Sensitivity to splicing modulation of BCL2 family genes defines cancer therapeutic strategies for splicing modulators

Abstract

Dysregulation of RNA splicing by spliceosome mutations or in cancer genes is increasingly recognized as a hallmark of cancer. Small molecule splicing modulators have been introduced into clinical trials to treat solid tumors or leukemia bearing recurrent spliceosome mutations. Nevertheless, further investigation of the molecular mechanisms that may enlighten therapeutic strategies for splicing modulators is highly desired. Here, using unbiased functional approaches, we report that the sensitivity to splicing modulation of the anti-apoptotic BCL2 family genes is a key mechanism underlying preferential cytotoxicity induced by the SF3b-targeting splicing modulator E7107. While BCL2A1, BCL2L2 and MCL1 are prone to splicing perturbation, BCL2L1 exhibits resistance to E7107-induced splicing modulation. Consequently, E7107 selectively induces apoptosis in BCL2A1-dependent melanoma cells and MCL1-dependent NSCLC cells. Furthermore, combination of BCLxL (BCL2L1-encoded) inhibitors and E7107 remarkably enhances cytotoxicity in cancer cells. These findings inform mechanism-based approaches to the future clinical development of splicing modulators in cancer treatment.

An Exon Skipping Screen Identifies Antitumor Drugs That Are Potent Modulators of Pre-mRNA Splicing, Suggesting New Therapeutic Applications

“…More recently proposals have appeared for two additional general mechanisms that may account for the observed selective action of SF3B1 targeted agents in certain cancers, the first proposes that ~11% of all cancers have a partial copy of wildtype SF3B1 protein, which renders these tumors sensitive to SF3B1 targeted drugs; (Paolella, Gibson et al 2017) another recent publication presents data which is consistent with the idea that certain tumors driven by BCL2A1, BCL2L2 and MCL1 are especially susceptible to SF3B1 targeted agents. (Aird, Teng et al 2019) It is certainly possible that multiple mechanisms can account for the selective tumor toxicity that has been observed with these agents, which supports the concept that these agents have good potential for broad application in cancer chemotherapy. (Lee and Abdel-Wahab 2016) Given these new insights into the relationships between carcinogenesis and spliceosome function we initiated a project aimed at the discovery of additional small molecules that target the spliceosome.…”

Apoptosis in Cancer Cells Is Induced by Alternative Splicing of hnRNPA2/B1 Through Splicing of Bcl-x, a Mechanism that Can Be Stimulated by an Extract of the South African Medicinal Plant, Cotyledon orbiculata

“…Natural product derivatives of Streptomyces bacteria such a pladienolide B or herboxidiene or isoginkgetin, a biflavonoid isolated from Ginko biloba , are inhibitors of the SF3B1 splicing factor that is required for constitutive splicing. Such compounds are generally toxic to most cells as they interfere with all splicing reactions, but tumor cells appear to be highly dependent on such constitutive splicing and so this chemotherapeutic approach has been taken into clinical trial with the SF3b targeting agent E7107 ( 51 ). Here we describe a novel mechanism of inhibiting splicing of key regulatory genes, in particular hnRNPA2B1 splicing, but also a number of others identified by RNASeq by an extract from the South African medicinal plant, Cotyledon orbiculata , or Pig's Ear.…”

Isoform-specific characterization implicates alternative splicing inAPOBEC3Bas a mechanism restricting APOBEC-mediated mutagenesis

“…Based on our observations that A3B1 291 and not A3A1 is expressed in bladder cancer cell lines, which have a high load of APOBEC-signature 292 mutations, it is likely that at least in these cell lines episodic APOBEC-mediated mutagenesis is 293 caused by the A3B1 activity. 294 Therapeutic targeting of AS to treat cancer is a rapidly developing field with several types of SF3B1 inhibitors, such as E7107 52,53 , an analog of pladienolide B, and H3B-8800 54 being evaluated for acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS) 36,51,54 . Because tumor cells depend 297 on wild-type SFs for survival, these drugs are particularly effective in killing cancer cells with 298 already impaired splicing machinery due to mutations in SFs, such as SRSF2 and SF3B1 54 .…”

“…Alternatively spliced isoforms of other APOBEC3 genes (APOBEC3H and APOBEC3F) have been 53 reported to generate enzymes with variable activity [16][17][18] , but the effects of AS in A3A and A3B on functional activities of these enzymes and relevant clinical outcomes have not been explored. Here, 55 we characterized AS in A3A and A3B in relation to APOBEC-mediated mutagenesis and explored the mechanisms of its regulation and possible therapeutic modulation.…”