Comprehensive Analyses of the Effects of the Small-Molecule Inhibitor of the UHM Domain in the Splicing Factor in Leukemia Cells.

Mutations in RNA splicing factor genes including , , and have been reported to contribute to development of myeloid neoplasms including myelodysplastic syndrome (MDS) and secondary acute myeloid leukemia (sAML). Chemical tools targeting cells carrying these mutant genes remain limited and underdeveloped. Among the four proteins, mutant U2AF1 (U2AF1) acquires an altered 3' splice site selection preference and co-operates with the wild-type U2AF1 (U2AF1) to change various gene isoform patterns to support MDS cells survival and proliferation. mutations in MDS cells are always heterozygous and the cell viability is reduced when exposed to additional insult affecting U2AF1 function. To investigate if the pharmacological inhibition of U2AF1 function can provoke drug-induced vulnerability of cells harboring , we conducted a fragment-based library screening campaign to discover compounds targeting the U2AF homology domain (UHM) in U2AF1 that is required for the formation of the U2AF1/U2AF2 complex to define the 3' splice site. The most promising hit () selectively inhibited growth of leukemia cell lines overexpressing and human primary MDS cells carrying . RNA-seq analysis of K562-U2AF1 following treatment with further revealed alteration of isoform patterns for a set of proteins that impair or rescue pathways associated with endocytosis, intracellular vesicle transport, and secretion. Our data suggested that further optimization of is warranted to obtain chemical probes that can be used to evaluate the therapeutic concept of inducing lethality to cells by inhibiting the U2AF1 protein.