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RNA splicing factor SF3B1 is recurrently mutated in various cancers, particularly in hematologic malignancies. We previously reported that coexpression of Sf3b1 mutation and Atm deletion in B cells, but not either lesion alone, leads to the onset of chronic lymphocytic leukemia (CLL) with CLL cells harboring chromosome amplification. However, the exact role of Sf3b1 mutation and Atm deletion in chromosomal instability (CIN) remains unclear. Here, we demonstrated that SF3B1 mutation promotes centromeric R-loop (cen-R-loop) accumulation, leading to increased chromosome oscillation, impaired chromosome segregation, altered spindle architecture, and aneuploidy, which could be alleviated by removal of cen-R- loop and exaggerated by deletion of ATM. Aberrant splicing of key genes involved in R-loop processing underlay augmentation of cen-R-loop, as overexpression of the normal isoform, but not the altered form, mitigated mitotic stress in SF3B1-mutant cells. Our study identifies a critical role of splice variants in linking RNA splicing dysregulation and CIN and highlights cen-R-loop augmentation as a key mechanism for leukemogenesis., Introduction Cancer genome sequencing has identified high-frequency mutations of splicing factor SF3B1 in hematologic malignancies such as myelodysplastic syndrome and chronic lymphocytic leukemia (CLL) (1-3). As one of the most [...]

Summary More than 80% of patients with the refractory anemia with ring sideroblasts subtype of myelodysplastic syndrome (MDS) have mutations in Splicing Factor 3B, Subunit 1 ( SF3B1 ). We generated a conditional knockin mouse model of the most common SF3B1 mutation, Sf3b1 K700E . Sf3b1 K700E mice develop macrocytic anemia due to a terminal erythroid maturation defect, erythroid dysplasia, and long-term hematopoietic stem cell (LT-HSC) expansion. Sf3b1 K700E myeloid progenitors and SF3B1 -mutant MDS patient samples demonstrate aberrant 3′ splice-site selection associated with increased nonsense-mediated decay. Tet2 loss cooperates with Sf3b1 K700E to cause a more severe erythroid and LT-HSC phenotype. Furthermore, the spliceosome modulator, E7017, selectively kills SF3B1 K700E -expressing cells. Thus, SF3B1 K700E expression reflects the phenotype of the mutation in MDS and may be a therapeutic target in MDS. [ABSTRACT FROM AUTHOR]

Genomic instability is a hallmark of human cancer, and results in widespread somatic copy number alterations. We used a genome-scale shRNA viability screen in human cancer cell lines to systematically identify genes that are essential in the context of particular copy-number alterations (copy-number associated gene dependencies). The most enriched class of copy-number associated gene dependencies was CYCLOPS (Copy-number alterations Yielding Cancer Liabilities Owing to Partial losS) genes, and spliceosome components were the most prevalent. One of these, the pre-mRNA splicing factor SF3B1, is also frequently mutated in cancer. We validated SF3B1 as a CYCLOPS gene and found that human cancer cells harboring partial SF3B1 copy-loss lack a reservoir of SF3b complex that protects cells with normal SF3B1 copy number from cell death upon partial SF3B1 suppression. These data provide a catalog of copy-number associated gene dependencies and identify partial copy-loss of wild-type SF3B1 as a novel, non-driver cancer gene dependency. DOI: http://dx.doi.org/10.7554/eLife.23268.001

Alterations in cellular homeostasis that affect protein folding in the endoplasmic reticulum (ER) trigger a signaling pathway known as the unfolded protein response (UPR). The initially cytoprotective UPR will trigger an apoptotic cascade if the cellular insult is not corrected; however, the proteins required to initiate this cell death pathway are poorly understood. In this study, we show that UPR gene expression is induced in cells treated with ER stress agents in the presence or absence of routine caspase-12 or human caspase-4 expression and in cells that overexpress Bcl-xL or a dominant negative caspase-9. We further demonstrate that ER stress-induced apoptosis is a caspase-dependent process that does not require the expression of caspase-12 or caspase-4 but can be inhibited by overexpression of Bcl-xL or a dominant negative caspase-9. Additionally, treatment of human and murine cells with ER stress agents led to the cleavage of the caspase-4 fluorogenic substrate, LEVD-7-amino-4-trifluoromethylcoumarin, in the presence or absence of caspase-12 or caspase-4 expression, whereas Bcl-xL or a dominant negative caspase-9 overexpression inhibited LEVD-7-amino-4-trifluoromethylcoumarin cleavage. These data suggest that caspase-12 and caspase-4 are not required for the induction of ER stress-induced apoptosis and that caspase-4-1ike activity is not always associated with an initiating event. [ABSTRACT FROM AUTHOR]

Mutations in components of the 3′ mRNA splicing machinery are found in almost 50% of myelodysplastic syndrome (MDS) cases. In this issue of Cancer Cell , Kim and colleagues, Colla and colleagues, and Shirai and colleagues report on the impact of mutated or dysregulated splicing factors to hematopoiesis, mRNA splicing, and MDS pathogenesis. [ABSTRACT FROM AUTHOR]

Hematopoietic stem and progenitor cells (HSPCs) maintain hematopoiesis throughout the lifetime of an organism. HSPC dysfunction can lead to disorders such as myelodysplastic syndrome (MDS). Spliceosome mutations are prevalent in MDS, but how splicing regulates HSPCs remains poorly understood. Using a zebrafish loss-of-function mutant for the top mutated splicing factor in MDS, splicing factor 3b, subunit 1 (sf3b1), we found that impaired splicing hindered HSPC specification. To identify Sf3b1-regulated transcripts, we performed RNA-sequencing on kdrl:gfp+ endothelial cells from sf3b1 mutant and unaffected siblings at 24hpf. ∼900 genes were mis-spliced with significant enrichment for Signaling Transducer and Activator of Transcription 3 (Stat3) pathway components. Mis-spliced Stat3 signaling components observed in sf3b1 mutants were predicted to dampen protein levels or inhibit functionality, and Stat3 target genes were significantly downregulated in sf3b1 mutants. Constitutively-active Stat3 overexpression in sf3b1 mutants partially suppressed the HSPC defect. Induced mis-splicing of stat3 using morpholinos caused a significant HSPC decrease in sf3b1 heterozygotes at 28hpf, but elicited no effect in wildtype embryos, demonstrating a synthetic lethal interaction. Inhibiting Stat3 with small molecule STATTIC similarly reduced HSPCs in heterozygous but not wildtype embryos. We next tested if STAT3 inhibition selectively affected SF3B1-mutated human cells. K562 cells expressing the MDS-associated SF3B1-K666N mutation were more sensitive to STAT3 inhibition with STATTIC than wildtype cells. Similarly, primary SF3B1-mutant MDS patient cells produced fewer hematopoietic colonies when treated with STATTIC than controls. Together, STAT3 inhibition is a conserved synthetic lethal vulnerability for SF3B1-mutated cells with potential to treat splicing factor-mutated MDS. [ABSTRACT FROM AUTHOR]

Summary SF3B1 is recurrently mutated in chronic lymphocytic leukemia (CLL), but its role in the pathogenesis of CLL remains elusive. Here, we show that conditional expression of Sf3b1- K700E mutation in mouse B cells disrupts pre-mRNA splicing, alters cell development, and induces a state of cellular senescence. Combination with Atm deletion leads to the overcoming of cellular senescence and the development of CLL-like disease in elderly mice. These CLL-like cells show genome instability and dysregulation of multiple CLL-associated cellular processes, including deregulated B cell receptor signaling, which we also identified in human CLL cases. Notably, human CLLs harboring SF3B1 mutations exhibit altered response to BTK inhibition. Our murine model of CLL thus provides insights into human CLL disease mechanisms and treatment. Graphical Abstract Highlights • Sf3b1-K700E mutation impairs 3′ splice site selection and induces cellular senescence • Sf3b1-K700E mutation in combination with Atm deletion causes CLL • CLL cells show genome instability and dysregulated BCR signaling • Human CLL cells with SF3B1 mutations show dysregulation of BCR signaling Yin et al. show that Sf3b1 -K700E mutation in mouse B cells induces cellular senescence, but deletion of Atm overcomes senescence and leads to the development of CLL-like disease. Both human and mouse CLL harboring mutant SF3B1 exhibit deregulated B cell receptor signaling and increased sensitivity to ibrutinib. [ABSTRACT FROM AUTHOR]