Alectinib enhances response to RBM39 degradation via SRPK1 inhibition

RNA splicing is a critical process in gene expression regulation and RNA splicing factors are increased in expression in many cancers. We have previously demonstrated that the molecular glue indisulam degrades RNA splicing factor RBM39 producing aberrant splicing transcripts that is very effective in high-risk neuroblastoma and can potentiate the sensitivity to DNA damaging agents in ovarian high-grade serous carcinoma. RNA splicing inhibitors have the ability to generate vulnerabilities that can be exploited for combinatorial therapeutic strategies. In this study, we employed combination drug screens to identify potential synergistic drug-drug interactions between indisulam and other FDA approved clinical compounds. We demonstrate that alectinib, a clinically approved ALK inhibitor, has strong potency against serine/arginine protein kinase 1 (SRPK1), a key modulator of RNA splicing. Combined treatment with alectinib and indisulam leads to synergistic cell growth inhibition, increased cell apoptosis and cell cycle arrest in multiple cancer cell lines including high-risk neuroblastoma. Co-treatment exacerbated RNA splicing defects in genes involved in DNA damage response and R-loop resolution, leading to R-loop accumulation and increased DNA damage. In the Th-MYCN/ALKF1174L neuroblastoma mouse model, combination therapy induced complete tumour regression and significantly improved survival rates compared with monotherapies. Thus, the combination of indisulam and alectinib is a promising approach to treat aggressive malignancies such MYCN-driven high-risk neuroblastoma, exploiting the hitherto untapped pharmacology of alectinib as a clinical RNA splicing inhibitor. Our work demonstrates the concept that co-targeting of functionally interdependent RNA splicing factors is a strategy that can yield new and highly synergistic anti-cancer combination therapies effective against otherwise hard-to-treat cancers.