and ENL coeluted on sizing columns together with the known ENL binding partner Polycomb3, suggesting the presence of a multiprotein complex. The overexpression of ENL alone activated a reporter construct and a mutational screen indicated the conserved YEATS domain as essential for this function. Overlay and pulldown-assays finally showed a specific and YEATS domain-dependent association of ENL with histones H3 and H1. In summary, our studies support a common role for nuclear MLL fusion partners in chromatin biology.

Mixed-lineage leukemia (MLL) fusion proteins are associated with a unique class of leukemia that is characterized by the simultaneous expression of lymphoid-specific as well as myeloid-specific genes. Here we report the first experimental model of MLL. Murine bone marrow cells were retrovirally transduced to express the MLL-eleven nineteen leukemia (MLL-ENL) fusion protein. When cultivated in flt-3 ligand, stem cell factor and interleukin-7 (IL-7) in a stroma-free culture system MLL-ENL-transduced as well as control cells showed a wave of B-lymphopoiesis. Whereas the controls exhausted their proliferative capacity in a CD19+/B220+ state, a continuously proliferating CD19-/B220+ cell population emerged in the MLL-ENL-transduced cultures. Despite the lymphoid surface marker, these cells were of monocytoid morphology. The immortalized cells contained unrearranged retrovirus, expressed MLL-ENL mRNA and were able to grow in syngenic recipients. From the diseased animals an MLL-ENL positive, B220+/CD19- cell type could be reisolated and cultivated in vitro. In analogy to human MLL, MLL-ENL-transformed cells not only coexpressed lymphocyte-specific (rag1, rag2, pax5, Tdt) and monocyte-specific genes (lysozyme, c-fms), but also showed rearrangements of the genomic immunoglobulin locus. This model shows that MLL-ENL influences events of early lineage determination and it will enable the investigation of the underlying molecular processes.

Chromosomal translocations that fuse the mixed lineage leukemia gene (MLL) to a variety of unrelated partner genes are frequent in pediatric leukemias. The novel combination of genetic material leads to the production of active oncoproteins that depend on the contributions of both constituents. In a search for a common function amongst the diverse group of MLL fusion partners we constructed artificial fusions joining MLL with generic transactivator and repressor domains (acidic blob, GAL4 transactivator domain, Herpes simplex VP16 activation domain, KRAB repressor domain). Of all constructs tested, only MLL-VP16 was able to transform primary bone marrow cells and to induce a block of early myeloid differentiation like an authentic MLL fusion. Interestingly, the transformation capability of the artificial MLL fusions was correlated with the transcriptional potential of the resulting chimeric protein but it was not related to the strength of the isolated transactivation domain that was joined to MLL. These results prove for the first time that a general biological function - transactivation - might be the common denominator of many MLL fusion partners.

Alterations of the proto-oncogene MLL (mixed lineage leukemia) are characteristic for a high proportion of acute leukemias, especially those occurring in infants. The activation of MLL is achieved either by an internal tandem duplication of 5' MLL exons or by chromosomal translocations that create chimeric proteins with the N-terminus of MLL fused to a variety of different partner proteins. A domain of MLL with significant homology to the eukaryotic DNA methyltransferases (MT domain) has been found to be essential for the transforming potential of the oncogenic MLL derivatives. Here we demonstrate that this domain specifically recognizes DNA with unmethylated CpG sequences. In gel mobility shifts, the presence of CpG was sufficient for binding of recombinant GST-MT protein to DNA. The introduction of 5-methylCpG on one or both DNA strands precluded an efficient interaction. In surface plasmon resonance a KD of approximately 3.3 x 10(-8) M was determined for the GST-MT/DNA complex formation. Site selection experiments and DNase I footprinting confirmed CpG as the target of the MT domain. Finally, this interaction was corroborated in vivo in reporter assays utilizing the DNA-binding properties of the MT domain in a hybrid MT-VP16 transactivator construct.

Investigation of the activity of a family of fusion proteins that cause aggressive leukemia suggests transcriptional elongation as a new mechanism for oncogenic transformation., Fusion proteins composed of the histone methyltransferase mixed-lineage leukemia (MLL) and a variety of unrelated fusion partners are highly leukemogenic. Despite their prevalence, particularly in pediatric acute leukemia, many molecular details of their transforming mechanism are unknown. Here, we provide mechanistic insight into the function of MLL fusions, demonstrating that they capture a transcriptional elongation complex that has been previously found associated with the eleven-nineteen leukemia protein (ENL). We show that this complex consists of a tight core stabilized by recursive protein–protein interactions. This central part integrates histone H3 lysine 79 methylation, RNA Polymerase II (RNA Pol II) phosphorylation, and MLL fusion partners to stimulate transcriptional elongation as evidenced by RNA tethering assays. Coimmunoprecipitations indicated that MLL fusions are incorporated into this complex, causing a constitutive recruitment of elongation activity to MLL target loci. Chromatin immunoprecipitations (ChIP) of the homeobox gene A cluster confirmed a close relationship between binding of MLL fusions and transcript levels. A time-resolved ChIP utilizing a conditional MLL fusion singled out H3K79 methylation as the primary parameter correlated with target expression. The presence of MLL fusion proteins also kept RNA Pol II in an actively elongating state and prevented accumulation of inhibitory histone methylation on target chromatin. Hox loci remained open and productive in the presence of MLL fusion activity even under conditions of forced differentiation. Finally, MLL-transformed cells were particularly sensitive to pharmacological inhibition of RNA Pol II phosphorylation, pointing to a potential treatment for MLL. In summary, we show aberrant transcriptional elongation as a novel mechanism for oncogenic transformation., Author Summary The expression level of a gene needs to be precisely adjusted to ensure proper function. Adjustments can be imposed at different stages during the overall process of gene expression, including transcription initiation, transcript elongation, and transcript processing. If control of one of these mechanisms fails, aberrant gene expression can occur, which may have severe consequences such as cellular transformation and the development of cancer. Here, we show that a class of aberrant fusion proteins that are causal in mixed-lineage leukemia (MLL) hijacks a transcriptional elongation complex. We analyze the architecture of this transcriptional elongation complex and demonstrate that the complex is targeted by MLL fusion proteins to genes that should normally be silenced to allow maturation of hematopoietic cells. We show that this mistargeting causes constitutive expression of the respective genes, which likely leads to inhibition of blood cell differentiation at a precursor cell stage in which the cells are highly proliferative. Such abnormal precursor cells have been shown previously to be resistant to normal differentiation signals and to form the leukemia-initiating population. We further show here that cells carrying MLL fusion proteins are more sensitive to chemical inhibition of transcriptional elongation than leukemic cells of different etiology. Our results propose transcriptional elongation as a new oncogenic mechanism and point to a potential specific therapy for this hard-to-cure leukemia.

The mixed-lineage leukemia (MLL) family of histone methyltransferases has become notorious for the participation of the founding member, MLL, in fusion proteins that cause acute leukemia. Despite structural conservation, no other MLL homolog has so far been found in a similar arrangement. Here, we show that fusion proteins based on Mll2, the closest relative of MLL, are incapable of transforming hematopoietic cells. Elaborate swap experiments identified the small CxxC zinc-binding region of Mll2 and an adjacent 'post-CxxC' stretch of basic amino acids as the essential determinants for the observed difference. Gel shift experiments indicated that the combined CxxC and post-CxxC domains of MLL and Mll2 possess almost indistinguishable DNA-binding properties in vitro. Within the cellular environment, however, these motifs guided MLL and Mll2 to a largely nonoverlapping target gene repertoire, as evidenced by nuclear localization, reporter assays, and measurements of homeobox gene levels in primary cells expressing MLL and Mll2 fusion proteins. Therefore, the CxxC domain appears to be a promising target for therapies aimed at MLL fusion proteins without affecting the general function of other MLL family members.

MLL fusion proteins are oncogenic transcription factors that are associated with aggressive lymphoid and myeloid leukemias. We constructed an inducible MLL fusion, MLL-ENL-ERtm, that rendered the transcriptional and transforming properties of MLL-ENL strictly dependent on the presence of 4-hydroxy-tamoxifen. MLL-ENL-ERtm-immortalized hematopoietic cells required 4-hydroxy-tamoxifen for continuous growth and differentiated terminally upon tamoxifen withdrawal. Microarray analysis performed on these conditionally transformed cells revealed Hoxa9 and Hoxa7 as well as the Hox coregulators Meis1 and Pbx3 among the targets upregulated by MLL-ENL-ERtm. Overexpression of the Hox repressor Bmi-1 inhibited the growth-transforming activity of MLL-ENL. Moreover, the enforced expression of Hoxa9 in combination with Meis1 was sufficient to substitute for MLL-ENL-ERtm function and to maintain a state of continuous proliferation and differentiation arrest. These results suggest that MLL fusion proteins impose a reversible block on myeloid differentiation through aberrant activation of a limited set of homeobox genes and Hox coregulators that are consistently expressed in MLL-associated leukemias.

The translocation t(11;19) is frequently found in acute leukemia in infants. This event truncates the proto-oncogene MLL and fuses the 5′ end of MLL in frame with the ENL gene. ENL contributes a crucial protein–protein interaction domain to the resulting oncoprotein MLL–ENL. Here we show by yeast two-hybrid assays, GST-pull-down experiments and in a far western blot analysis that this domain is necessary and sufficient to recruit a novel member of the human Polycomb protein family (hPc3). hPc3 RNA was detected throughout the human hematopoietic system. Similar to other Polycomb proteins hPc3 acts as a transcriptional repressor. The ENL-hPc3 interaction was verified by mutual co-precipitation of the proteins from cell extracts. ENL and hPc3 tagged with fluorescent proteins co-localized in living cells in a nuclear dot pattern. An internal region of hPc3 was responsible for binding to ENL. Finally, hPc3 binds to the C-terminus of AF9, another common MLL fusion partner. The recruitment of a repressive function by ENL opens up a new insight into a possible mechanism of leukemogenesis by the fusion protein MLL–ENL.

Translocations of the chromosomal locus 11q23 that disrupt the MLL gene (alternatively ALL-1 or HRX) are frequently found in children's leukemias. These events fuse the MLL amino terminus in frame with a variety of unrelated proteins. Up to date, 16 different fusion partners have been characterized and more are likely to exist. No general unifying property could yet be detected amongst these proteins. We show here that the frequent MLL fusion partner ENL at 19p13.1 interacts with the human homologue of the mouse Abl-Interactor 1 (ABI1) protein. ABI1 in turn, is fused to MLL in the t(10;11)(p11.2;q23) translocation. ABI1 was identified as an ENL binding protein by a yeast two-hybrid screen. The interaction of ENL and ABI1 could be verified in vitro by far-Western blot assays and GST-pulldown studies as well as in vivo by co-immunoprecipitation experiments. A structure-function analysis identified an internal region of ENL and a composite motif of ABI1 including an SH3 domain as mutual binding partners. These data introduce novel aspects that might contribute to the understanding of the process of leukemogenesis by MLL fusion proteins.

Abstract 2443 MLL fusion proteins are potent leukemogenic agents that are created by chromosomal translocations. These events join the N-terminus of the histone methyltransferase MLL to a variety of different fusion partners. Some time ago we showed that a subgroup of frequently occurring MLL fusion partners, including ENL, assemble a novel transcriptional elongation complex termed EAP [1,2] (elongation assisting proteins, later also called AEP for AF4-ENL proteins [3] or SEC for super elongation complex [4]). Aberrant recruitment of EAP to targets normally under control of MLL leads to abnormal stimulation of transcriptional elongation through the activity of pTEFb (positive transcription elongation factor b). This is accompanied by enhanced H3K79 methylation catalyzed by the histone methyltransferase DOT1L that also interacts directly with EAP. As a consequence MLL-targets, like the clustered Hox-homeobox genes, are ectopically expressed and contribute to hematopoietic transformation. Paradoxically, we also observed a persistent copurification of EAP with members of the polycomb repressive complex 1 (PRC1). PRC1 inhibits gene expression and ubiquitinylates H2A. Here we confirm the association of EAP with PRC1 and we show that interaction of ENL and CBX8 (chromobox 8) is necessary for EAP to neutralize the repressive function of PRC1 as prerequisite for efficient Hox expression and transformation. Mass spectrometry and immunological detection verified that ENL is also present in biochemical preparations of PRC1. A study of the architecture of this interaction demonstrated that a CBX8-ENL dimer bridges the PRC1 core to EAP. Interestingly, an analysis of the binding interfaces revealed that EAP would be able to home in on PRC1 engaged chromatin whereas the reverse was not possible because Dot1l and CBX8 could not bind ENL simultaneously. This also suggested that the activity of these two chromatin modifying activities is mutually exclusive. Indeed CBX8 counteracted MLL-ENL in vivo. Introduction of CBX8 into MLL-ENL expressing cells opposed transformation, reduced H3K79 methylation and induced H2A ubiquitinylation at key targets for MLL fusions like the Hox-locus. Deletion of the ENL interaction domain from CBX8 but preserving its PRC1 dependent functions created a “super-repressor” indicating that EAP recruitment via ENL is able to attenuate PRC1 activity. This seems to be a normal function of EAP that exists independently of the MLL fusion context as overexpression of ENL lead to derepression of polycomb controlled genes also in embryonic stem cells. In agreement with these results an elongation reporter system revealed that EAP can completely offset PRC1 repression but only if direct interaction between ENL and CBX8 is possible. During hematopoietic differentiation genes involved in the decision between self renewal and differentiation are often controlled by transcriptional elongation. PRC1 has been found to play a role in this setting and obviously MLL fusion proteins have found yet another method to interfere with this process. Disclosures: No relevant conflicts of interest to declare.

The mixed lineage leukemia (MLL) family of histone methyltransferases has become notorious for the participation of the founding member MLL in fusion proteins that cause acute leukemia. Despite a high overall structural conservation no other MLL homolog has been found involved in leukemogenic fusion proteins. This surprising fact might be either due to a relative genomic stability of the MLL2 locus that prevents chromosomal translocations or MLL2 might be altogether incapable of contributing to oncogenic fusions because of functional constraints. Here we demonstrate the latter to be true for fusion proteins based on MLL2, the closest relative of MLL. A MLL2-ENL protein constructed in analogy to the highly leukemogenic MLL-ENL was incapable of transforming primary hematopoietic cells. Elaborate swap experiments identified the zinc binding “CxxC”- region of MLL2 and an adjacent “post-CxxC” stretch of basic amino acids as the essential determinants for the observed difference between MLL and MLL2. Surprisingly gel shift experiments indicated that the CxxC and post-CxxC domains of MLL and MLL2 conferred almost indistinguishable in vitro DNA binding properties. However, in vivo these motifs guided MLL-ENL and MLL2-ENL to a largely non-overlapping gene repertoire. Divergent nuclear localization, a distinct potency to activate a MLL model promoter in reporter assays, and measurements of homeobox gene levels in primary cells expressing MLL and MLL2 fusion proteins all argued for a separate target site selection of the two fusions. Therefore, the CxxC domain appears to be largely responsible for target finding and as a consequence this domain is a promising object for therapies aimed at MLL fusion proteins without affecting the general function of other MLL family members.

Chromosomal translocations at 11q23 are characteristic for a subset of particularly aggressive acute lymphoid and myeloid leukemias. This event fuses the mixed lineage leukemia (MLL) gene to a puzzling variety of seemingly unrelated fusion partners to create novel transcription factors with potent oncogenic activity. Despite the molecular heterogeneity, MLL−associated leukemias show similar clinical presentations and an almost identical gene expression pattern regardless of the translocation partner. We and others previously identified interactions between individual MLL translocation partners suggesting that these might share a common mechanism for transformation. To characterize these interactions in more detail we generated a HEK293−derived producer line expressing a FLAG−tagged derivative of the frequent fusion partner ENL. Double affinity purification of nuclear extracts on FLAG and ENL antibody resins reproducibly yielded a macromolecular complex of 10 proteins we term MPAC, for MLL Partner Associated Complex, which in addition to ENL includes the MLL fusion partners AF4, AF9 and AF5q31, and two components involved in transcriptional elongation: pTEFb and DOT1L. The pTEFb dimer consists of cyclin T1/2 and CDK9 and is responsible for serine−2 phosphorylation of the C−terminal repeat domain of elongating RNA Polymerase II. DOT1L is the only known histone methyltransferase that catalyzes dimethylation of H3K79, a modification introduced during elongation of actively transcribed transcription units. Surprisingly, PC3 and RING1b, members of the polycomb repressive complex I were also identified in the MPAC complex. Further examination demonstrated a direct interaction of ENL with DOT1L through C−terminal interaction domains by yeast 2−hybrid, pulldown and colocalization experiments. Knock−down of ENL diminished global H3K79 dimethylation and also impaired various promoters in transient reporter assays suggesting the MPAC complex is involved in transcriptional regulation mediated by DOT1L, even in the absence of MLL fusion proteins. In summary, our results indicate that the most common MLL fusion partners are associated in an hitherto undescribed complex involved in transcriptional elongation.

Summary Stimulation of transcriptional elongation is a key activity of leukemogenic MLL fusion proteins. Here, we provide evidence that MLL-ENL also inhibits Polycomb-mediated silencing as a prerequisite for efficient transformation. Biochemical studies identified ENL as a scaffold that contacted the elongation machinery as well as the Polycomb repressive complex 1 (PRC1) component CBX8. These interactions were mutually exclusive in vitro, corresponding to an antagonistic behavior of MLL-ENL and CBX8 in vivo. CBX8 inhibited elongation in a specific reporter assay, and this effect was neutralized by direct association with ENL. Correspondingly, CBX8-binding-defective MLL-ENL could not fully activate gene loci necessary for transformation. Finally, we demonstrate dimerization of MLL-ENL as a neomorphic activity that may augment Polycomb inhibition and transformation.