Harnessing the E3 ligase SPOP for targeted degradation of the NUP98::KDM5A fusion oncoprotein

NUP98-rearranged (NUP98-r) acute myeloid leukemia (AML) is associated with poor clinical outcomes and represents a major therapeutic challenge due to the lack of strategies for the direct elimination of NUP98-fusion oncoproteins. While targeted degradation of cancer-driving oncoproteins is an attractive strategy, the molecular mechanisms controlling NUP98 fusion oncoprotein stability are not known. Here, we used CRISPR/Cas9 screening to identify the E3 ligase SPOP as a direct regulator of NUP98 oncofusion stability and a novel tumor suppressor in NUP98-r AML. SPOP loss caused a selective increase of NUP98 fusion oncoprotein levels, and promoted leukemia cell proliferation. Leveraging this specificity, we show that induced proximity of SPOP and the NUP98::KDM5A fusion oncoprotein via a bioPROTAC approach induced full clearance of the fusion oncoprotein, and drove terminal differentiation and apoptosis of NUP98-r leukemia cells in vitro and in vivo. Altogether, our study identifies the SPOP E3 ligase as a direct regulator of NUP98 oncofusion stability and presents a blueprint for redirecting the ubiquitin proteasome system to selectively target cancer driving fusion oncoproteins. Overall design: HEK293T cells: NUP98::KDM5A-expressing or wild-type HEK293T cells were subjected to 3' mRNA-sequencing to study effects of the introduction of NUP98::KDM5A. GFP-NUP98::KDM5A-driven AML cells: Cells were transduced with SPOP-bioPROTAC or empty vector constructs. Doxycycline was added to cells to induce expression of the constructs. On days 3 and 6 post induction, cells were sent for RNA sequencing to assess changes to the transcriptional landscape upon bioPROTAC-mediated NUP98::KDM5A degradation.