RBM15-MKL1 fusion protein promotes leukemia via m6A methylation and WNT pathway activation

Mayday, M. Y.; Biancon, G.; Wei, M.; Ramirez, C.; Moratti, I.; Pintado-Urbanc, A. P.; Wang, L.; Espinosa, J. A.; Simon, M. D.; Ofir-Rosenfeld, Y.; Rausch, O.; Tebaldi, T.; Halene, S.; Krause, D. S.

doi:10.1101/2025.02.19.638991

bioRxiv · 10.1101/2025.02.19.638991

RBM15-MKL1 fusion protein promotes leukemia via m6A methylation and WNT pathway activation

Mayday, M. Y.·Biancon, G.·Wei, M.·Ramirez, C.·Moratti, I.·Pintado-Urbanc, A. P.·Wang, L.·Espinosa, J. A.·Simon, M. D.·Ofir-Rosenfeld, Y.·Rausch, O.·Tebaldi, T.·Halene, S.·Krause, D. S.

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Abstract

Acute megakaryoblastic leukemia driven by the RBM15-MKL1 fusion protein (RM-AMKL) is the only known recurrent mutation involving the N6-methyladenosine (m6A) writer complex. Dysregulation of m6A modification affects RNA fate and is linked to oncogenesis. Inhibition of m6A deposition via inhibition of the METTL3 writer protein has anti-tumour activity, but the mechanism underlying its efficacy and cancer specificity remains unclear. We treated murine RM-AMKL cells with a novel METTL3 inhibitor, STM3675, and showed apoptosis in vitro and prolonged survival of mice transplanted with RM-AMKL, implicating m6A as an essential component of AMKL and identifying Wnt signalling as a key driver of leukemogenesis. To elucidate the mechanism by which m6A contributes to leukemogenesis we employed a multi-omic approach, combining transcriptome-wide assessment of RNA binding, methylation and turnover. We show for the first time that RM retains the RNA-binding and m6A-modifiying functions of its RBM15 component, while also selectively regulating distinct mRNA targets, particularly genes involved in Wnt signalling including Frizzled. Frizzled genes are upregulated by RM and downregulated in RM-AMKL cells in response to METTL3 inhibition, providing an m6A-dependent explanation for their upregulation. Direct Frizzled knockdown reduced RM-AMKL growth, which was partially rescued by treatment with a {beta}-catenin agonist, underscoring a functional role of Wnt signalling in RM-AMKL. Human AMKLs show elevated Wnt pathway and Frizzled gene expression, highlighting the relevance of our work. Together, our findings reveal that RM-specific m6A modifications and activation of Wnt signalling are critical drivers of RM-AMKL, highlighting these pathways as potential therapeutic targets. Key PointsO_LIRM retains functional abilities of RBM15 and additionally interacts with Wnt-related transcripts to increase expression of Fzd proteins. C_LIO_LIThe METTL3 writer complex and WNT signalling pathways are essential for RM-driven leukemia. C_LI

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Mayday, M. Y., Biancon, G., Wei, M., Ramirez, C., Moratti, I., Pintado-Urbanc, A. P., Wang, L., Espinosa, J. A., Simon, M. D., Ofir-Rosenfeld, Y., Rausch, O., Tebaldi, T., Halene, S., Krause, D. S.. 2025-02-24. RBM15-MKL1 fusion protein promotes leukemia via m6A methylation and WNT pathway activation. https://doi.org/10.1101/2025.02.19.638991

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