Blood cancers are frequently driven by chromosomal translocations that generate disease-causing fusion proteins — formed by the joining of fragments of two proteins. Fusion proteins that involve the regulatory protein mixed lineage leukaemia (MLL) are commonly found in aggressive paediatric leukaemias and are associated with poor prognosis. There is, therefore, a great need to develop therapeutic strategies for leukaemias that involve MLL-rearranged (MLL-r) fusion proteins. In this issue, Erb et al. and Wan et al. converge on the identification of the protein ENL as a crucial factor for the viability of MLL-r cells in leukaemia.
Histone proteins are structural and signalling factors around which DNA is wrapped in cells. Their modification by the addition or removal of molecular groups regulates gene expression. A notable structural feature of ENL is a distinctive fold of about 75 amino acids called a YEATS domain, which is a reader of acetylation — it recognizes and associates with residues of the amino acid lysine in histones that have been modified by the addition of an acetyl moiety. Erb et al. and Wan et al. provide compelling evidence that this 'reader' ability of ENL on acetylated histones is crucial to the induction of MLL-r leukaemia.
MLL fusion partners are predominantly related to two protein complexes implicated in epigenetic regulation — the modulation of gene expression independently of DNA sequence. The first is the super elongation complex (SEC), which facilitates a phase of gene transcription called elongation. The second is the DOT1L-containing complex (DotCom), which adds methyl groups to the residue lysine 79 on histone H3 (abbreviated as H3K79). The translocations that generate these fusions typically occur on one of the two sets of chromosomes present in mammals.
The prevailing view is that MLL-containing fusion proteins promote the localization of SEC and DotCom, containing proteins encoded on both chromosomes (fusion and normal non-fused proteins), to regions of the genome where they drive the expression of genes that promote the development of leukaemia.
Erb et al. and Wan et al. uncover another, complementary mechanism of SEC and DotCom stabilization. The groups found that inactivation of ENL impaired the function of SEC and DotCom in MLL-r cells. The ability of ENL to physically associate with both SEC and DotCom suggests a model in which the protein — through recognition of acetylated H3 by its YEATS domain — coordinates SEC and DotCom stabilization and activity at abnormal regions of the genome.
This new model raises the possibility that drugs such as small-molecule inhibitors that target the ENL YEATS domain could selectively kill leukaemic MLL-r cells. Other cell types seem to be largely tolerant of ENL loss, but SEC, DotCom and ENL are ubiquitously expressed, so it will be important to understand the molecular basis of this difference in tolerance as such drugs are developed.
The requirement for ENL in MLL-r leukaemias is consistent with observations that properly regulated DOT1L activity is necessary for the development and maintenance of MLL-r cells. H3K79 methylation has long been associated, circumstantially, with genes actively undergoing transcription, and as the regulatory mechanisms that govern DOT1L activity come into sharper focus, a major unanswered question is how the signals encoded by this histone modification could directly influence transcription.
Methyl–lysine signals are typically connected to downstream processes by mechanisms analogous to those involved in the YEATS domain's reading of acetyl–lysine signals. Reader domains have been identified for all major histone methylation sites apart from H3K79. Furthermore, methylated lysines can be dynamically regulated by demethylase enzymes, but a demethylase that removes methyl groups at H3K79 is yet to be identified. Erb et al. and Wan et al. provide further motivation to find readers and demethylases for H3K79 methylation, which would be predicted to intersect with ENL-mediated signalling under both physiological and pathological conditions.
There is an emerging appreciation that epigenetic regulators can have fundamental roles in disease. This awareness has ushered in focused efforts to develop inhibitors that target these mechanisms to treat cancer. A DOT1L inhibitor has been evaluated in a clinical trial for MLL-r leukaemias (see go.nature.com/2lquysj for details). Intriguingly, Erb et al. showed that treating cells with a DOT1L inhibitor in conjunction with an ENL mutant that cannot recognize acetylated lysine suppressed the leukaemia-promoting gene-expression program more effectively than disruption of either protein alone, suggesting synergistic cooperation between these interventions.
Wan et al. also investigated the potential of combinatorial therapy to treat MLL-r leukaemia, targeting acetyl–lysine binding by both the ENL YEATS domain and another reader of lysine acetylation — the bromodomain of BET family proteins. BET proteins normally interact with SEC and promote transcriptional elongation. Drugs called BET inhibitors disrupt the binding of BET proteins to acetyl–lysine moieties, and there are currently about 20 clinical trials testing the efficacy of these drugs as cancer treatments. Wan and colleagues found that perturbation of the ENL YEATS domain combined with treatment with the BET inhibitor JQ1 was highly toxic to MLL-r leukaemic cells.
The effects of these combinatorial interventions highlight how the integration of multiple modified histone signals is instrumental in establishing the distinct epigenetic state of MLL-r leukaemia. As such, these cancers may be susceptible to a multi-pronged targeting approach that could increase therapeutic efficacy while mitigating the emergence of drug resistance, which is a risk with single-drug approaches.
Historically, drug hunters have focused on targeting enzymatic activities rather than protein–protein interactions. However, there is growing excitement — in part owing to the success of BET inhibitors — about therapies that target diverse reader domains. The binding pocket of the YEATS domain is attractive for drug development, because it is deep and amenable to the accommodation of acetyl–lysine along with larger analogous modifications. Thus, the discovery that MLL-r leukaemias are reliant on ENL not only provides fundamental insight into how cells integrate signals relating to transcription, but also has provocative implications for the treatment of a complex human disease.