Targeting SUMOylation dependency in human cancer stem cells through a unique SAE2 motif revealed by chemical genomics

Natural products (NP) encompass a rich source of bioactive chemical entities. Hence, NPs-derived compounds represent the majority of drugs currently approved to treat cancer. Here, we used human cancer stem cells (CSCs) in a chemical genomics campaign with NP chemical space to interrogate extracts from diverse strains of actinomycete for anti-cancer properties. We identified a compound (SCCRI025044), capable of selectively inhibiting human CSC function vs. normal stem cell (SC) counterparts. Biochemical and molecular studies revealed that SCCRI025044 exerts inhibition on human CSCs through the small ubiquitin-like modifier (SUMO) cascade, found to be hyperactive in human CSCs. SCCRI025044 impedes SUMOylation pathway via direct targeting of the SAE1/2 complex. Treatment of patient-derived CSCs resulted in reduced levels of SUMOylated proteins and suppression of progenitor and stem cell capacity measured in vitro and in vivo. Our study overcomes a barrier in chemically inhibiting oncogenic SUMOylation activity and uncovers a unique role for SAE2 in human CSC biology. Duplicates of each drug treatment were compared to vehicle control (DMSO) for each cell type, also in duplicate.