Deubiquitinase USP6 stabilizes oncogenic RUNX1 fusion proteins to promote the leukemic progression
RUNX1-rearranged leukemia is one of the most common subtypes of patients with recurrent genetic abnormalities. Although a majority of RUNX1-rearranged patients are likely to respond well to standard chemotherapy, the risks of relapse and long-term adverse effects still persist. RUNX1 fusions generated by rearrangement are pivotal oncogenic drivers, with over 70 distinct fusions involving various partners including RUNX1/ETO and ETV6/RUNX1 having been characterized. Thus, elucidating their regulatory mechanism may help to find novel therapeutic strategies. Herein, we first clarify a universal deubiquitinase USP6-involved mechanism that enhances the protein stability of RUNX1 fusions with different partners. Importantly, In RUNX1-rearranged leukemia, USP6 is specially upregulated in RUNX1-rearranged leukemia and strongly linked to poor patient outcomes. Mechanically, USP6 stabilizes RUNX1 fusions to facilitate the formation of phase separation, leading to robust transcriptional activation of differentiation inhibitory and stemness maintenance pathways. Depletion of USP6 dramatically inhibits proliferation and induced differentiation of RUNX1-rearranged leukemia in vitro and in vivo. Subsequent phenotypic screening identifies marketed drug Auranofin as the first USP6 inhibitor, which induces significant degradation of different RUNX1 fusions. Furthermore, Auranofin effectively induced myeloid differentiation of RUNX1-rearranged cells and arrested xenograft tumor growth. Notably, Auranofin selectively showed a strong therapeutic effect on RUNX1-rearranged patients-derived leukemia blasts. Together, these findings not only uncover a new biological function of deubiquitinase USP6 in regulating transcriptional activity of RUNX1 fusions, but also validates USP6 as well as Auranofin as the promising drug target and candidate for RUNX1-rearranged leukemia. Overall design: Gene expression profiling analysis of RNA-seq data for KASUMI-1 cells  treated with lentivirus-USP6