Targeting MBNL1-mediated alternative splicing in MLL-fusion leukemia

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Proposal Summary/Abstract: Though outcomes for pediatric acute leukemia have improved dramatically over the last few decades, infant leukemia is a particularly aggressive disease which remains difficult to cure even with chemotherapy intensification and bone marrow transplant. Most of these leukemias carry a rearrangement of the MLL gene, a phenomenon also seen in some de novo acute myeloid leukemias (AML) as well as therapy-related AML, and studies have demonstrated that a common gene expression program underlies these leukemias regardless of lineage. Through preliminary studies, we have found that MLL-fusion leukemias express high levels of MBNL1, an RNA binding protein that regulates alternative RNA splicing. We have also identified an alternative splicing (AS) signature unique to MLL-fusion leukemia, and show that MBNL1 loss causes reversion of this signature and impairs MLL-fusion leukemia cell growth. We thus hypothesize that MBNL1 is a critical regulator of an MLL-fusion specific AS program, and that disruption of this program via MBNL1 inhibition leads to leukemia cell death. To test these hypotheses, our specific aims are 1) to determine the mechanism underlying MLL-fusion leukemia dependence on MBNL1, and 2) optimize characteristics of a small-molecule MBNL1 inhibitor as a treatment for MLL-fusion leukemia. To achieve the first aim, we will characterize changes in key cell growth and death pathways which we hypothesize are responsible for the effects seen with genetic knockdown. We will also identify novel MBNL1-mRNA interactions in MLL-fusion leukemia using CLIP-seq (cross-linking immunoprecipitation with RNAseq). For the second aim, we have shown as a proof of concept that a small molecule inhibitor of MBNL1 can induce MLL-fusion leukemia cell death. This compound requires optimizations for potency, which we will achieve by applying medicinal chemistry principles. Furthermore, we have used its structural characteristics and published crystal structures to initiate an in silico screen of a proprietary compound library. This proposal will advance our understanding of the role of AS in the pathogenesis of MLL-fusion leukemia, while also directly leading to a first-in-class therapy for this disease. The applicant, who is currently an instructor in the Division of Oncology at Cincinnati Children’s Hospital Medical Center, will execute this research plan while simultaneously engaging in structured didactics and receiving close individual guidance from a panel of mentors as described in the application. These scientists possess significant expertise in the molecular pathogenesis of leukemia. The experiments, mentoring, and structured classwork described in this career development plan will position the applicant to successfully transition into an independent researcher and physician-scientist, with expertise in the role of RNA binding proteins in leukemia pathogenesis.