Increased sensitivity of SF3B1 mutated uveal melanoma by spliceosome inhibition

Abstract

Purpose : Effective treatment of uveal melanoma (UM) patients with metastatic disease is unfortunately not yet available. Twenty percent of UM harbors a mutation in splicing factor gene SF3B1, suggesting that an aberrant spliceosome function plays a vital role in tumorigenesis. Inhibiting the spliceosome could prevent formation of aberrant transcripts. Splicing inhibitors (e.g. E7107) have been shown to exploit the preferential sensitivity of spliceosome compromised cells to these compounds. E7107 targets the SF3B subunit 1 and interferes with splicing by binding non-covalently to the SF3B subunit of the U2 snRNP complex. This prevents the U2 snRNP complex to bind to the pre-mRNA branch point. We have studied the effect of E7107 using UM cell lines (Mel202 and 92.1) and SF3B1 and BAP1 mutated primary ex vivo tumor slices.

Methods : Cell lines and ex vivo tumor slices were exposed for 24h to different concentrations of E7107. Tumor slices were stained with H&E, BAP1, MelanA, MIB-1 and caspase-3 antibodies. RNA was isolated for transcriptome and gene expression analysis. The type and number of alternative and aberrant transcripts was evaluated after exposure to E7107 with the MISO and FRASER analysis, respectively.

Results : Of twenty UM slices were included from September 2018-2021. E7107 exposed on UM cell lines showed decreased cell viability and increased apoptosis. This effect was significant in SF3B1 mutated cells compared to SF3B1 wild-type cells (p = 0.0004). A similar effect was observed in UM tumor slices. A decrease in MIB-1 (proliferation) positive cells and increase in caspase-3 (apoptosis) positive cells was observed. Furthermore, a decrease in mainly aberrant transcript formation was observed after E7107 exposure, especially at a concentration of 5 nM E7107. Ninety-seven transcripts had a decrease in aberrant transcripts after E7107 exposure, and this effect was mostly in exon skipping/intron retention.

Conclusions : This study demonstrates that SF3B1 mutated UM cells are more sensitive to splicing inhibitor E7107 compared to SF3B1 wild-type UM cells. Splicing inhibitors such as E7107 have therapeutic potential in SF3B1 mutated UM. Further research is recommended to assess and maximize the efficacy of E7107 as well as other potential splicing inhibitors in a therapeutic setting. An optimal dose should be determined with no serious adverse events but high enough for an increased effect in mutated cells.

This abstract was presented at the 2022 ARVO Annual Meeting, held in Denver, CO, May 1-4, 2022, and virtually.