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MBNL1 Regulates Essential Alternative RNA Splicing Patterns in MLL-Rearranged Leukemia

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MBNL1 Regulates Essential Alternative RNA Splicing Patterns in MLL-Rearranged Leukemia ARTICLE https://doi.org/10.1038/s41467-020-15733-8 OPEN MBNL1 regulates essential alternative RNA splicing patterns in MLL-rearranged leukemia Svetlana S. Itskovich1,9, Arun Gurunathan 2,9, Jason Clark 1, Matthew Burwinkel1, Mark Wunderlich3, Mikaela R. Berger4, Aishwarya Kulkarni5,6, Kashish Chetal6, Meenakshi Venkatasubramanian5,6, ✉ Nathan Salomonis 6,7, Ashish R. Kumar 1,7 & Lynn H. Lee 7,8 Despite growing awareness of the biologic features underlying MLL-rearranged leukemia, 1234567890():,; targeted therapies for this leukemia have remained elusive and clinical outcomes remain dismal. MBNL1, a protein involved in alternative splicing, is consistently overexpressed in MLL-rearranged leukemias. We found that MBNL1 loss significantly impairs propagation of murine and human MLL-rearranged leukemia in vitro and in vivo. Through transcriptomic profiling of our experimental systems, we show that in leukemic cells, MBNL1 regulates alternative splicing (predominantly intron exclusion) of several genes including those essential for MLL-rearranged leukemogenesis, such as DOT1L and SETD1A.Wefinally show that selective leukemic cell death is achievable with a small molecule inhibitor of MBNL1. These findings provide the basis for a new therapeutic target in MLL-rearranged leukemia and act as further validation of a burgeoning paradigm in targeted therapy, namely the disruption of cancer-specific splicing programs through the targeting of selectively essential RNA binding proteins. 1 Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA. 2 Cancer and Blood Diseases Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA. 3 Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA. 4 College of Medicine, University of Cincinnati School of Medicine, Cincinnati, OH 45267, USA. 5 Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH 45221, USA. 6 Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA. 7 Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH 45229, USA. 8 Division of Oncology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA. 9These ✉ authors contributed equally: Svetlana S. Itskovich, Arun Gurunathan. email: [email protected] NATURE COMMUNICATIONS | (2020)11:2369 | https://doi.org/10.1038/s41467-020-15733-8 | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-020-15733-8 eciprocal chromosomal translocations of the mixed lineage MBNL1 expression compared to normal CD34+ cord blood cells Rleukemia (MLL) gene with one of over 70 fusion partners (Supplementary Fig. 1D). A similar phenomenon was observed in are commonly found in a subset of aggressive leukemias Lin- mouse bone marrow cells transduced with the MA9 retro- including infant leukemia, and are associated with poor out- virus (Supplementary Fig. 1E) MBNL1 was recently demonstrated come1–3. Regardless of the fusion partner and the type of leu- to be a direct target of the MLL-AF4 fusion protein in patient- kemia (acute myeloid leukemia (AML) or acute lymphoblastic derived ALL cell lines as well as in an experimental retroviral leukemia (ALL)) all MLL-rearranged leukemias share a common model20,29. To determine whether this observation applied to gene expression profile that is distinct from that of non−MLL- leukemia cells bearing different MLL-fusion partners, we analyzed rearranged leukemias4,5. Analysis of MLL-rearranged signatures MLL-fusion protein (MLL-N and fusion partner C-terminus if reveals that muscleblind-like 1 (MBNL1) is one of the most applicable) and H3K79me2 chromatin immunoprecipitation fol- consistently overexpressed genes in MLL-rearranged leukemia lowed by deep sequencing (ChIP-seq) datasets from THP-130 and compared to other leukemias3–6. ML-231 cell lines (with MLL-AF9 and MLL-AF6 respectively), as Muscleblind-like 1 (MBNL1) is an RNA-binding protein that well as from the MV4;1130, RS4;1132, and SEM33 cell lines which has been shown to regulate RNA alternative splicing, localization, bear an MLL-AF4 fusion. We found evidence of MLL-N/fusion-C and integrity7–11. Alternative splicing of pre-mRNA is a key binding to the MBNL1 promoter and gene body, along with mechanism regulating eukaryotic gene expression by expanding H3K79me2 enrichment across all cell lines studied (Fig. 1c). To genome coding diversity. MBNL1 has previously been shown to experimentally verify the observed interactions between MLL- regulate alternative splicing in the fetal-to-adult transition in fusion proteins and MBNL1, we used transformed human CD34+ heart, muscle, and brain9. Sequestration of MBNL1 due to cells bearing a repressible MA9 oncogene where doxycycline binding to expanded poly-CUG repeats in the dystrophia myo- treatment represses MA9 expression34,35. Nuclear extracts iso- tonica protein kinase (DMPK) mRNA is a main contributor to lated at different intervals demonstrated a decrease in MBNL1 the pathogenesis of myotonic dystrophy type 1 (DM1), a syn- expression directly correlating with MA9 downregulation drome characterized by muscle weakness, cardiac abnormalities, (Fig. 1d). intellectual disability, and cataracts. The sequestration of MBNL1 We then performed short hairpin RNA (shRNA) knockdown results in missplicing of target mRNAs, leading to the clinical studies of MBNL1 in human leukemia cell lines to test its features12. Moreover, MBNL1 and MBNL2 are known to play a requirement for leukemia cell growth. We screened commercially central role in regulating the pattern of alternative splicing events available lentiviral shRNAs and chose two that showed the most that control embryonic cell pluripotency13. Knockdown of Mbnl1 consistent and efficient knockdown of MBNL1 mRNA (Supple- in murine fetal liver cells leads to blockade of terminal ery- mentary Fig. 2A) and protein (Fig. 2a), hereafter referred to as thropoiesis through deregulation of alternative splicing of Ndel1 shMBNL1-64 and -65. There was substantial growth inhibition of mRNA14. MLL-rearranged cell lines following MBNL1 knockdown both in Abnormalities in RNA processing, particularly splicing, have liquid culture (Fig. 2b–d) and in colony forming unit (CFU) assays been associated with cancer, including AML and ALL)indepen- (Supplementary Figs. 2B–C). However, MBNL1 knockdown did dent of spliceosome mutations15–19. The increased expression of not significantly affect growth of non-MLL-rearranged leukemic MBNL1 in MLL-rearranged leukemia described above, as well as cells (Fig. 2e–g) bearing a variety of different oncofusions (BCR- evidence that the MLL-fusion complex directly binds the MBNL1 ABL in K562, RUNX1-RUNXT1 in Kasumi-1) despite efficient promoter20, suggest that MBNL1-mediated RNA splicing may be knockdown (Supplementary Fig. 2D–H). important to the pathogenesis of MLL-rearranged leukemias. The To determine the requirement for MBNL1 in leukemia in vivo, mechanism of action and extent of essentiality of MBNL1 in we transduced two primary patient AML samples bearing MLL MLL-rearranged leukemogenesis, however, remains unknown. fusions (one MLL-AF9 and one MLL-AF10) with shMBNL1-64 In this report, through a combination of functional genomic or a non-targeting (NT) control. Transduction efficiency ranged studies, pharmacologic inhibition, and comprehensive analysis of from 67 to 85% (Venus+). Bulk cells were transplanted into alternative splicing we demonstrate that MBNL1 is required in immune-deficient NSGS mice. At the time of visible illness, all MLL-rearranged leukemia. mice showed robust human cell engraftment (ranging from 92.4 to 99.4% in the MLL-AF9 group and 7.6–40.2% in the MLL-AF10 group) in the bone marrow. Bone marrow from mice trans- Results planted with shNT-transduced cells contained Venus+ cells MBNL1 is required for the propagation of human MLL- (range 6.9–78% of all human cells), whereas the majority of mice rearranged leukemia in vitro and in vivo. To confirm the rele- transplanted with shMBNL1-64 had virtually no Venus+ fraction vance of MBNL1 expression in MLL-rearranged leukemia, we first (Fig. 2h). One mouse transplanted with shMBNL1-64-transduced compared multiple gene expression studies which identified dif- MLL-AF9 patient cells had 62.4% Venus+; this mouse was ferentially expressed genes between MLL-rearranged and MLL- removed from analysis after qRT-PCR analysis revealed lack of wildtype leukemias4,6,21,22. We began by examining the inter- MBNL1 knockdown. To show broad applicability of knockdown, section of these gene expression signatures, and found that we repeated this experiment using an MLL-AF9/NRASG12D cell MBNL1 expression was a common feature of these signatures line, with similar results (Supplementary Fig. 3A–C)36. These data across both acute myeloid and lymphoblastic leukemias (Fig. 1a). suggest that MBNL1 is essential for leukemia propagation in vivo. We further examined MBNL1 expression across two major pri- As an alternative approach, we tested the effects of MBNL1 mary patient datasets evaluating both AML and ALL, and con- inhibition achieved by biochemical means. Recently, an MBNL1- sistently found high MBNL1 expression in MLL-rearranged specific inhibitor that prevents MBNL1 binding to its targets was patient samples23–28 (Supplementary Figs. 1A–C). We subse- identified in a high-throughput
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