Abstract 5987: Targeting the spliceosome in high-risk B-cell acute lymphoblastic leukemia

Abstract

Abstract The outcome for children with high-risk B-cell acute lymphoblastic leukemia (B-ALL) is poor. Disease relapse is speculated to be due to leukemia cells escaping treatment. Our group discovered a unique cell subpopulation in B-ALL that has the capacity to initiate leukemia and is resistant to treatment. Transcriptome studies of this cell population highlight a unique RNA regulation process, specifically RNA splicing. In B-ALL, dysregulated splicing is reported to be associated with drug resistance and disease relapse. SF3B1 is a core component of the spliceosome and an essential protein in the RNA splicing process. SF3B1 inhibition is therapeutic in many cancers. In our current studies, we investigated the therapeutic potential of pladienolide B (Plad-B), an SF3B1 inhibitor, in B-ALL. SF3B1 protein expression was significantly higher in cell lines (Reh and JM1) and 28 primary B-ALL samples (14 each for standard-risk and high-risk), regardless of the risk group, than in normal B-cells (NBs) and hematopoietic stem cells (HSCs). Plad-B showed significant dose-dependent cytotoxicity in the cell lines with IC50 of 1.2nM and 0.6nM, respectively, and three harvested high-risk patient-derived xenograft (PDX) samples with almost the same IC50 as the cell lines. Plad-B did not show cytotoxicity in NBs and HSCs at the same tested concentrations. In vivo efficacy of Plad-B was tested using an Reh xenograft mouse model and a high-risk PDX model. Plad-B, as a single drug treatment, significantly prolonged survival in both models (p<0.01). G2/M cell cycle arrest and apoptosis induction were observed at 24 hours after Plad-B treatment in Reh and JM1. Splicing events were examined by RNA-seq in the treated cells at different time points (15 min, 30 min, and 60 min). Plad B demonstrated rapid splicing inhibition as early as 15 min post-treatment and, at 60 min, splicing was inhibited in 1,669 genes, including apoptosis-associated genes. 2,625 differential splicing events were observed in these genes with ~96% from intron retention and exon skipping. Furthermore, 202 genes showed significant changes in their expression over this time frame. Most of the genes were rapidly downregulated in the treatment group compared to the control, and some were slowly downregulated. There were also some genes which were upregulated, either rapidly or slowly, compared to the control. We demonstrated that Plad-B induced short pro-apoptotic spliced isoforms, instead of anti-apoptotic forms, in BCL2L1 and MCL-1, as early as 60 min after treatment. In conclusion, these data demonstrated the therapeutic potential of SF3B1 inhibition in high-risk B-ALL. Plad-B rapidly inhibited splicing in many genes and downregulated the anti-apoptotic forms of apoptosis-associated genes, leading to cell apoptosis. In future studies, we will identify the downstream targets of Plad-B and further investigate the mechanism of rapid apoptosis induction by SF3B1 inhibition. Citation Format: Yuki Murakami, Hiroaki Konishi, Clifford Tepper, John McPherson, Noriko Satake. Targeting the spliceosome in high-risk B-cell acute lymphoblastic leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5987.