Synthesis of an RBM39 Degrader That Downregulates CEP192 and Induces Disorganized Spindle Structures

Abstract

RBM39 is an essential component of the spliceosome, playing a critical role in maintaining mRNA integrity. Its depletion significantly exacerbates RNA splicing defects and demonstrates potent anticancer activity. To identify key effectors following RBM39 depletion, we employed a multiomics approach to directly compare two structurally distinct compounds, CB039 and Indisulam. Through proteomic analysis, RNA sequencing, and DepMap dependency assessment, CEP192 emerged as a crucial gene, exhibiting dependency in 96% of the 1,100 analyzed cancer cell lines. In eight cancer cell lines, treatment with both CB039 and Indisulam consistently induced CEP192 exon 42 skipping and reduced CEP192 protein levels. Mechanistically, either CB039 treatment or RNA interference-mediated CEP192 knockdown led to a significant increase in spindle disorganization, as well as chromosome condensation and failed segregation. In conclusion, our characterization of the downstream effects of RBM39 depletion provides novel insights into the therapeutic potential of RBM39 degraders.