Selective Targeting of Spliceosome-Mutant Myeloid Malignancies with H3B-8800: An Oral SF3b Modulator

H3B-8800 is a newly discovered, potent, and orally bioavailable compound that modulates the SF3b complex, a component of the spliceosome. It has shown efficacy in treating myeloid malignancies with spliceosome mutations, which are common in myelodysplastic syndrome (MDS), chronic myelomonocytic leukemia (CMML), and acute myeloid leukemia (AML). The compound was found to selectively target cells with spliceosome mutations, leading to preferential lethality compared to their wildtype (WT) counterparts.

H3B-8800 was identified through medicinal chemistry efforts and demonstrated a strong binding affinity to SF3b complexes, whether containing WT or mutant SF3B1 protein. It induced a dose-dependent modulation of splicing in both biochemical and cellular assays. The compound's selectivity was confirmed through resistance observations in cells with the SF3B1R1074H mutation, known to confer resistance to other splicing modulators.

In isogenic AML cells with specific spliceosome mutations, H3B-8800 exhibited preferential inhibition of cell growth. In vivo, it showed dose-dependent splicing modulation and tumor growth inhibition in mice with SF3B1K700E knock-in K562 cells, and improved survival in mice with Srsf2P95H/MLL-AF9 mouse AML cells.

RNA-seq analysis revealed that H3B-8800 induced splicing alterations, such as intron retention and exon skipping, with a preference for shorter, GC-rich introns. Notably, many genes affected by H3B-8800 encode spliceosome components, suggesting that spliceosome-mutant cells are particularly dependent on the normal expression of these proteins.

To explore H3B-8800's therapeutic potential in CMML, a xenotransplantation model was developed using CD34+ cells from CMML patients. H3B-8800 significantly reduced leukemic burden in spliceosome-mutant CMML patient-derived xenografts (PDX) and decreased leukemia-initiating cells compared to vehicle treatment.

The findings indicate that H3B-8800 presents a novel therapeutic strategy with selective lethality for myeloid cells with spliceosome mutations. Despite the importance of splicing, CMML/AML cells without spliceosome mutations were less sensitive to H3B-8800. The compound is currently under clinical evaluation for patients with MDS, AML, and CMML.