Spliceosome Genes Research Articles

Aberrant expression of CPSF1 promotes head and neck squamous cell carcinoma via regulating alternative splicing.

Alternative mRNA splicing increases protein diversity, and alternative splicing events (ASEs) drive oncogenesis in multiple tumor types. However, the driving alterations that underlie the broad dysregulation of ASEs are incompletely defined. Using head and neck squamous cell carcinoma (HNSCC) as a model, we hypothesized that the genomic alteration of genes associated with the spliceosome may broadly induce ASEs across a broad range of target genes, driving an oncogenic phenotype. We identified 319 spliceosome genes and employed a discovery pipeline to identify 13 candidate spliceosome genes altered in HNSCC using The Cancer Genome Atlas (TCGA) HNSCC data. Phenotypic screens identified amplified and overexpressed CPSF1 as a target gene alteration that was validated in proliferation, colony formation, and apoptosis assays in cell line and xenograft systems as well as in primary HNSCC. We employed knockdown and overexpression assays followed by identification of ASEs regulated by CPSF1 overexpression to identify changes in ASEs, and the expression of these ASEs was validated using RNA from cell line models. Alterations in expression of spliceosome genes, including CPSF1, may contribute to HNSCC by mediating aberrant ASE expression.

Transcriptome profiling reveals the high incidence of hnRNPA1 exon 8 inclusion in chronic myeloid leukemia

Chronic myeloid leukemia (CML) is a malignancy that evolves through a multi-step process. Alternative splicing of several genes has been linked to the progression of the disease, but involvement of alternations in splicing profiles has not been reported. RNA-seq of peripheral blood mononuclear cell (PBMC) samples characterized the differentially expressed and spliced transcripts in five CML chronic phase (CP) and five blast phase (BP) patients, and five healthy controls. Global splicing alteration analysis detected 6474 altered splicing events altered between CML and healthy samples, including many of the previously reported splicing variants and showing a more profound altered splicing deregulation in BP samples. Functional clustering of differentially spliced genes in CP revealed a preferred enrichment relating to cell signaling, while the spliceosome pathway was most overrepresented in BP samples. One differentially spliced spliceosome gene hnRNPA1 showed two splice isoforms; the longer isoform contained exon 8 was preferentially expressed in the BP patients, and the short one excluding exon 8 was specific to healthy controls. Our findings suggested that alternative splicing deregulation played a central role during the progression of CML from CP to BP, and the longer isoform of hnRNPA1 might represent a diagnostic marker and therapeutic target for CML.

Pan-cancer analysis identifies mutations in SUGP1 that recapitulate mutant SF3B1 splicing dysregulation

The gene encoding the core spliceosomal protein SF3B1 is the most frequently mutated gene encoding a splicing factor in a variety of hematologic malignancies and solid tumors. SF3B1 mutations induce use of cryptic 3' splice sites (3'ss), and these splicing errors contribute to tumorigenesis. However, it is unclear how widespread this type of cryptic 3'ss usage is in cancers and what is the full spectrum of genetic mutations that cause such missplicing. To address this issue, we performed an unbiased pan-cancer analysis to identify genetic alterations that lead to the same aberrant splicing as observed with SF3B1 mutations. This analysis identified multiple mutations in another spliceosomal gene, SUGP1, that correlated with significant usage of cryptic 3'ss known to be utilized in mutant SF3B1 expressing cells. Remarkably, this is consistent with recent biochemical studies that identified a defective interaction between mutant SF3B1 and SUGP1 as the molecular defect responsible for cryptic 3'ss usage. Experimental validation revealed that five different SUGP1 mutations completely or partially recapitulated the 3'ss defects. Our analysis suggests that SUGP1 mutations in cancers can induce missplicing identical or similar to that observed in mutant SF3B1 cancers.

Spliceosomal Protein Gene BmSPX Regulates Reproductive Organ Development in Bombyx mori.

Sex determination and differentiation are nearly universal to all eukaryotic organisms, encompassing diverse systems and mechanisms. Here, we identified a spliceosomal protein gene BmSPX involved in sex determination of the lepidopeteran insect, Bombyx mori. In a transgenic silkworm line that overexpressed the BmSPX gene, transgenic silkworm males exhibited differences in their external genitalia compared to wild-type males, but normal internal genitalia. Additionally, transgenic silkworm females exhibited a developmental disorder of the reproductive organs. Upregulation of BmSPX significantly increased the expression levels of sex-determining genes (BmMasc and BmIMP) and reduced the female-type splice isoform of Bmdsx, which is a key switch gene downstream of the sex-determination pathway. Additionally, co-immunoprecipitation assays confirmed an interaction between the BmSPX protein and BmPSI, an upstream regulatory factor of Bmdsx. Quantitative real-time PCR showed that BmSPX over-expression upregulated the expression of the Hox gene abdominal-B (Adb-B), which is required for specification of the posterior abdomen, external genitalia, and gonads of insects, as well as the genes in the Receptor Tyrosine Kinase (RTK) signaling pathway. In conclusion, our study suggested the involvement of BmSPX, identified as a novel regulatory factor, in the sex-determination pathway and regulation of reproductive organ development in silkworms.

Clinicopathologic characterisation of myeloid neoplasms with concurrent spliceosome mutations and myeloproliferative-neoplasm-associated mutations

AimsSpliceosome genes (SF3B1, SRSF2, U2AF1 and ZRSR2) are commonly mutated in myeloid neoplasms, particularly in myelodysplastic syndromes (MDS). JAK2, MPL and CALR mutations are associated with myeloproliferative neoplasms (MPN). Although...

Therapeutic Options in Myelodysplastic Syndromes Following Hypomethylating Agent Failure

Hypomethylating agents (HMA) azacitidine and decitabine are standard of care for the treatment of myelodysplastic syndromes (MDS). Although HMA have revolutionised the treatment of MDS, only approximately half of patients respond to these agents with variable duration of effect, known as primary and secondary HMA failure, respectively. Therapeutic options following HMA failure remain limited; however, growing understanding of the pathogenesis underlying MDS has resulted in the development of multiple targeted therapies showing varying degrees of success in clinical trials. Drugs that target molecular alterations (such as abnormal histone regulation, IDH mutations, and spliceosome gene mutations), abnormal signalling pathways (such as the multikinase inhibitor rigosertib), cellular apoptosis (such as the Bcl2 inhibitor venetoclax), and immune checkpoint inhibition are under development. Agents recently approved for use in higher-risk acute myeloid leukaemia, such as FLT3-inhibitors and CPX-351, are also being studied in MDS. Several more agents, including two first-in-class agents, a novel immune regulator targeting CD47, and pevonedistat, a NEDD8-activating enzyme inhibitor, are under investigation. In the absence of established therapeutic approaches following HMA failure, decisions in therapy should be based on the type of HMA resistance as well as the patient’s clinical and molecular characteristics. As targeted therapies continue to be developed, a comprehensive re-evaluation of the patient including the mutational profile at the time of HMA failure may reveal new treatment options. Here, emerging therapeutic approaches to HMA failure in MDS are reviewed.

Myelodysplastic Syndrome with Excess Blasts and Secondary Acute Myeloid Leukemia: Same Disease with Different Blast Count

Introduction: The World Health Organization (WHO) diagnoses acute myeloid leukemia (AML) if ≥20% myeloid blasts are present in peripheral blood or bone marrow. Consequently a patient with even 19% blasts is often ineligible for an "AML study". A less arbitrary means to define "AML" and myelodysplastic syndromes ("MDS") emphasizes biologic features. Here, focusing on patients with WHO-defined MDS with excess (5-19%) blasts (MDS-EB) or AML with myelodysplasia-related changes (AML-MRC) or therapy-related (t-AML) (WHO defined secondary AML), we compared morphologic blast percentage (MBP) with the frequency of mutations in genes belonging to different functional groups, and with the variant allele frequency (VAF) for individually mutated genes. Methods: 328 adults with WHO-defined AML (de novo and secondary; n=149) or MDS (n=179) and with mutational analysis by next-generation sequencing (NGS) performed at the University of Washington Hematopathology Laboratory between 2015-2017 were included. Of these, 86 had MDS-EB and 49 had secondary AML. Mutational analysis was performed using a customized, amplicon-based assay, TruSeq Custom Amplicon (Illumina, San Diego, CA). Custom oligonucleotide probes targeted specific mutational hotspots in ASXL1, CBL, CEBPA, CSF3R, EZH2, FBXW7, FGFR1, FLT3, GATA1, GATA2, HRAS, IDH1, IDH2, JAK2, KIT, KMT2A, KRAS, MAP2K1, MPL, NOTCH1, NPM1, NRAS, PDGFRA, PHF6, PTEN, RB1, RUNX1, SF3B1, SRSF2, STAG2, STAT3, TET2, TP53, U2AF1, WT1, and ZRSR2. VAF ≥5% was required to identify point mutations. Spearman's correlation coefficient was used to examine the relation between VAF of individually mutated genes and MBP. The Mann Whitney test served to compare the distribution of VAF in AML (≥20% blasts) vs. MDS (<20% blasts), before and after exclusion of subgroups as described below. Fisher's exact test was used to compare incidence of mutations. Results: 96% of cases had ≥one mutation in the 36 genes tested using NGS. Considering all 328 patients, mutations in tumor suppressor and cohesin complex genes were similarly frequent in MDS and AML, whereas spliceosomal genes, in particular SF3B1 and SRSF2, were more frequently mutated in MDS than in AML (46% vs. 26%, p<0.001). Mutations in epigenetic modifiers were more common in AML than MDS (54% vs. 42%, p= 0.035) as were transcription factor mutations (52% vs. 28%, p<0.001). However comparisons limited to MDS-EB vs. AML-MRC/t-AML, indicated the differences observed when comparing all MDS and all AML were less apparent, both statistically and more perhaps importantly with respect to observed frequencies. For example, spliceosomal gene mutations were found in 35% in MDS-EB and 27% in AML-MRC/t-AML (p=0.34) vs. 46% and 26% in all MDS and all AML. NPM1 mutations were detected in only 8% of AML-MRC/t-AML vs. 3% in MDS-EB but 29% for all AML. Results were analogous with FLT3 ITD, FLT3 TKD, and JAK2 mutations. Examining 20 individually mutated genes detected in ≥ 10 patients only with SRSF2 (p=0.04), did distribution of VAF differ statistically according to whether blast percentage was <20% versus ≥20%. Conclusions: The similar prevalence of mutations in different functional categories in MDS-EB and AML-MRC/t-AML suggests these entities are two manifestations of the same disease. We believe it appropriate to combine these WHO entities allowing patients in each to be eligible for both AML and MDS trials. Disclosures Othus: Glycomimetics: Other: Data Safety and Monitoring Committee; Celgene: Other: Data Safety and Monitoring Committee. Walter:Amgen: Consultancy; Boston Biomedical: Consultancy; Agios: Consultancy; Argenx BVBA: Consultancy; Astellas: Consultancy; BioLineRx: Consultancy; BiVictriX: Consultancy; Covagen: Consultancy; Daiichi Sankyo: Consultancy; Jazz Pharmaceuticals: Consultancy; Kite Pharma: Consultancy; New Link Genetics: Consultancy; Pfizer: Consultancy, Research Funding; Race Oncology: Consultancy; Seattle Genetics: Research Funding; Amphivena Therapeutics: Consultancy, Equity Ownership; Boehringer Ingelheim: Consultancy; Aptevo Therapeutics: Consultancy, Research Funding. Becker:Accordant Health Services/Caremark: Consultancy; AbbVie, Amgen, Bristol-Myers Squibb, Glycomimetics, Invivoscribe, JW Pharmaceuticals, Novartis, Trovagene: Research Funding; The France Foundation: Honoraria.

Prognostic Impact of a Composite Genetic Profile Defined By Cytogenetics and Next Generation Sequencing at Diagnosis on Treatment Outcomes Following Allogeneic Hematopoietic Stem Cell Transplantation in Acute Myeloid Leukemia

Prognostic Impact of a Composite Genetic Profile Defined By Cytogenetics and Next Generation Sequencing at Diagnosis on Treatment Outcomes Following Allogeneic Hematopoietic Stem Cell Transplantation in Acute Myeloid Leukemia

The Splicing Factor RBM17 Supports Leukemia Stem Cell Self-Renewal

Background: Acute myeloid leukemia (AML) is thought to be sustained by sub-populations of leukemia stem cells (LSCs), which possess the capacity for self-renewal and differentiation and are believed to be responsible for disease initiation, relapse and chemoresistance. There is therefore an urgent need to develop therapies that target the LSC population to achieve effective AML treatment. To date there has been limited success in this endeavor, highlighting the importance of gaining a more comprehensive understanding of the mechanistic elements that underpin LSC function. Aberrant alternative splicing is recognized as a key driver of cancer. In the context of AML, genome-wide sequencing studies have shown that approximately one third of genes are differentially spliced in primitive CD34+ cells in AML patients compared to those obtained from normal controls. In particular, LSCs also have a unique splicing profile when compared to normal aging HSCs, underscoring the importance of understanding the mechanistic controls of aberrant splicing in LSC function. Results: Previous studies examining the link between aberrant splicing and AML focused on spliceosome genes with somatic mutations in AML patients. To examine mechanisms that mediate aberrant alternative splicing in LSC beyond splicing factor mutations, we performed a data-mining survey of 203 known mRNA splicing factors. Strikingly, RNA-binding motif protein 17 (RBM17) is the only splicing factor that is both strongly linked to poor AML prognosis and significantly elevated in LSC-enriched subsets of primary AML samples based on a recent study of 78 AML samples with normal karyotype. RBM17 has been implicated in regulating alternative splicing and cancer chemotherapy resistance. However, its function in AML or LSCs is not known. From our studies, we found that the level of RBM17 protein is elevated in the phenotypically primitive subsets of primary AML samples (n=8, RBM17+%: 67.42% in CD34+ versus 34.66% in CD34-fractions). Depletion of RBM17 with shRNAs in 3 human primary AML samples resulted in reduced colony formation compared to shScramble controls. More importantly, knockdown of RBM17 in a primary AML sample greatly impeded AML engraftment in immune-deficient mice (mean of 0.89 control versus mean of 0.1671 and 0.3171 shRNAs), suggesting that RBM17 is required for the stem and progenitor potential of AML and maintenance of LSC populations. Intriguingly, in contrast to the situation for the malignant hierarchy, the level of RBM17 in normal HSCs is lower than that in more committed cell populations in the normal hematopoietic system. To determine if RBM17 plays different roles in malignant LSC and normal hematopoietic stem and progenitor cells (HSPCs), we depleted RBM17 with shRNAs in human cord blood (CB) derived CD34+ HSPCs, and found RBM17 knockdown had negligible adverse impact on both CB total colony and primitive GEMM colony outputs and yielded no increase in apoptosis, indicating no defects were apparent to primitive cells of CB as read out in vitro. To uncover the molecular mechanisms underlying the role of RBM17 in LSC functions, we preformed RBM17 eCLIP-seq in the K562 and HL60 human leukemic cell lines. We then cross-analyzed the CLIP-seq datasets with a published ENCODE RNA-seq dataset (RBM17 knockdown in K562 cells), where we found RBM17 directly binds to transcripts of stem cell program-related genes and regulates the splicing of these genes, including MADD (MAP kinase activating death domain) and MRPS18C (mitochondrial ribosomal protein S18C). We further demonstrated that the splicing patterns of MADD and MRPS18C are mediated by RBM17 in primary AML samples. In our ongoing functional validation experiments, isoform-specific knockdown of MADD or MRPS18C splice variants downstream of RBM17 impeded colony forming capacity and induced myeloid differentiation in the MOLM13 AML cell line. These results suggest that RBM17-mediated splicing events impact primitive cell function in AML. Conclusion: We have identified RBM17 as a novel LSC-regulating factor, plays an important role in maintaining AML LSC function through regulating the alternative splicing of stem cell program-related genes. The potential LSC-selective role for RBM17, along with its downstream splicing events, represent promising putative therapeutic targets whose modulation could offer attractive therapeutic windows in AML treatment. Disclosures No relevant conflicts of interest to declare.

SM09419, a Novel, Small-Molecule CDC-like Kinase (CLK) Inhibitor, Demonstrates Strong Inhibition of the Wnt Signaling Pathway and Antitumor Effects in Mantle Cell Lymphoma Models

Mantle cell lymphoma (MCL) is a B-cell non-Hodgkin lymphoma (NHL) that accounts for ~7% of all NHL in the U.S. MCL is associated with aberrant activation of the Wnt signaling pathway, which plays a key role in the survival and maintenance of MCL-initiating cells. Many MCL patients experience relapse and subsequent disease progression due to chemoresistance following initial therapy; hence, novel therapies are needed. CLKs regulate the activity of serine/arginine-rich splicing factors (SRSFs) that modulate spliceosome assembly, mRNA splicing, and gene expression. SM09419 is a novel, oral, small-molecule pan-CLK inhibitor that potently inhibits the Wnt pathway. The purpose of these studies was to examine the antitumor activity of SM09419 in preclinical models of MCL. SM09419 potently inhibited both CLK1-CLK4 (IC50 for all <0.02 µM) and Wnt signaling pathway (average EC50=0.068 µM) activities. In REC-1 and GRANTA-519 MCL cells, SM09419 dose-dependently inhibited SRSF6 phosphorylation and potently suppressed expression of Wnt-related genes (CCND1, LEF1, TCF7) and proteins vs. vehicle. In tests on 5 MCL cell lines, cell proliferation was strongly impaired by SM09419 across all lines (average EC50=0.102 µM [0.021-0.236]). SM09419 also induced apoptosis in REC-1 and GRANTA-519 cells, increasing caspase 3/7 activation and PARP cleavage while reducing survivin and MCL-1 expression vs. vehicle. In vivo antitumor effects and tolerability of oral SM09419 (QD 20-21 days) were assessed in mice bearing REC-1 and JeKo-1 flank xenografts (n=5/group). In REC-1 xenografts, strong tumor growth inhibition (TGI) vs. vehicle occurred in mice treated with 12.5, 25, and 50 mg/kg SM09419 (TGI 88% [p<0.01], 100%, and 100% [p<0.001], respectively), and the two highest doses induced complete tumor regression in all mice from D14. Similarly, in JeKo-1 xenografts, SM09419 (12.5 and 25 mg/kg) induced significant TGI vs. vehicle (71% and 100%, respectively; p<0.0001) with complete tumor regression at 25 mg/kg, whereas acalabrutinib (50 mg/kg BID) was not efficacious (27% TGI) when tested in parallel. SM09419 25mg/kg induced reversible suppression of phospho-SRSF6 protein and inhibited Wnt pathway-related gene expression (TCF7 and DVL2) in JeKo-1 tumors in a single-dose PD study, demonstrating downstream target engagement in vivo. SM09419 was also assessed in 2 patient-derived xenograft (PDX) mouse models of MCL. PDX cells were injected intravenously and treatment was initiated upon 8-12% engraftment of human CD45+CD19+ cells in peripheral blood. In the first model, derived from a patient who was progressive after 8 modalities including ibrutinib, SM09419 (25 mg/kg QD) increased survival vs. vehicle (100% through D26 vs. 0% by D12, respectively; n=6/group) and suppressed MCL engraftment in the blood (12% at D26 vs. 69% at D8 and D12, respectively; p=0.002) and bone marrow (30% at D26 vs. 91% at D8 and D12, respectively; p=0.002). In the second model, derived from a patient refractory after ibrutinib and anti-PDL1 treatment, SM09419 (25 mg/kg QD) significantly suppressed MCL engraftment vs. vehicle in the blood (8% vs. 72%), bone marrow (20% vs. 57%), and spleen (15% vs. 96%) at D28 (study end; p<0.001 for all; n=4/group). In addition, SM09419 greatly inhibited splenomegaly vs. vehicle (0.04 g vs. 0.4 g, respectively; p<0.001). In a subsequent experiment in the same model, mice (n=7/group) were treated with 12.5 or 25 mg/kg SM09419 or vehicle for 12 weeks (to D85). Blood MCL engraftment at D41 was significantly lower in mice treated with SM09419 (40% at 12.5 mg/kg and 23% at 25 mg/kg) vs. vehicle (88%; p<0.01 and p<0.001, respectively). SM09419 dose-dependently increased survival (28.6% at 12.5 mg/kg and 85.7% at 25 mg/kg at D85) vs. vehicle (0% at D63); survival was maintained in both dose groups during post-treatment monitoring (to D99). SM09419 was well tolerated in all tested mouse models based on body weight measurements. In summary, SM09419 potently inhibited SRSF6 phosphorylation Wnt signaling pathway activity, and cell proliferation and induced apoptosis in MCL cell lines. The strong in vivo antitumor effects observed as a single agent suggest that SM09419 may provide a clinical benefit for patients with treatment-resistant or refractory MCL. A Phase 1 study assessing safety, tolerability, and pharmacokinetics of SM09419 in subjects with advanced hematologic malignancies is being initiated. Disclosures Chung: Samumed, LLC: Employment, Equity Ownership. Creger:Samumed, LLC: Employment, Equity Ownership. Sitts:Samumed, LLC: Employment, Equity Ownership. Chiu:Samumed, LLC: Employment, Equity Ownership. Mak:Samumed, LLC: Employment, Equity Ownership. KC:Samumed, LLC: Employment, Equity Ownership. Tam:Samumed, LLC: Employment, Equity Ownership. Bucci:Samumed, LLC: Employment, Equity Ownership. Stewart:Samumed, LLC: Employment, Equity Ownership. Phalen:Samumed, LLC: Employment, Equity Ownership. Cha:Samumed, LLC: Employment, Equity Ownership.

Dysregulation of Splicing Patterns in MDS Induced By the S100A9/Fto Axis

We previously reported that S100A9 promotes ineffective hematopoiesis and the development of MDS in a feed forward age-dependent fashion. Nonetheless, the precise mechanism by which S100A9 may foster DNA damage in MDS remains unclear. We recently showed that S100A9 directs overexpression of the fat-mass and obesity-associated gene (FTO) encoding an m6A RNA demethylase, which leads to nuclear exclusion of SRSF2. Removal of SRSF2 from its functional domain in the nucleosome leads to stalling of RNA polymerase II and formation of the nucleic acid R-loops, comprising DNA:RNA hybrids with the associated non-template single-stranded DNA. S100A9/FTO axis activation leads to SRSF2 deregulation through suppression of its main nuclear transport protein RanBP2, thereby stalling transcription machinery with resulting accumulation of nuclear R-loops and cytosolic/extracellular RNA:DNA hybrids. Persistent R-loops induce DNA damage while also compromising DNA repair. Here we identify an S100A9/FTO-regulated pathway responsible for induction of genomic instability through the accumulation of cytoplasmic RNA:DNA hybrids and modification of the spliceosomal patterns of aged S100A9Tg mice matching MDS hematopoietic stem and progenitor cells (HSPC). We first investigated which components of the S100A9/FTO axis are critical to hematopoiesis and those that are important for both the development of RNA:DNA hybrids and γH2AX activation. We analyzed the contribution of RanBP2 and the effects of elimination of R-loop formation via overexpression of RNAse H1, an enzyme that removes stalled R-loops in the nucleus by degrading DNA-hybridized RNA, thereby reducing the accumulation of cytoplasmic RNA:DNA hybrids. CRISPR knock-down of RanBP2 showed that the protein is critical for accumulation of yH2AX defined by double stranded breaks (DSB). Importantly, overexpression of RNAse H1 degraded R-loops and restored colony-forming capacity, indicating that RNA:DNA hybrids induced by the S100A9/FTO have profound effects on hematopoietic potential. However, while the FTO exclusion of SRSF2 from the nucleus explains the accumulation of γH2AX, it should potentially impact global RNA splicing. To investigate this, we performed a comparative RNAseq analysis on WT and S100A9Tg mice (young and old) to understand both changes induced through the normal aging process as well as those compounded by S100A9. We found that genes linked to splicing, RNA development, nucleotide excision repair and genomic instability and ribosome function were downregulated in aged S100A9Tg mice. Further analysis comparing splicing patterns of S100A9Tg and WT mice with human MDS BM HSPC led to ~200 common genes that were analyzed further. These genes showed that there are splicing changes enriched in spliceosomal assembly and mRNA splice selection site genes. We also found that the enriched genes affect the nucleolus and ribosome formation matching what is seen phenotypically with MDS. Dysregulation of these pathways are highly consistent with our observations of the pathways affected by the S100A9/FTO-induced inflammaging process, validating our hypothesis of S100A9 as a common initiator of dysfunction that can give rise to MDS. Importantly, our data demonstrates the potential for spliceosomal dysfunction regardless of the presence of spliceosomal mutations in MDS. We are currently in the process of performing both DRIPseq and m6A-seq of primary human MDS specimens and S100A9Tg mice to further assess the role of the S100A9/FTO pathway in the selection of sites for RNA/DNA hybrid formation and rise of genomic dysfunction that gives rise to MDS. We conclude that S100A9/FTO-induced nuclear exclusion of SRSF2 aids in the formation of RNA:DNA-hybrids that lead to genomic instability and the disruption of normal spliceosomal patterns in both human HSPC and the S100A9Tg MDS murine model, representing a previously uncharacterized mechanism contributing to MDS pathogenesis. Our studies provide evidence that targeting this cascade offers significant potential for development of novel, biologically rational therapeutics for MDS. Disclosures List: Celgene: Membership on an entity's Board of Directors or advisory committees, Research Funding.

SM09419, a Novel, Small-Molecule CDC-like Kinase (CLK) Inhibitor, Demonstrates Strong Inhibition of the Wnt Signaling Pathway and Antitumor Effects in FMS-like Tyrosine Kinase 3 (FLT3)-Mutant Acute Myeloid Leukemia Models

Acute myeloid leukemia (AML) with the FLT3 internal tandem duplication (FLT3-ITD) mutation accounts for ~25% of all AMLs, carries a poor prognosis, and is prone to relapse despite targeted therapy. FLT3 mutations are associated with aberrant activation of the Wnt signaling pathway, which itself is implicated in AML initiation/progression and is required for the self-renewal and survival of leukemic stem cells. CLKs regulate the activity of serine/arginine-rich splicing factors (SRSFs) that modulate spliceosome assembly, mRNA splicing, and gene expression. SM09419 is a novel, oral, small-molecule pan-CLK inhibitor that potently inhibits the Wnt pathway. These studies examined the antitumor activity of SM09419 as a single agent and in combination with targeted and standard therapies in preclinical models of FLT3-ITD AML. In MV-4-11 and MOLM-13 AML cells carrying the FLT3-ITD mutation, SM09419 dose-dependently inhibited SRSF6 phosphorylation and potently suppressed expression of Wnt pathway-related genes (CCND1, MYC, TCF7, DVL2). The effect on cell proliferation was tested in 8 AML cell lines with varying mutation profiles as well as 26 different leukapheresis-derived primary human AML cells. Proliferation was strongly impaired by SM09419 across all tested cell lines (average EC50=0.2 + 0.048 µM]); MV-4-11 and MOLM-13 cells had EC50 of 0.049 and 0.144 µM, respectively. SM09419 also potently inhibited proliferation in all primary AML cells (average EC50=0.048 + 0.0097 µM) regardless of FLT3 mutation status, cytogenetics, or AML diagnosis (de novo or relapsed/refractory). SM09419 also induced apoptosis in MV-4-11 and MOLM-13 cells, increasing caspase 3/7 activation and PARP cleavage while reducing survivin and MCL-1 expression relative to vehicle. In vivo antitumor effects and tolerability of oral SM09419 (QD) alone or combined with either midostaurin (FLT3 inhibitor) or venetoclax (BCL2 inhibitor) and/or azacitidine were assessed in FLT3-ITD xenograft models (n=5-6/group). In MOLM-13 xenografts, SM09419 (12.5 and 25 mg/kg) induced strong tumor growth inhibition (TGI) vs. vehicle at Day 14 (TGI 52% [p<0.05] and 74% [p<0.001], respectively). Midostaurin (50 mg/kg) induced significant TGI vs. vehicle (50%, p<0.05), which was increased when administered in combination with 12.5 mg/kg SM09419 (81%, p<0.001). In MV-4-11 xenografts, single-agent SM09419 (6.25, 12.5, and 25 mg/kg) induced significant TGI vs. vehicle (56% [p<0.05], 94%, and 95% [p<0.001], respectively) at Day 26 with tumor regression in all mice dosed at 12.5 mg/kg and 25 mg/kg. In a subsequent experiment, midostaurin (50 mg/kg) alone and combined with 6.25 mg/kg SM09419 for 23 days induced tumor regression in MV-4-11 xenografts (100% TGI vs. vehicle, p<0.0001). After treatment discontinuation, tumor regression was maintained in all mice (6/6) treated with the combination for 26 days, whereas tumor regrowth was immediately observed in midostaurin-treated mice. In another MV-4-11 xenograft study, the combination of 6.25mg/kg SM09419 with azacitidine (0.8 mg/kg QD) and/or venetoclax (25 mg/kg QD) induced significant TGI (95-98% vs. vehicle, p<0.001) with tumor regression at Day 26. Azacitidine + venetoclax induced 79% TGI (p<0.001), but no tumor regression was observed. The triple combination induced tumor regression in all mice and complete regressions in 4/6 mice (67%); it had a greater effect on slowing tumor regrowth after treatment discontinuation vs. a single agent or doublet. SM09419 alone or in combination was well tolerated in these xenograft models based on body weight measurements. In summary, SM09419 potently inhibited SRSF6 phosphorylation and Wnt signaling pathway activity and induced apoptosis in FLT3-ITD cell lines. It also inhibited proliferation in cell lines and primary AML cells regardless of FLT3 status. The strong in vivo antitumor effects observed as combination treatment suggest that SM09419 combined with standard therapies may provide a clinical benefit by slowing or preventing relapse in AML with a marker of poor prognosis such as FLT3-ITD. A Phase 1 study assessing safety, tolerability, and pharmacokinetics of SM09419 in subjects with advanced hematologic malignancies is being initiated. Disclosures Chung: Samumed, LLC: Employment, Equity Ownership. Creger:Samumed, LLC: Employment, Equity Ownership. Sitts:Samumed, LLC: Employment, Equity Ownership. Chiu:Samumed, LLC: Employment, Equity Ownership. Mak:Samumed, LLC: Employment, Equity Ownership. KC:Samumed, LLC: Employment, Equity Ownership. Tam:Samumed, LLC: Employment, Equity Ownership. Bucci:Samumed, LLC: Employment, Equity Ownership. Stewart:Samumed, LLC: Employment, Equity Ownership. Phalen:Samumed, LLC: Employment, Equity Ownership. Cha:Samumed, LLC: Employment, Equity Ownership.

SM09419, a Novel, Small-Molecule CDC-like Kinase (CLK) Inhibitor, Demonstrates Strong Inhibition of the Wnt Signaling Pathway and Antitumor Effects in Tumor Protein p53 (TP53)-Mutant Acute Myeloid Leukemia Models

Acute myeloid leukemia (AML) with TP53 mutation makes up ~13% of AML cases and is an aggressive, treatment-resistant subtype with dismal prognosis and limited therapeutic options. Aberrant activation of the Wnt signaling pathway is associated with AML initiation/progression and is required for the self-renewal and survival of leukemic stem cells, making Wnt signaling inhibition a potential therapeutic modality for adverse AML. CLKs regulate the activity of serine/arginine-rich splicing factors (SRSFs) that modulate spliceosome assembly, mRNA splicing, and gene expression. SM09419 is a novel, oral, small-molecule pan-CLK inhibitor that potently inhibits the Wnt pathway in a Wnt signaling reporter assay. The purpose of these studies was to examine the antitumor activity of SM09419 as a single agent and in combination with standard therapies in preclinical models of TP53 mutant (TP53mut) AML. In TF-1a and KG-1a AML cells with TP53 mutations, SM09419 dose-dependently inhibited SRSF6 phosphorylation and potently suppressed expression of Wnt-related genes (LEF1, MYC, DVL2) and proteins vs. vehicle. The effect of SM09419 on cell proliferation was tested in 6 TP53mut AML cell lines. Proliferation was strongly impaired by SM09419 across all cell lines (EC50=0.23 + 0.056 µM). SM09419 significantly induced apoptosis in TF-1a and KG-1a cells, increasing caspase 3/7 activation and PARP cleavage while reducing survivin and MCL-1 expression relative to vehicle. In addition, SM09419 potently inhibited cell proliferation when tested in 27 leukapheresis-derived human primary AML cell lines (EC50=0.046 + 0.0061 µM) regardless of TP53 status, cytogenetics, or AML diagnosis (de novo or relapsed/refractory). In vivo antitumor effects and tolerability of oral SM09419 (QD) alone or combined with cytarabine (Ara-C), venetoclax (VEN), or azacytidine (AZA) were assessed in mice bearing TP53mut flank xenografts (n=5-15/group). In TF-1a xenografts, SM09419 (12.5 and 25 mg/kg) induced significant tumor growth inhibition (TGI) vs. vehicle at D20 (TGI 55-56% [p<0.01]). VEN (50mg/kg) was not effective (3% TGI) and combining VEN with SM09419 had no additional benefit (52%-60% TGI). In Kasumi-1 xenografts, SM09419 (12.5 and 25 mg/kg), AZA (0.8 mg/kg), and VEN (25 mg/kg) induced TGI vs. vehicle of 87%, 95% (both p<0.0001), 72% (p<0.001), and 48% (NS), respectively at D18. SM09419 25 mg/kg alone induced tumor regression in 40% (2/5) of the mice. SM09419 (12.5 mg/kg) + VEN induced greater TGI vs. vehicle (96%, p<0.0001) with tumor regression in 80% (4/5) of the mice, while AZA + VEN induced 79% TGI (p<0.001) with no tumor regression. In KG-1a xenografts, single-agent SM09419 (12.5 and 25 mg/kg) and Ara-C (10mg/kg) induced significant TGI vs. vehicle (53%, 98%, and 80% [p<0.001], respectively) at D28 but VEN (12.5mg/kg) did not (35% TGI). The combination of SM09419 (12.5 mg/kg) + VEN (12.5 mg/kg) improved TGI (98%) vs. vehicle. Tumor regression was seen in all mice with single-agent SM09419 (25 mg/kg) and 12.5 mg/kg + VEN. In another KG-1a xenograft study, mice were treated with combinations of SM09419 (12.5 mg/kg), AZA (0.8 mg/kg), and VEN (25 mg/kg) for 20 days followed by 21 days of SM09419 (25 mg/kg) or vehicle maintenance in some groups. SM09419 + VEN, SM09419 + AZA, and AZA + VEN induced TGI of 95%, 64%, and 58%, respectively (all p<0.0001), with 80% (12/15) regression in SM09419 + VEN. The triplet induced 91% TGI but was not well tolerated due to GI toxicity. In the maintenance phase, SM09419 given QD or QOD greatly slowed tumor regrowth vs. vehicle at D41 in mice previously treated with SM09419 + VEN (80% and 72% TGI [p<0.001], respectively). SM09419 QD maintenance therapy also slowed tumor regrowth following AZA + VEN (p<0.0001). SM09419 alone and in combination (except with AZA + VEN) was well tolerated in all tested xenografts. In summary, SM09419 potently inhibited SRSF phosphorylation and Wnt pathway signaling and induced apoptosis in TP53mut AML cell lines. It also inhibited proliferation in cell lines and primary AML cells regardless of TP53 status. Strong in vivo antileukemic effects were observed with SM09419 as a single agent or in combination with other AML therapies, suggesting that it is a potential treatment for hard-to-treat AML subtypes such as TP53mut AML. A Phase 1 study assessing safety, tolerability, and pharmacokinetics of SM09419 in subjects with advanced hematologic malignancies is being initiated. Disclosures Chung: Samumed, LLC: Employment, Equity Ownership. Creger:Samumed, LLC: Employment, Equity Ownership. Sitts:Samumed, LLC: Employment, Equity Ownership. Chiu:Samumed, LLC: Employment, Equity Ownership. Mak:Samumed, LLC: Employment, Equity Ownership. KC:Samumed, LLC: Employment, Equity Ownership. Tam:Samumed, LLC: Employment, Equity Ownership. Bucci:Samumed, LLC: Employment, Equity Ownership. Stewart:Samumed, LLC: Employment, Equity Ownership. Phalen:Samumed, LLC: Employment, Equity Ownership. Cha:Samumed, LLC: Employment, Equity Ownership.

Genomic Profiling of a Phase III Clinical Trial of Interferon Versus Hydroxyurea in MPN Patients Reveals Mutation-Specific and Treatment-Specific Patterns of Response

Background: To investigate the role of genomics in determining response and resistance to front line treatment in MPN, we performed somatic mutational profiling of the DALIAH trial, a randomized controlled phase III trial of interferon versus hydroxyurea in newly diagnosed MPN patients. Methods: We performed genomic analyses on 202 pre-treatment primary MPN samples obtained from patients enrolled on the DALIAH trial (NCT01387763) and 135 samples obtained after 24 months of treatment. Genomic profiling comprised targeted next generation sequencing (NGS) of 100 genes, selected on the basis of their known or suspected involvement in the pathogenesis of myeloid malignancies, and 1609 informative single nucleotide polymorphisms (SNPs) on chromosome 9p. Clinicohematological response was determined by central review using ELN 2009 (ET, PV and pre-MF) and EUMNET 2005 (PMF) criteria. We evaluated the association of somatic mutations with clinical parameters and with attainment of clinicohematological complete response (CR) at 24 months. Results: Prior to treatment, 191 of 202 (95%) patients had somatic mutations, including 93% with canonical MPN phenotypic drivers: JAK2 (74%), CALR (14%), and MPL (5%). Among those with JAK2 mutations 37% had JAK2 copy-neutral loss of heterozygosity (JAK2 CN-LOH). Patients with PV were more likely to have JAK2 CN-LOH (p = 0.0001) as compared with patients with other MPN subtypes. At baseline, patients with JAK2 CN-LOH had significantly higher hemoglobin (p = 0.0001), higher white blood cell count (WBC, p = 0.002) and lower platelet count (p=0.0001) than patients without JAK2 CN-LOH. Mutations in TET2 (24%), DNMT3A (16%), and ASXL1 (10%) were the most frequent co-occurring non-MPN phenotypic driver mutations and they occurred across all MPN subtypes. In addition, 5% of patients had spliceosome gene mutations, and 6% had mutations in genes involved in RAS/MAPK signaling. Patients with TET2, DNMT3A or ASXL1 mutations were significantly older than patients without these mutations (p= 0.0001) and there was a significant association between the presence of a TET2, DNMT3A or ASXL1 mutation and prior stroke (p = 0.004). There were no other significant associations between somatic mutation status and baseline clinical characteristics. The probability of attaining clinicohematological CR at 24 months was independent of baseline somatic mutations. Among patients with JAK2 mutations who remained on interferon treatment at 24 months, those with CR had a greater reduction in mean variant allele fraction (VAF) (28% to 8%, p<0.0001) than those who did not achieve CR (34% to 23%, p=0.03). In contrast, the mutant CALR VAF did not significantly decline in either those achieving CR with interferon treatment (16% to 12%, p=0.38) or those not achieving CR (20% to 16%, p=0.35). In patients with JAK2 mutations treated with hydroxyurea, CR at 24 months was associated with a change in VAF (mean 24% to 13%, p=0.04). Among patients who remained on treatment for 2 years, 44 mutations in 35 patients were newly detected or expanded on serial sampling. DNMT3A mutations were the most frequently acquired, accounting for 41% of new mutations. ASXL1, TET2, PPM1D, TP53, IDH2, and CBL mutations were also recurrently acquired. 97% of patients who acquired new mutations were JAK2-mutant. Among those with acquired DNMT3A mutations, 85% were treated with interferon, and 23% had CR at 24 months. Among those that acquired non-DNMT3A mutations, 38% were treated with interferon and 47% had CR at 24 months. The VAF of newly detected mutations was low (median 1.5%), and half of the patients with newly acquired mutations had at least 50% reduction in JAK2V617F VAF, suggesting that new mutations could either have arisen independently or be subclonal to the dominant JAK2-mutant clone. Conclusions: Using sequential genomic analyses of a phase III clinical trial of interferon versus hydroxyurea in MPN patients, we found mutation-specific and treatment-specific patterns of response. We uncovered distinct patterns of response to interferon in JAK2-mutant MPN as compared with CALR-mutant MPN. We found that DNMT3A mutations were the most frequent acquired mutations at 24 months and that these were enriched in patients treated with interferon. In aggregate, these results provide insights into molecular response and resistance to interferon and inform the clinical use of interferon in MPN patients. Disclosures Hansen: Alexion: Research Funding. Neuberg:Pharmacyclics: Research Funding; Madrigal Pharmaceuticals: Equity Ownership; Celgene: Research Funding. Hasselbalch:Novartis: Research Funding; AOP Orphan Pharmaceuticals: Other: Data monitoring board. Lindsley:Jazz Pharmaceuticals: Research Funding; Takeda Pharmaceuticals: Consultancy; Medlmmune: Research Funding. Mullally:Janssen: Research Funding.

Critical Requirement of U2AF1 in the Maintenance and Function of Hematopoietic Stem Cells

Mutations in the RNA spliceosome genes have been frequently found in myelodysplastic syndromes (MDS). U2AF1 is involved in the recognition of the 3' splice site required for the recruitment of the U2 snRNP during pre-mRNA splicing. U2AF1 mutations have been identified in ~11% cases of MDS and are associated with poor prognosis. However, the role of wild type U2AF1 in normal hematopoiesis has remained unknown. To determine the role of U2AF1 in hematopoietic stem/progenitor cell (HSPC) function and normal hematopoiesis, we have generated a conditional U2AF1 knockout (floxed) mouse. We crossed the U2AF1 floxed mouse with Mx1Cre mouse and the expression of Cre recombinase was induced with pI-pC injection at 4 weeks after birth. All induced Mx1Cre;U2AF1fl/fl (U2AF1-deleted) mice became moribund or died between 11-12 days after pI-pC induction. U2AF1-deleted mice exhibited marked decrease in bone marrow (BM) cellularity and significantly reduced numbers of WBC, neutrophil, RBC and platelet counts in their peripheral blood compared with control animals. Flow cytometric analyses revealed a dramatic decrease in myeloid, erythroid and megakaryocytic precursor cells in U2AF1-deficient mice compared with control animals. Hematopoietic progenitor colony assays showed a marked decrease in myeloid (CFU-GM), erythroid (BFU-E), and megakaryocytic (CFU-Mk) colonies in the BM of U2AF1-deficient mice. Histopathologic analysis revealed severe BM aplasia in U2AF1-deficient mice. Together, these data suggest that deletion of U2AF1 results in profound defects in hematopoietic development. The fatal BM failure in U2AF1-deficient mice prompted us to examine the HSPC compartments in the BM of these animals. We observed a marked decrease in Lin-Sca-1+c-kit+(LSK) and long-term hematopoietic stem cells (LT-HSC), short-term HSC (ST-HSC), and multipotential progenitors (MPP) as well as early progenitors including common myeloid progenitors (CMP), granulocyte-macrophage progenitors (GMP), and megakaryocyte-erythroid progenitors (MEP) in the BM of U2AF1-deficient mice, indicating a defect at the earliest stage of adult hematopoietic development. To determine whether the loss of HSCs in U2AF1-deficient animals is cell autonomous, BM cells from uninduced control (U2AF1fl/fl; no cre) and Mx1Cre;U2AF1fl/fl mice were transplanted into lethally irradiated WT C57BL/6 mice. Six weeks after transplantation, recipients were injected with pI-pC to induce the deletion of U2AF1. All the recipients of U2AF1-deficient BM became moribund within 14 days after pI-pC induction. Deletion of U2AF1 in the recipient animals resulted in pancytopenia and marked decrease in HSC/progenitors, myeloid, erythroid and megakaryocytic cells similar to that observed in the primary U2AF1-deficient mice, suggesting that the hematopoietic defects in U2AF1-deficient HSCs is cell intrinsic. We performed competitive repopulation assays to further evaluate the function of U2AF1-deficient HSCs. BM cells from uninduced control (U2AF1fl/fl; no cre) and Mx1Cre;U2AF1fl/fl mice (CD45.2+) were mixed with CD45.1+competitor BM cells at a ratio of 1:1 and then transplanted into lethally irradiated congenic recipient animals (CD45.1+). Chimerism analysis in the transplanted animals revealed that U2AF1-deficient mice BM cells were completely unable to compete with WT BM cells. The percentages of U2AF1-deficient CD45.2+(donor-derived) LSK, myeloid, B and T cells were markedly reduced in the recipient animals compared with wild type U2AF1 BM donor at 16 weeks after transplantation, indicating that U2AF1-deficiency impairs the repopulation capacity of the HSCs. To gain insights into the mechanism by which U2AF1controls HSC maintenance and function,we performed RNA-sequencing on purified LSK cells from control and U2AF1-deleted mice. Analysis of RNA-sequencing data revealed significant down regulation of genes related to HSC maintenance, cell cycle and JAK-STAT pathway in U2AF1-deficient LSK cells compared with control LSK. RNA sequencing also identified significantly altered splicing events in several important genes in U2AF1-deficient LSK cells. The most commonly altered splicing events were exon skipping/inclusion. We also observed increased phospho-H2AX and DNA damage in U2AF1-deficient BM cells. Overall, our results suggest an essential role for U2AF1 in the maintenance and function of hematopoietic stem cells. Disclosures No relevant conflicts of interest to declare.

CSIG-28. ROLE OF ALTERNATIVE SPLICING IN CONFERRING SPATIAL HETEROGENEITY SIGNATURES IN GBM

Abstract Therapeutic interventions induce cell stress to trigger apoptosis in tumor cells. Specific cellular stressors, including those initiated by radio-chemotherapy, activate distinct pro-death proteins through a multitude of mechanisms. Apoptosis consists of highly regulated pathways involving post-translational modifications and cleavage of proteins leading to sequential inactivation of the main cellular processes e.g. cell cycle progression. Recently, we demonstrated that apoptotic bodies/ApoEVs in GBM transfer spliceosomal machinery components to neighboring cells, which are subsequently internalized and confer survival advantage through changes in mRNA splicing. Following the validation of the role of RBM11, a spliceosomal component in the said intercellular communication, we extended our findings in the characterization of spatially distinct clonally derived sphere lines from tumor edge and core-located tissues from GBM patients. We analyzed the expression of spliceosomal genes in edge and core-derived clones and found spatially distinct splicing capabilities and that the genes that were affected by alternative splicing events in edge and core cells have different splicing of genes that are involved in ubiquitination and regulate cell cycle progression. Downstream analyses revealed that the most promising target is MDM2. Importantly, this gene regulates cell cycle via ubiquitination. Further, western blot revealed differential expression of both RBM11 and MDM2 in egde and core-derived clones.Collectively, the data so far provides motivation for the possibility of finding cellular vulnerabilities in the splicing machinery and thus actionable targets for intervention that accounts for the bearings of spatial heterogeneity.

Regulation of the Neurospora Circadian Clock by the Spliceosome Component PRP5.

Increasing evidence has pointed to the connection between pre-mRNA splicing and the circadian clock; however, the underlying mechanisms of this connection remain largely elusive. In the filamentous fungus Neurospora crassa, the core circadian clock elements comprise White Collar 1 (WC-1), WC-2 and FREQUENCY (FRQ), which form a negative feedback loop to control the circadian rhythms of gene expression and physiological processes. Previously, we have shown that in Neurospora, the pre-mRNA splicing factors Pre-mRNA-processing ATP-dependent RNA helicase 5 (PRP5), protein arginine methyl transferase 5 (PRMT5) and snRNA gene U4-2 are involved in the regulation of splicing of frq transcripts, which encode the negative component of the circadian clock system. In this work we further demonstrated that repression of spliceosomal component sRNA genes, U5, U4-1, and prp5, affected the circadian conidiation rhythms. In a prp5 knockdown strain, the molecular rhythmicity was dampened. The expression of a set of snRNP genes including prp5 was up-regulated in a mutant strain lacking the clock component wc-2, suggesting that the function of spliceosome might be under the circadian control. Among these snRNP genes, the levels of prp5 RNA and PRP5 protein oscillated. The distribution of PRP5 in cytosol was rhythmic, suggesting a dynamic assembly of PRP5 in the spliceosome complex in a circadian fashion. Silencing of prp5 caused changes in the transcription and splicing of NCU09649, a clock-controlled gene. Moreover, in the clock mutant frq9, the rhythmicity of frq I-6 splicing was abolished. These data shed new lights on the regulation of circadian clock by the pre-RNA splicing, and PRP5 may link the circadian clock and pre-RNA splicing events through mediating the assembly and function of the spliceosome complex.

Ring sideroblasts in AML are associated with adverse risk characteristics and have a distinct gene expression pattern

AbstractRing sideroblasts (RS) emerge as result of aberrant erythroid differentiation leading to excessive mitochondrial iron accumulation, a characteristic feature for myelodysplastic syndromes (MDS) with mutations in the spliceosome gene SF3B1. However, RS can also be observed in patients diagnosed with acute myeloid leukemia (AML). The objective of this study was to characterize RS in patients with AML. Clinically, RS-AML is enriched for ELN adverse risk (55%). In line with this finding, 35% of all cases had complex cytogenetic aberrancies, and TP53 was most recurrently mutated in this cohort (37%), followed by DNMT3A (26%), RUNX1 (25%), TET2 (20%), and ASXL1 (19%). In contrast to RS-MDS, the incidence of SF3B1 mutations was low (8%). Whole-exome sequencing and SNP array analysis on a subset of patients did not uncover a single genetic defect underlying the RS phenotype. Shared genetic defects between erythroblasts and total mononuclear cell fraction indicate common ancestry for the erythroid lineage and the myeloid blast cells in patients with RS-AML. RNA sequencing analysis on CD34+ AML cells revealed differential gene expression between RS-AML and non RS-AML cases, including genes involved in megakaryocyte and erythroid differentiation. Furthermore, several heme metabolism-related genes were found to be upregulated in RS- CD34+ AML cells, as was observed in SF3B1mut MDS. These results demonstrate that although the genetic background of RS-AML differs from that of RS-MDS, they have certain downstream effector pathways in common.

Hotspot SF3B1 mutations induce metabolic reprogramming and vulnerability to serine deprivation.

Cancer-associated mutations in the spliceosome gene SF3B1 create a neomorphic protein that produces aberrant mRNA splicing in hundreds of genes, but the ensuing biologic and therapeutic consequences of this missplicing are not well understood. Here we have provided evidence that aberrant splicing by mutant SF3B1 altered the transcriptome, proteome, and metabolome of human cells, leading to missplicing-associated downregulation of metabolic genes, decreased mitochondrial respiration, and suppression of the serine synthesis pathway. We also found that mutant SF3B1 induces vulnerability to deprivation of the nonessential amino acid serine, which was mediated by missplicing-associated downregulation of the serine synthesis pathway enzyme PHGDH. This vulnerability was manifest both in vitro and in vivo, as dietary restriction of serine and glycine in mice was able to inhibit the growth of SF3B1MUT xenografts. These findings describe a role for SF3B1 mutations in altered energy metabolism, and they offer a new therapeutic strategy against SF3B1MUT cancers.

Mutations in spliceosome genes and therapeutic opportunities in myeloid malignancies.

Since the discovery of RNA splicing more than 40 years ago, our comprehension of the molecular events orchestrating constitutive and alternative splicing has greatly improved. Dysregulation of pre‐mRNA splicing has been observed in many human diseases including neurodegenerative diseases and cancer. The recent identification of frequent somatic mutations in core components of the spliceosome in myeloid malignancies and functional analysis using model systems has advanced our knowledge of how splicing alterations contribute to disease pathogenesis. In this review, we summarize our current understanding on the mechanisms of how mutant splicing factors impact splicing and the resulting functional and pathophysiological consequences. We also review recent advances to develop novel therapeutic approaches targeting splicing catalysis and splicing regulatory proteins, and discuss emerging technologies using oligonucleotide‐based therapies to modulate pathogenically spliced isoforms.