Modulation of SF3B1 causes global intron retention and downregulation of the B-cell receptor pathway in chronic lymphocytic leukemia

Splicing factor SF3B1 is frequently mutated in chronic lymphocytic leukemia (CLL) patients and has been suggested as a potential therapeutic target. In this study, we performed RNA-seq analysis to evaluate the global impact of SF3B1 modulator sudemycin D6 (SD6) on alternative splicing. Our analysis revealed significant increases in global intron-retention in SD6-treated CLL cells. Pathway analysis of the genes associated with increased intron-retention suggested that B-cell receptor (BCR), protein ubiquitination, and PI3K signaling pathways were among the top canonical pathways being affected by SD6. The increases in intron-retention were inversely correlated with deceases in mRNA and protein levels of the affected BCR/PI3K pathway molecules such as BLNK, BTK, AKT1, PLCγ2 and PI3Kδ. SD6 also induced a time-dependent exon-skipping event in mRNA of MCL1 and resulted in significant down-regulation of another anti-apoptotic gene TRAF1, which may contribute to the SD6-induced apoptosis. Finally, SD6 can overcome the pro-survival and pro-growth signals and synergize with ibrutinib, idelalisib and venetoclax to induce apoptosis in primary CLL cells co-cultured with bone marrow stromal cells and in the presence of T-cell-derived cytokines. Cumulatively, these results provide a strong rationale for future clinical development of spliceosome modulators and combinatory therapies based on spliceosome modulators in CLL. To determine the global impacts of SD6 treaments on transcriptome in CLL cells, we performed RNA-seq analysis in MEC1 and GM12878 cell lines treated with 125nM for three different time points (2, 6, and 24 hours), respectively.