Differential Regulation of c-Myc/Lin28 Discriminates Subclasses of Rearranged MLL Leukemia

Rearrangements of the 11q23 locus account for ~70% of infant ALL and ~50% of infant AML¹ and about 10% of leukemia overall. The prognosis for 11q23 patients is generally poor, however, outcomes vary depending on the fusion partner². Rearrangements fuse the N-terminus of MLL with one of >70 different partner genes that includes both nuclear and cytoplasmic proteins. Despite the different intracellular localization of these partner proteins, to date, all studied MLL fusion proteins (MLL-FPs) localize to chromatin in the nucleus and drive aberrant transcriptional activation. Recent seminal work by a number of groups has revealed that several of the most common nuclear translocation partner genes (including AF9, ENL, AFF1 (AF4), AFF4 (AF5q31), AF10, AF17 and ELL) assemble into a transcriptional activation complex that includes p-TEFb and/or the histone H3K79 methyltransferase DOT1l. Translocation of MLL with members of this complex results in deregulated transcriptional activation of target genes. Conversely, oligomerization motifs are necessary for transformation following 11q23 translocation with a cytoplasmic partner. However, these mechanisms fail to explain different survival outcomes observed in patients. Further, the transcriptional programs induced in these diverse 11q23 leukemias are currently not well understood. In this study, we examined the genome wide expression profiles in leukemic cells transformed by several MLL-FPs representative of nuclear translocations [t(9;11) (MLL-AF9), t(10;11) (MLL-AF10) and t(11;19) (MLL-ENL)] or cytoplasmic translocations [t(1;11) (MLL-AF1p), t(6;11) (MLL-AF6) and t(11;17) (MLL-Gas7)]. Leukemia cell lines established from mouse bone marrow cells expressing these MLL-FPs proliferated at different rates and mice transplanted with the transformed cells develop leukemia with different latencies remarkably consistent with differences observed in patients harboring different MLL translocations. To elucidate differences in the gene programs induced by different MLL-FPs we performed genome wide expression profiling by RNA-sequencing. These data demonstrated that while the MLL-AF9 and MLL-ENL fusion proteins induce very similar gene programs, the cytoplasmic fusion proteins (MLL-AF6, MLL-AF1p and MLL-GAS7) all possess unique gene signatures. We then performed a pathway analysis comparing nuclear fusion proteins and cytoplasmic fusion proteins and discovered the Myc transcription factor program as one of the top distinguishing features. Myc overexpression significantly increased the growth rate of slow-growing cells that also had low intrinsic Myc, while the growth rate change of more highly proliferative cells was minimal. While all leukemic cell lines were sensitive to the BET inhibitor JQ1 which regulates c-Myc expression, greater sensitivity was observed in those with low c-Myc expression demonstrating the universal importance of this gene program. The Myc target and micro RNA binding protein Lin28B is also differentially expressed between nuclear and cytoplasmic fusions. Negative regulation of miR-150 by Lin28B was observed in all MLL-FP cell lines, which is necessarily downregulated in 11q23 leukemias. We then investigated another Lin28B microRNA target let-7. Interestingly, let-7g expression was significantly increased in MLL-FP transformed cells associated with the longest disease latency. These data demonstrate that differential activation of the c-Myc/Lin28 program accounts for changes in let-7g expression and is associated with MLL-FP disease latency. These data also suggest that patients harboring different 11q23 rearrangements will respond differentially to therapeutic targeting of c-Myc expression dependent on fusion partner.

References:

1. Krivtsov AV, Armstrong SA. MLL translocations, histone modifications and leukaemia stem-cell development. Nature reviews Cancer. 2007;7(11):823-833.

2. Balgobind BV, Raimondi SC, Harbott J, et al. Novel prognostic subgroups in childhood 11q23/MLL-rearranged acute myeloid leukemia: results of an international retrospective study. Blood. 2009;114(12):2489-2496.