RUNX1 aberrations in blast-phase chronic myeloid leukaemia induce the RNA-binding protein SPATS2L, which promotes growth, survival and stress granule assembly.

RUNX1 is a critical regulator of hematopoiesis. In CML, somatic RUNX1 mutations and RUNX1::MECOM/EVI1, are associated with TKI resistance and progression to BP-CML. To examine post-transcriptional dysregulation downstream of RUNX1 aberrations, we used orthogonal organic phase separation to characterise the RNA-binding proteome of RUNX1 deficient BP-CML cells. RUNX1 depleted BP-CML cells exhibited significant alterations to RBPs involved in stress response pathways and translation/ribosome-biogenesis. Furthermore, RUNX1 depletion or expression of RUNX1::EVI1 in BP-CML cells induced expression and RNA binding activity of SPATS2L, a component of stress granules (SG). Whilst RUNX1 depletion increased SG-assembly, SPATS2L depletion reduced SG-assembly and inhibited the growth/survival of multiple BP-CML cell lines. Homoharringtonine (HHT), used historically in TKI-resistant CML, ablated SG-assembly in BP-CML cells with RUNX1 depletion, and primary BP-CML cells with LOF/hypomorphic RUNX1 mutations were preferentially sensitised to HHT. Suppressing SPATS2L expression induced by RUNX1 depletion, reduced SG-forming capacity and increased the HHT-sensitivity of RUNX1 depleted BP-CML cells, suggesting SPATS2L contributes to therapeutic resistance in RUNX1 mutated CML. Finally, we demonstrate that SGs may contribute more widely to TKI-resistance in this setting. This study suggests that SPATS2L/SG induction could be critical to RUNX1-mutant leukemias, and, provides preliminary evidence for a mutationally-targeted approach in CML with RUNX1 aberrations.