Mutant U2AF1-expressing cells are sensitive to pharmacological modulation of the spliceosome

Shirai, Cara Lunn; White, Brian S.; Tripathi, Manorama; Tapia, Roberto; Ley, James N; Ndonwi, Matthew; Kim, Sanghyun P.; Shao, Jin; Carver, Alexa; Sáez, Borja; Fulton, Robert S.; Fronick, Catrina C.; O’Laughlin, Michelle; Lagisetti, Chandraiah; Webb, Thomas R.; Graubert, Timothy A.; Walter, Matthew J.

doi:10.1038/ncomms14060

Cited by 101 publications

(78 citation statements)

References 46 publications

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“…Based on these results, we hypothesize that synergistic apoptosis induced by MYC induction and CLK inhibition might therefore be because of the concomitant perturbation of different splicing pathways. To support this hypothesis, a synthetic lethality between mutant splicing factors is proposed because of clinical observations that splicing factor mutation exclusively occurs (Yoshida et al , ; Haferlach et al , ; Dvinge et al , ), as well as pharmacological SF3B1‐mediated splicing modulators kill cells harboring mutant forms of SRSF2 or U2AF1 more effectively (Lee et al , ; Shirai et al , ).…”

Section: Discussionmentioning

confidence: 99%

Anti‐tumor efficacy of a novel CLK inhibitor via targeting RNA splicing and MYC‐dependent vulnerability

et al. 2018

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The modulation of pre‐mRNA splicing is proposed as an attractive anti‐neoplastic strategy, especially for the cancers that exhibit aberrant pre‐mRNA splicing. Here, we discovered that T‐025 functions as an orally available and potent inhibitor of Cdc2‐like kinases (CLKs), evolutionally conserved kinases that facilitate exon recognition in the splicing machinery. Treatment with T‐025 reduced CLK‐dependent phosphorylation, resulting in the induction of skipped exons, cell death, and growth suppression in vitro and in vivo. Further, through growth inhibitory characterization, we identified high CLK2 expression or MYC amplification as a sensitive‐associated biomarker of T‐025. Mechanistically, the level of CLK2 expression correlated with the magnitude of global skipped exons in response to T‐025 treatment. MYC activation, which altered pre‐mRNA splicing without the transcriptional regulation of CLKs, rendered cancer cells vulnerable to CLK inhibitors with synergistic cell death. Finally, we demonstrated in vivo anti‐tumor efficacy of T‐025 in an allograft model of spontaneous, MYC‐driven breast cancer, at well‐tolerated dosage. Collectively, our results suggest that the novel CLK inhibitor could have therapeutic benefits, especially for MYC‐driven cancer patients.

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Section: Discussionmentioning

confidence: 99%

Anti‐tumor efficacy of a novel CLK inhibitor via targeting RNA splicing and MYC‐dependent vulnerability

et al. 2018

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“…These findings may have therapeutic relevance, because it is speculated that CCND3 mutations confer sensitivity to CDK4/CDK6 inhibitors, 22 whereas those in U2AF1 confer sensitivity to spliceosome inhibitors. 25 Other mutations affecting genes involved in transcriptional regulation (CEBPA, CREBBP, DDX3X, and PBRM1) and chromatin remodeling (KMT2C [MLL3], KDM6A, and KDM5C) were also identified (supplemental Figure 3A-B).…”

Section: Resultsmentioning

confidence: 99%

Genomic analysis of hairy cell leukemia identifies novel recurrent genetic alterations

Durham¹,

Getta

Dietrich

et al. 2017

Blood

110

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Key Points• KMT2C mutations occur in 15% and 25% of patients with cHCL and vHCL, respectively, along with CCND3 and U2AF1 mutations each in 13% of vHCLs.• NF1, NF2, N/KRAS, and IRS1 alterations contribute to clinical resistance to vemurafenib treatment in patients with cHCL.Classical hairy cell leukemia (cHCL) is characterized by a near 100% frequency of the BRAFV600E mutation, whereas ∼30% of variant HCLs (vHCLs) have MAP2K1 mutations. However, recurrent genetic alterations cooperating with BRAFV600E or MAP2K1 mutations in HCL, as well as those in MAP2K1 wild-type vHCL, are not well defined. We therefore performed deep targeted mutational and copy number analysis of cHCL (n 5 53) and vHCL (n 5 8). The most common genetic alteration in cHCL apart from BRAFV600E was heterozygous loss of chromosome 7q, the minimally deleted region of which targeted wild-type BRAF, subdividing cHCL into those hemizygous versus heterozygous for the BRAFV600E mutation. In addition to CDKN1B mutations in cHCL, recurrent inactivating mutations in KMT2C (MLL3) were identified in 15% and 25% of cHCLs and vHCLs, respectively. Moreover, 13% of vHCLs harbored predicted activating mutations in CCND3.A change-of-function mutation in the splicing factor U2AF1 was also present in 13% of vHCLs. Genomic analysis of de novo vemurafenib-resistant cHCL identified a novel gain-of-function mutation in IRS1 and losses of NF1 and NF2, each of which contributed to resistance. These data provide further insight into the genetic bases of cHCL and vHCL and mechanisms of RAF inhibitor resistance encountered clinically. (Blood. 2017;130(14):1644-1648

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“…88 Primary human MDS/AML cells with mutant U2AF1 had impaired proliferation after treatment with SD1 in vitro compared with cells lacking splicing factor mutations and in vivo treatment of mice with SD6 reverted aberrant hematopoietic progenitor expansion in an inducible mouse model of mutant U2AF1. 89 FD-895 caused induction of apoptosis in CLL cells in vitro (independent of SF3B1 genotype) at nanomolar concentrations, similar to PB. 90 A semisynthetic analog (17S-FD-895) with improved pharmacokinetic properties 91 administered to immunodeficient mice engrafted with primary human AML samples reduced their repopulating activity in secondary transplants and reverted the splicing signature in leukemia stems cells from "secondary AML-associated" to "healthy aging."…”

Section: Splicing Modulatorsmentioning

confidence: 99%

Splicing factor gene mutations in hematologic malignancies

Sáez

Walter

Graubert

2017

Blood

Self Cite

101

103

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Alternative splicing generates a diversity of messenger RNA (mRNA) transcripts from a single mRNA precursor and contributes to the complexity of our proteome. Splicing is perturbed by a variety of mechanisms in cancer. Recurrent mutations in splicing factors have emerged as a hallmark of several hematologic malignancies. Splicing factor mutations tend to occur in the founding clone of myeloid cancers, and these mutations have recently been identified in blood cells from normal, healthy elderly individuals with clonal hematopoiesis who are at increased risk of subsequently developing a hematopoietic malignancy, suggesting that these mutations contribute to disease initiation. Splicing factor mutations change the pattern of splicing in primary patient and mouse hematopoietic cells and alter hematopoietic differentiation and maturation in animal models. Recent developments in this field are reviewed here, with an emphasis on the clinical consequences of splicing factor mutations, mechanistic insights from animal models, and implications for development of novel therapies targeting the precursor mRNA splicing pathway. (Blood. 2017;129(10):1260-1269 IntroductionThe control of messenger RNA (mRNA) processing is a crucial component of gene regulation. The precursor messenger RNA (premRNA) sequence contains exons that flank introns, which are removed during splicing.1 Human genes are remarkably complex, containing an average of 8 exons, with introns composing up to 90% of the pre-mRNA sequence.2,3 Up to 94% of human genes generate multiple mRNA isoforms. [4][5][6] The spliceosome is a multiprotein complex consisting of 5 small nuclear ribonucleoproteins (snRNPs) and more than 150 proteins that recognizes the elements near intron-exon boundaries and the branch site that catalyzes the excision of intronic regions. Additional trans-acting factors including SR proteins bind the cis-regulatory sequences (exonic and intronic silencers and enhancers) to promote or prevent spliceosome assembly. [7][8][9] The complexity of regulatory elements that control proper splicing makes this process not only critical to maintain tissue homeostasis, but also highly susceptible to hereditary and somatic mutations that are involved in disease. This review will discuss the implications of aberrant splicing on human disease, with a focus on the impact of somatic mutations in trans-acting splicing factors in hematologic malignancies. Splicing and diseaseA comprehensive analysis of The Cancer Genome Atlas (TCGA) project RNA sequencing (RNA-seq) data from 16 tumor types and matched normal tissue revealed evidence of global alternative splicing involving a variety of splicing junctions, including cassette exons, retrained introns, and competing 59 and 39 splice sites (SSs). 10 In particular, acute myeloid leukemia (AML) cells showed the largest number of alternative spliced events among tumor types.10 Recent evidence from analysis of paired DNA and RNA-seq data from TCGA has shown that somatic mutations affecting splicing regulatory sequences (sp...

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Mutant U2AF1-expressing cells are sensitive to pharmacological modulation of the spliceosome

Cited by 101 publications

References 46 publications

Anti‐tumor efficacy of a novel CLK inhibitor via targeting RNA splicing and MYC‐dependent vulnerability

Anti‐tumor efficacy of a novel CLK inhibitor via targeting RNA splicing and MYC‐dependent vulnerability

Genomic analysis of hairy cell leukemia identifies novel recurrent genetic alterations

Splicing factor gene mutations in hematologic malignancies

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