H3B-8800, an orally available small-molecule splicing modulator, induces lethality in spliceosome-mutant cancers

Abstract

Genomic analyses of cancer have identified recurrent point mutations in the RNA splicing factor–encoding genes SF3B1, U2AF1, and SRSF2 that confer an alteration of function1,2,3,4,5,6. Cancer cells bearing these mutations are preferentially dependent on wild-type (WT) spliceosome function7,8,9,10,11, but clinically relevant means to therapeutically target the spliceosome do not currently exist. Here we describe an orally available modulator of the SF3b complex, H3B-8800, which potently and preferentially kills spliceosome-mutant epithelial and hematologic tumor cells. These killing effects of H3B-8800 are due to its direct interaction with the SF3b complex, as evidenced by loss of H3B-8800 activity in drug-resistant cells bearing mutations in genes encoding SF3b components. Although H3B-8800 modulates WT and mutant spliceosome activity, the preferential killing of spliceosome-mutant cells is due to retention of short, GC-rich introns, which are enriched for genes encoding spliceosome components. These data demonstrate the therapeutic potential of splicing modulation in spliceosome-mutant cancers.

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Figure 1: H3B-8800 modulates splicing of WT and mutant SF3B1 spliceosomes in vitro and preferentially kills SF3B1-mutant cells.
Figure 2: H3B-8800 modulates splicing and selectively kills SF3B1-mutant leukemia cells in vivo.
Figure 3: H3B-8800 demonstrates preferential activity on SRSF2-mutant leukemia in PDX mice.
Figure 4: H3B-8800 inhibits splicing of short, GC-rich introns and affects splicing of mRNAs encoding spliceosome components.

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Acknowledgements

We thank H3 Biomedicine employees for their support in this project. A.Y. was supported by grants from the Aplastic Anemia and Myelodysplastic Syndromes (MDS) International Foundation and the Lauri Strauss Leukemia Foundation. O.A.-W. was supported by grants from the Edward P. Evans Foundation, the Taub Foundation, the Department of Defense Bone Marrow Failure Research Program (BM150092 and W81XWH-12-1-0041), National Institutes of Health National Heart, Lung and Blood Institute (R01 HL128239), the Josie Robertson Investigator Program, an award from the Starr Foundation (I8-A8-075), the Leukemia and Lymphoma Society (2314-17) and the Pershing Square Sohn Cancer Research Alliance.

Author information

G.K., S. Prajapati, J.W., and X.L guided and performed the medicinal chemistry efforts that led to identification of H3B-8800. E. Park, A.A.A., B.C., and P.F. performed the in vitro biochemical assays. A.Y., A.C., B.C., R.D., C.K., L.L., P.K., C. Mackenzie, Y.M., T.T., H.Y., P.Z., P.G.S., and S.B. performed experiments and analyses of H3B-8800 performance in in vitro cellular assays. M.T., E.S., G.L., E. Pazolli, C. Meeske, P.G.S., M.W., and S.B. performed studies and analyzed data from the cell line xenografts. V.K. and E. Padron provided patient materials used for PDX models. A.Y., S.C-W.L., J.T., and O.A.-W. generated PDX models and performed PDX experiments and analyses. M.S., S. Peng, and L.Y. performed RNA-seq analyses. O.A.-W., M.S., A.A.A., P.G.S., and S.B. wrote the manuscript.

Correspondence to Silvia Buonamici.

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Competing interests

M.T., B.C., M.S., A.A.A., B. Chan, B. Caleb, A.C., R.D., P.F., C.K., G.K., L.L., P.K., X.L., C. Mackenzie, C. Meeske, Y.M., E. Park, S. Peng, S. Prajapati, T.T., J.W., M.W., H.Y., L.Y., P.Z., P.G.S. and S.B. are employees of H3 Biomedicine, Inc., and E.S. and G.L. are employees of Eisai, Inc.

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Seiler, M., Yoshimi, A., Darman, R. et al. H3B-8800, an orally available small-molecule splicing modulator, induces lethality in spliceosome-mutant cancers. Nat Med 24, 497–504 (2018). https://doi.org/10.1038/nm.4493

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