SF3B1 WT Research Articles

SF3B1 mutant-induced missplicing of MAP3K7 causes anemia in myelodysplastic syndromes

SF3B1 is the most frequently mutated RNA splicing factor in cancer, including in ∼25% of myelodysplastic syndromes (MDS) patients. SF3B1-mutated MDS, which is strongly associated with ringed sideroblast morphology, is characterized by ineffective erythropoiesis, leading to severe, often fatal anemia. However, functional evidence linking SF3B1 mutations to the anemia described in MDS patients harboring this genetic aberration is weak, and the underlying mechanism is completely unknown. Using isogenic SF3B1 WT and mutant cell lines, normal human CD34 cells, and MDS patient cells, we define a previously unrecognized role of the kinase MAP3K7, encoded by a known mutant SF3B1-targeted transcript, in controlling proper terminal erythroid differentiation, and show how MAP3K7 missplicing leads to the anemia characteristic of SF3B1-mutated MDS, although not to ringed sideroblast formation. We found that p38 MAPK is deactivated in SF3B1 mutant isogenic and patient cells and that MAP3K7 is an upstream positive effector of p38 MAPK. We demonstrate that disruption of this MAP3K7-p38 MAPK pathway leads to premature down-regulation of GATA1, a master regulator of erythroid differentiation, and that this is sufficient to trigger accelerated differentiation, erythroid hyperplasia, and ultimately apoptosis. Our findings thus define the mechanism leading to the severe anemia found in MDS patients harboring SF3B1 mutations.

Whole Transcriptome Analysis Identifies Distinct Gene Expression Profiles between SF3B1mut and SF3B1 wt Myelodysplastic Syndrome with Ring Sideroblasts

Background and aims - The 2016 revised WHO classification incorporated somatic mutation in SF3B1 spliceosome gene within the diagnostic criteria of myelodysplastic syndrome (MDS) with ring sideroblasts (RS). However, SF3B1wt MDS-RS display significantly different clinical features and outcome from those of SF3B1mut MDS-RS. Recently, the recognition of SF3B1-mutant MDS as a distinct nosologic entity has been proposed to overcome this limitation.Methods - To evaluate the biological relevance of this proposal, we studied a consecutive cohort of 132 MDS with RS >5% using a pangenomic approach (targeted-DNA sequencing, genome-wide copy number variation analysis and bulk RNA-sequencing of CD34+ bone marrow mononuclear cells). 16 age-matched healthy individuals and 43 MDS-SLD/MLD negative for both splicing mutation and RS were included in this study as controls.Results - Unsupervised clustering analysis based on mutation profiles identified two major clusters predicted by SF3B1 mutation (87 MDS-RS-SF3B1mut and 45 MDS-RS-SF3B1wt). The most recurrently mutated genes in MDS-RS-SF3B1wt were TP53(40%), SRSF2(38%), TET2 (33%), ASXL1 (21%) and DNMT3A (12%). SRSF2 and TP53 mutations were found to be mutually exclusive with SF3B1 (p-value <0.05), whereas no difference was found in TET2, DNMT3A and ASXL1 frequencies between MDS-RS-SF3B1 mutand MDS-RS-SF3B1wt subgroups. TP53-mutated MDS-RS exhibited shorter overall survival (median 1.3 years, log-rank p-value<0.0001) compared to SF3B1mut (median 7.6 years), SRSF2mut (median 3.4 years) and MDS-RS without the abovementioned aberrations (median 4.4 years). Notably, allelic imbalances analysis of oncogenic variants identified a significant enrichment of TP53 biallelic inactivation in MDS-RS-SF3B1wt (64% vs 0, p<0.01).Differential gene expression analysis results were incorporated into a specific expression signature highly predictive of MDS-RS-SF3B1 mutand MDS-RS-SF3B1wt subgroups (Figure 1). The resulting gene clusters were classified in RS-specific genes (cluster 1 and 2) and SF3B1-specific genes (cluster 3 and 4). RS-specific genes comprising heme and hypoxia genes were enriched (Figure 2AB) and correlated with RS percentage (p<0.01). Pathway analysis revealed a specific downregulation of adhesion molecules and an upregulation of G-protein coupled receptor signaling molecules in MDS-RS-SF3B1mut. Among SF3B1-specific genes (Figure 2CD), we confirmed ABCB7 downregulation and identified new molecular targets that may concur to the pathophysiology of SF3B1-driven myeloid neoplasms.Conclusions - This study contributes to unveil molecular features of SF3B1-mutant MDS and provides further evidence to support recognition of somatic SF3B1 mutation as a disease-defining genetic lesion. DisclosuresPapaemmanuil: Isabl Technologies: Divested equity in a private or publicly-traded company in the past 24 months; Kyowa Hakko Kirin Pharma: Consultancy.

Mutational Profile and Analysis of Lower-Risk Myelodysplastic Syndromes (MDS) Patients Treated with Luspatercept: Phase 2 PACE-MDS Study

Background: Management of anemia is a common therapeutic challenge in patients (pts) with MDS. Luspatercept (ACE-536), a fusion protein containing modified activin receptor type IIB, is being developed for treatment of anemia in lower-risk MDS. Luspatercept acts as a ligand trap for GDF11 and other TGF-β family ligands to suppress Smad2/3 signaling, promote late-stage erythroid differentiation, and increase hemoglobin (Hgb) levels (Suragani R, Nat Med, 2014; Attie K, Am J Hematol, 2014). Luspatercept has demonstrated clinical activity in ring-sideroblast positive (RS+,≥15% in bone marrow) MDS pts and comparable responses in non-RS+ pts with EPO<500 U/L. While RS+ pts have distinct clinical and molecular features including SF3B1 splicing mutations, non-RS+ pts have a more heterogeneous population of mutations.Aims: This ongoing, phase 2, multicenter, open-label study followed by a long-term extension (ext) study evaluates the effects of luspatercept in pts with lower-risk MDS. Endpoints include long-term safety and tolerability, erythroid response (IWG HI-E), RBC transfusion independence (RBC-TI,≥8 weeks), and duration of HI-E. New analyses focus on clinical, molecular, and bone marrow morphological features of disease and factors associated with luspatercept response.Methods: Inclusion criteria: MDS IPSS low or int-1, age ≥18 yr, Hgb<10 g/dL (if <4U RBC/8 wks), no prior HMA, no current lenalidomide or erythropoiesis-stimulating agent (ESA). The dose-escalation phase of the study is completed. An expansion cohort was added to this phase 2 study to evaluate response in pts not qualified for the phase 3 MEDALIST trial (for regularly transfused RS+ pts refractory to ESA or EPO>200 U/L). These include pts with low transfusion burden (<4U RBC/8 weeks) and either 1) RS+ with baseline EPO ≤200 U/L or 2) non-RS+ and any EPO level. Non-RS+ pts allowed up to 6U RBC/8 wks. Pts treated every 3 weeks subcutaneously for up to 5 doses (titration up to 1.75 mg/kg) in the base study (NCT01749514) and are then eligible for long-term treatment up to 5 additional years (NCT02268383).Results: Data (as of 13Apr2017) were available for 88 pts treated at therapeutic dose levels (≥0.75 mg/kg) in both the base and ext studies. 88 pts were evaluable for IWG HI-E and 60 pts were evaluable for RBC-TI (baseline transfusions of ≥2 units/8 wks). 75 pts were evaluable for mutational data analysis.Baseline characteristics are shown in Table 1. In pts with mutational data, the most common mutations were SF3B1 (57%), TET2 (39%), DNMT3A (21%), ASXL1 (17%), and SRSF2 (11%). Response by subgroup is shown in Table 2.Responses were observed in both RS+ and non-RS+ pts of various mutational backgrounds. Many pts possessed mutations in multiple genes; pts carrying SF3B1 mutations tended to have increased response rates compared to SF3B1 WT pts. Other commonly observed (>10%) mutations (TET2, DNMT2A, ASXL1, and SRSF2) demonstrated similar responses in pts when either mutated or not. Longer-term data on all pts plus additional exploratory analyses of molecular, cellular, and morphologic parameters and their relationship to response will be presented at the meeting.Luspatercept has been well tolerated, with seven possibly related grade 3 non-serious adverse events (AE): ascites, blast cell count increase, blood bilirubin increase, bone pain, hypertension, platelet count increase, and pleural effusion and four possibly related SAEs as of 15June2017: ataxia, general physical health deterioration, muscle weakness, and myalgia. Related AEs in >2 pts were headache, fatigue, hypertension, bone pain, diarrhea, arthralgia, injection site erythema, myalgia, and peripheral edema.Conclusions: Lower-risk MDS pts treated long-term with luspatercept demonstrated robust and sustained increases in Hgb and decreases in transfusion burden and a high rate of RBC-TI. Encouraging responses were seen across EPO levels up to 500 U/L in both RS+ and non-RS+ patients. The presence of an SF3B1 mutation was associated with a higher response in this initial cohort of pts and responses were also observed in SF3B1 WT pts with mutations typically associated with poor prognosis (e.g., ASXL1). The data support continued study of luspatercept in MDS pts, including aPhase 3 study in regularly-transfused RS+ pts with lower-risk MDS according to IPSS-R (MEDALIST study; NCT02631070; fully enrolled) and a future Phase 3 study planned in first-line lower-risk MDS pts. [Display omitted] DisclosuresPlatzbecker:Acceleron: Consultancy, Honoraria, Research Funding; Novartis: Consultancy, Research Funding; Celgene: Consultancy, Honoraria, Research Funding; Janssen: Consultancy, Honoraria, Research Funding. Kiewe:Acceleron: Consultancy, Honoraria, Research Funding. Germing:Novartis: Honoraria, Research Funding; Janssen: Honoraria; Celgene: Honoraria, Research Funding. Götze:Celgene: Honoraria; Novartis: Honoraria; BMS: Honoraria; Abbvie: Honoraria. Radsak:Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel support, Research Funding; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel support; Gilead: Other: Travel support; Acceleron: Research Funding. Wilson:Acceleron: Employment, Equity Ownership. Zhang:Acceleron: Employment, Equity Ownership. Rovaldi:Acceleron: Employment, Equity Ownership. Laadem:Celgene: Employment, Equity Ownership. Sherman:Acceleron: Employment, Equity Ownership. Attie:Acceleron: Employment, Equity Ownership. Reynolds:Acceleron: Employment, Equity Ownership. Linde:Acceleron: Employment, Equity Ownership. Giagounidis:Celgene: Consultancy; Acceleron: Consultancy.

SF3B1 Splicing Mutation in the Context of Therapy Related MDS

Background: Therapy related myelodysplastic syndromes (t-MDS) account for 10-20% of all myelodysplastic syndromes (MDS). They are associated with poor outcome namely driven by high occurrence of poor risk cytogenetics and TP53 mutations. Acquired SF3B1 splicing mutation is the sole somatic mutation (SM) associated with favorable outcome in de novo MDS and is described among 80% of patients with ring sideroblasts (RS) subytpe. The prognostic value of SF3B1 SM in the context of t-MDS has not been reported. We aimed to compare the outcomes of patients with SF3B1 mutation (mut) between t-MDS and de novo MDS, and the outcome among t-MDS patients harboring SF3B1 mut to those with SF3B1 wild type t-MDS. Patients and Methods: Patients with myelodysplastic syndrome seen at Moffitt Cancer Center between 2013 and 2019 were evaluated and included for analysis. SF3B1 mutational status was assessed via next generation sequencing. We included patients with known SF3B1 status. These patients were further stratified into de novo MDS and those with t-MDS. Further, outcomes of t-MDS patients were evaluated based on SF3B1-mut vs SF3B1-WT. Baseline characteristics were compared by chi square (categorical variables) and t- test (continuous variables). Survival estimates were calculated using the Kaplan-Meier method from date of diagnosis and groups were compared using log-rank test. Multivariate survival analysis performed by means of Cox proportional hazards regression. Results: In a large cohort of patients with myelodysplastic syndrome, 320 patients were identified with SF3B1 SM who were classified as de novo MDS (n=289) and t-MDS (n=31). Baseline characteristics were similar among both groups with t-MDS patients being slightly older and harboring high risk cytogenetics. Mutational distribution was also similar except for CBL which was more observed in t-MDS compared to de novo (10% vs 1%, p-value =.002). AML, transformation rate was 12.5% vs 12.9% for de novo MDS and t-MDS respectively, p-value .943. Median overall survival (OS) in those with de novo MDS SF3B1-mut vs t-MDS SF3B1-mut was 103 months vs 59 months, p-value .001. t-MDS patients were then stratified by wild type SF3B1 (SF3B1-WT) and SF3B1-mut. Of the 272 t-MDS in our database with known SF3B1 status, 31 were SF3B1-mut (11%). Of those with SF3B1-mut, 60% were classified as MDS-RS compared to 4.1% of those SF3B1-wt with t-MDS. Complex cytogenetics were seen in 37.4% vs 10.3% of patients with SF3B1-WT vs SF3B1-mut, p-value .009. TP53 mutation was seen in 36.1% SF3B1-WT vs 10% SF3B1-mut, p-value .004. AML transformation rate was 34.4% in SF3B1-WT compared to 12.9% SF3B1-mut, p-value .016. Median overall survival was17 months in SF3B1-WT vs 43 months in SF3B1-mut, p-value .004. Conclusion: In our study, SF3B1 mutations are more commonly seen in de novo than in therapy related MDS. De novo MDS SF3B1-mut had better outcomes compared to t-MDS SF3B1-mut although rate of AML transformation was similar. In patients with therapy related MDS, those with SF3B1-mut had better outcomes than those with SF3B1-WT. Additionally complex cytogenetics, TP53 mutation, and transformation to AML occurred more with SF3B1-WT than with SF3B1-mut. In the absence of SF3B1 mut, t-MDS with ring sideroblasts has been reported to have higher rate of TP53 mut compared to de novo MDS-RS. To our knowledge, our data is first to suggest that among t-MDS patients, SF3B1-mut may portend a better prognosis. Disclosures Padron: BMS: Research Funding; Novartis: Honoraria; Kura: Research Funding; Incyte: Research Funding. Sallman:Celgene, Jazz Pharma: Research Funding; Agios, Bristol Myers Squibb, Celyad Oncology, Incyte, Intellia Therapeutics, Kite Pharma, Novartis, Syndax: Consultancy. Komrokji:Acceleron: Honoraria; Geron: Honoraria; Agios: Honoraria, Speakers Bureau; AbbVie: Honoraria; JAZZ: Honoraria, Speakers Bureau; Incyte: Honoraria; Novartis: Honoraria; BMS: Honoraria, Speakers Bureau.

MDS-254: SF3B1 Splicing Mutation in the Context of Therapy-Related MDS

Context: Acquired SF3B1 splicing mutation is the sole somatic mutation associated with favorable outcome in MDS and is described among 80% of patients with the ring sideroblasts subtype. Objective: Evaluate clinical characteristics and outcomes of SF3B1-mt in therapy-related MDS (t-MDS) Design: We identified all patients with MDS harboring the SF3B1 mutation at Moffitt Cancer Center and compared t-MDS to de novo MDS. Additionally, we evaluated those with t-MDS and further stratified them into wild-type SF3B1 (SF3B1-WT) and SF3B1-mut and compared these two groups. Results: In a large cohort of patients with MDS, we identified 320 patients with SF3B1 mutations. These were further stratified to de novo MDS (n=289) and those with therapy-related MDS (n=31). Baseline characteristics and concomitant mutations were similar among both groups, except for concomitant CBL in de novo MDS vs in t-MDS (1% vs 10%; p = 0.002). Transformation to AML between dn-MDS SF3B1-mut vs t-MDS SF3B1-mut was 12.5% vs 12.9%, respectively (p = 0.943). Median overall survival in those with de novo MDS SF3B1-mut vs t-MDS SF3B1-mut was 103 months vs 59 months, p = 0.001. During further investigation of all therapy-related MDS patients, were then stratified by wild-type SF3B1 (SF3B1-WT) and SF3B1-mut. Of the 272 t-MDS, 31 were SF3B1-mut (11%). Complex cytogenetics was seen in 37.4% vs 10.3% of patients with SF3B1-WT vs SF3B1-mut, p = 0.009. Concomitant TP53 mutations were seen in 36.1% SF3B1-WT vs 10% SF3B1-mut, p = 0.004. AML transformation was 34.4% in SF3B1-WT compared to 12.9% SF3B1-mut, p-value 0.016. Median overall survival was 17 months in SF3B1-WT vs 43 months in SF3B1-mut, p = 0.004. Conclusions: SF3B1 mutations are more commonly seen de novo than in therapy-related MDS. After comparison, baseline characteristics and concomitant mutations were similar; however, de novo MDS SF3B1-mut had better outcomes versus t-MDS SF3B1-mut, although incidence of transformation to AML was similar. In patients with therapy-related MDS, those with SF3B1-mut had better outcomes than those with SF3B1-WT. Additionally, complex cytogenetics, concomitant TP53 mutation, and transformation to AML occurred more with SF3B1-WT than with SF3B1-mut. Our data suggest that SF3B1-mut compared to SF3B1-WT in t-MDS may portend a better prognosis; however, further studies are warranted to confirm this finding.

Marrow Ring Sideroblasts Are Highly Predictive for TP53 Mutation in MDS with Excess Blasts

Background: Myelodysplastic syndrome with ring sideroblasts (MDS-RS) is defined by the World Health Organization (WHO) as ring sideroblasts (RS) ≥15% or ≥5% with associated SF3B1 mutation and no excess blasts (EB). In MDS-RS, SF3B1 mutation defines a homogenous group with isolated erythroid dysplasia and favorable prognosis (Malcovati et al. Blood 2015). Given the separate WHO classification, patients with MDS-EB frequently are not tested for RS. SF3B1-wild type (wt) MDS with RS also has not been well characterized. Therefore, herein we characterized MDS with RS, focusing on SF3B1-wt and implications of molecular subsets. Patients and Methods: Between 2013 and 2018, 157 MDS and MDS/MPN patients with RS ≥5% and next generation sequencing performed within 6 months of diagnosis at Moffitt Cancer Center were identified with clinical variables obtained at date of diagnosis. Quantification of RS was performed in all cases by hematopathology. Baseline characteristics were compared by Fisher's exact test (categorical variables) and Mann-Whitney test (continuous variables). Survival estimates were calculated using the Kaplan-Meier method from date of diagnosis and groups were compared using log-rank test. Multivariate survival analysis performed by means of Cox proportional hazards regression. Pearson correlation coefficient was used in correlative analyses. Results: A total of 75 SF3B1-mutant (mt) and 82 SF3B1-wt cases with MDS (141) or MDS/MPN (13) and RS were identified. Median age was 71 years (38-89) with male and Caucasian predominance (62% and 94%, respectively). In the SF3B1-wt cohort, there were 77 MDS and 5 MDS/MPN patients. The MDS patients consisted of 2 MDS-SLD, 15 MDS-MLD, 3 MDS-RS-SLD, 17 MDS-RS-MLD, 24 MDS-EB1 and 16 MDS-EB2. The majority of SF3B1-wt patients (58%) were high or very high risk based on the Revised International Prognostic Scoring system (IPSS-R). Median RS% was significantly lower in SF3B1-wt compared to SF3B1-mt (18% (5-50) vs 35% (5-83) p &lt;0.0001). TP53 was the most common mutation (54%) in the SF3B1-wt cohort (n=44; Figure 1). Additional mutations observed in &gt;10% of the SF3B1-wt cohort were DNMT3A 18% (n=15), TET2 16% (n=13) and U2AF1 16% (n=13). Non-SF3B1 spliceosome mutations represented 27% (n=22) of the SF3B1-wt cohort. TP53-mt and non-SF3B1 spliceosome-mt were observed at significantly higher prevalence in SF3B1 wt vs mt patients (p&lt;0.0001 and p=0.003). In univariate analysis, IPSS-R, TP53 and DNMT3A were associated with worse overall survival in SF3B1-wt patients (OS). In multivariate analysis including age, IPSS-R and BMT, only TP53 was an independent covariate for inferior survival (HR 6.3; 95% CI 2.4-16.6 p&lt;0.0001). Given the high frequency of mutations, we then focused on TP53-mt RS patients. In the total cohort of patients with RS≥5%, 77% of MDS-EB1 and 68% of MDS-EB-2 were TP53-mt. In SF3B1 wt patients with RS≥5% and excess blasts, TP53 mutation was identified in 79% (n=19) and 81% (n=13) of MDS-EB-1 and MDS-EB-2 patients, respectively (p&lt;0.0001 TP53-mt MDS-EB vs other). 3 patients were co-mutant for TP53 and SF3B1. Increased RS as defined as &gt;15% vs 5-15% resulted in improved OS in the TP53-mt cohort (median OS 13.5 vs 8.6 months; HR 0.36 95% CI 0.14-0.93 p=0.034). In multivariate analysis including age, IPSS-R and BMT, the survival advantage was maintained (HR 0.35 95% CI 0.14-0.93 p=0.034). Increased RS did not significantly improve OS in any other somatic mutation. Response to hypomethylating agents was similar between TP53-mt RS &gt;15% vs 5-15% (Complete remission (CR) 21% vs 17% p=1.0 and overall response rate (ORR) 52% vs 42% p=.72). No TP53-mt RS patients responded to lenalidomide (0/4). The proportion of patients receiving allogeneic stem cell transplant was similar between TP53-mt RS &gt;15% vs 5-15% (14% vs 22% p=0.69). There was no difference in distribution of TP53-mt between 5-15% RS cohort vs &gt;15% (55% n=26 vs 51% n=18 p=0.82). Finally, TP53 VAF did not correlate with RS percentage (p=.393) Conclusions: In our study, MDS-RS-EB was highly concordant with the presence of TP53 mutation occurring in 80% of SF3B1-wt patients. In TP53 mutant patients, increased ring sideroblast % was an independent covariate associated with a significant survival advantage. As therapy targeting TP53 emerges, the ability to rapidly predict TP53 mutation status based on presence of ring sideroblasts should be a priority. Figure Disclosures Komrokji: Agios: Consultancy; celgene: Consultancy; pfizer: Consultancy; DSI: Consultancy; JAZZ: Consultancy; Incyte: Consultancy; Novartis: Speakers Bureau; JAZZ: Speakers Bureau. List:Celgene: Membership on an entity's Board of Directors or advisory committees, Research Funding. Sallman:Abbvie: Speakers Bureau; Novartis: Speakers Bureau; Jazz: Research Funding; Incyte: Speakers Bureau; Celyad: Membership on an entity's Board of Directors or advisory committees; Celgene: Research Funding, Speakers Bureau.

Dependency of Spliceosomal Mutant MDS on Innate Immune Signaling

Mutations in genes encoding RNA splicing factors constitute the most common class of genetic alterations in patients with myelodysplastic syndromes (MDS). These occur as heterozygous point mutations at specific amino acid residues in SF3B1, SRSF2, and U2AF1, and are almost always mutually exclusive with one another. Recent studies have identified that mutations in each of these genes results in activation of the innate immune signaling through altered splicing of mRNAs encoding key enzymes in this pathway. Now, through an unbiased genetic screen as well as focused genetic studies, we have identified that SF3B1-mutant MDS depends on aberrant immune signaling for cell survival.Recent work has identified that aberrant splicing of MAP3K7 (also known as TAK1; TGF-b Activating Kinase 1) is pervasive across SF3B1-mutant human and mouse cells and results in reduced MAP3K7 protein expression and increased NF-κB signaling. Consistent with this, Map3k7 haploinsufficiency in myeloid cells is known to cause myeloproliferation, while at the same time, complete loss of Map3k7 is intolerable for hematopoietic cells. We therefore hypothesized that partial inhibition of MAP3K7 might preferentially impact SF3B1-mutant cells. To test this hypothesis, we generated mice with inducible deletion of 1 or 2 copies of Map3k7 (Mx1-cre Map3k7fl/+,Mx1-cre Map3k7fl/fl) alone or in the presence of mutant Sf3b1K700E (Mx1-cre Map3k7fl/+Sf3b1K700E/+,Mx1-cre Map3k7fl/flSf3b1K700E/+), along with all controls (Mx1-cre Sf3b1+/+ Map3k7+/+ (Wildtype; WT) and Mx1-cre Sf3b1K700E/+ mice). We then performed bone marrow transplantation (BMT) to assess the effect of Map3k7 deletion on aberrant hematopoiesis driven by mutant SF3B1. Consistent with prior reports, heterozygous deletion of Map3k7did not affect repopulating potential in BMT assays compared to controls while homozygous deletion of Map3k7 resulted in complete failure of hematopoiesis (Figure A). Interestingly, however, in the presence of Sf3b1K700E mutation, deletion of a single copy of Map3k7 completely rescued the hematopoietic defects characteristic of mutant SF3B1 in both mature and immature cells (Figure B-C). These data suggest that inhibition of residual MAP3K7 function may preferentially target SF3B1-mutant MDS cells.In parallel to the above studies, we also performed a negative selection RNAi screen to uncover novel genetic dependencies in SF3B1-mutant myeloid neoplasms. We performed pooled lentiviral infection of shRNAs targeting ~2,200 genes encoding proteins which are drug targets (“The Druggable Genome”) under the control of a doxycycline-inducible vector in isogenic K562 cells expressing the two most commonly occurring SF3B1 mutations, SF3B1K666N and SF3B1K700E, from the endogenous SF3B1 locus. Two individual clones per SF3B1-mutant line were used to improve the robustness of the screen. On Day 21 following shRNA activation, genes with ≥3 shRNAs depleted in SF3B1-mutant cells while remaining unchanged in parental K562 cells were selected. This identified 101 candidates that are potentially synthetic-lethal with SF3B1 mutation (Figure D). Interestingly, pathway analysis of these potential candidates revealed of genes involved in immune and inflammatory signaling as well as in metabolic processes (Figure E). Further target validation was performed using in vitro competitive growth assay in K562 cells, and another set of SF3B1 isogenic lymphoid leukemia cell lines (NALM-6) expressing the same mutations. This revealed consistent dependency of SF3B1-mutant cells on STAT1, an essential component of the interferon (IFN) signaling pathway (Figure F). Upon exposure to Type-I IFNs, SF3B1-mutant K562 cells showed increased transcriptional response in IFN-responsive genes containing interferon stimulated response elements (ISREs) compared with SF3B1 WT cells (Figure G). These data highlight that SF3B1-mutant cells are hyper-responsive to IFN signaling and require intact IFN-signaling responses for cell survival.Taken together, the above studies indicate that sustained IFN signaling as well as activated innate immune signaling downstream of TAK1 are required for the survival of SF3B1-mutant myeloid cells. These results therefore have important therapeutic implications as they suggest that pharmacologic inhibition of STAT1/Type I IFN activation and/or TAK1 may serve as important therapeutic agents for SF3B1-mutant MDS. DisclosuresNo relevant conflicts of interest to declare.

Mutations in the RNA Splicing Factor SF3B1 Promote Transformation through MYC Stabilization

Mutations in the RNA splicing factor SF3B1 are recurrent in CLL and myeloid neoplasms but their functional role in promoting tumorigenesis remain poorly understood. While SF3B1 mutations have been identified as promoting use of aberrant 3' splice sites (3'ss), consistent identification of mis-spliced transcripts and pathways that functionally link mutant SF3B1 to transformation remains elusive. Moreover, large-scale analyses of the impact of mutant SF3B1 on gene expression and gene regulatory networks, which may be distinct from aberrant splicing changes, remain to be performed. We therefore sought to elucidate the effects of SF3B1 mutations across hematopoietic malignancies and cancer lineages at the level of both mRNA splicing and expression. To this end, we collected RNA-seq data from 79 tumors and 12 isogenic cell lines harboring SF3B1 hotspot mutations. The most frequent hotspot, K700E, was the most common mutation in CLL and breast cancers while mutations at position R625 were restricted to melanomas (Figure A, B).Regulatory network analysis of differentially expressed genes in SF3B1 mutated CLL identified MYC as the top master regulator (Figure C). MYC activation in SF3B1 mutated CLL was also verified by differential expression analyses (Figure D) and was common to SF3B1K700E mutant cancers while absent in cancers with mutations affecting R625. Taken together, these observations suggested that tumors harboring SF3B1K700E mutations activate the MYC transcriptional program.We next sought to verify the effects of c-Myc activation by mutant Sf3b1 in the B-cell lineage in vivo. We crossed Cd19-cre Sf3b1K700E/+ mice with Eμ-Myc transgenic mice to generate Cd19-cre+ control, Sf3b1K700E/+, Eμ-MycTg/+, and Sf3b1K700E/+Eμ-MycTg/+ double-mutant mice. While control or single mutant primary mice did not develop disease over one year, double-mutant mice developed a lethal B-cell malignancy. This effect was consistent in serial transplantation, where mice transplanted with double-mutant cells had shorter survival compared to single-mutant controls (Figure E). These data provide the first evidence that SF3B1 mutations contribute to tumorigenesis in vivo.To understand the molecular mechanism for MYC activation across SF3B1 mutant human and mouse cells, we analyzed RNA-seq data from CLL patients, isogenic Nalm-6 cells, and splenic B-cells from the mouse models. This revealed a significant overlap in aberrant (3'ss) events across SF3B1 mutant samples. Interestingly, mis-spliced events across mouse and human SF3B1K700E mutant samples identified aberrant 3'ss usage and decay of PPP2R5A (Figure F), a gene whose product has previously been shown to regulate c-MYC protein stability and the only gene whose aberrant splicing was most prominent in K700E compared with R625 mutant SF3B1. PPP2R5A is a subunit of the PP2A phosphatase complex that dephosphorylates Serine 62 (S62) of c-MYC, resulting in an unstable form of c-MYC that is a substrate for proteasomal degradation. Consistent with this, SF3B1K700E mutant cells exhibited dramatic increase in S62-phosphorylated c-MYC and increased stability of c-MYC protein. MYC expression, stability, and S62 phosphorylation could be abrogated in SF3B1 mutant cells by restoring PPP25RA expression. In addition to c-MYC S62 phosphorylation, PPP2R5A-containing PP2A reduced S70 phosphorylation of BCL2 (a modification important for apoptosis induction) in SF3B1 mutant cells. To functionally evaluate the importance of impaired PP2A enzymatic activity in SF3B1 mutant cells further, we assessed the therapeutic potential of the FDA-approved oral PP2A activator, FTY-720. SF3B1 mutant cells were more sensitive to FTY-720 treatment than SF3B1 WT counterparts, experiencing growth arrest at lower concentration (Figure G). Moreover, both S62-phosphorylated c-MYC and S70-phosphorylated BCL2 decreased in a dose-dependent manner upon treatment with FTY-720 (Figure H).Here through combined evaluation of the effects of the SF3B1 mutation on splicing, gene expression, and transcriptional networks across cancer types, we identify a novel mechanism by which mutant SF3B1-mediated alterations in RNA splicing contribute to activation of oncogenic MYC through effects on MYC proteolysis. Moreover, these data highlight a novel therapeutic approach targeting the impact of mutant SF3B1 on post-translational modification of MYC. DisclosuresMato:Janssen: Consultancy, Honoraria; Celgene: Consultancy; Prime Oncology: Speakers Bureau; TG Therapeutics: Research Funding; Regeneron: Research Funding; Abbvie: Consultancy; Sunesis: Honoraria, Research Funding; Acerta: Research Funding; AstraZeneca: Consultancy; Pharmacyclics: Consultancy, Honoraria, Research Funding.

Response to Treatment Among SF3B1 Mutated Myelodysplastic Syndromes (MDS): A Case-Control Study from the MDS Clinical Research Consortium (MDS CRC)

IntroductionSomatic mutations in SF3B1 ,a gene encoding a core component of RNA splicing machinery, have been identified in patients (pts) with myelodysplastic syndrome (MDS). The SF3B1 mutation (MT) is more commonly detected in pts with ring sideroblasts (RS) morphology and is associated with favorable outcome. The pattern of response among SF3B1 mutated MDS pts to available treatment options, including erythropoiesis stimulating agents (ESA), hypomethylating agents (HMA) and lenalidomide is not known. The distinct underlying disease biology among such pts may alter response to treatment.MethodsPts treated at MDS CRC institutions with MT vs wild-type SF3B1 (WT) controls were matched 1:2. Matching criteria were age at diagnosis, year of diagnosis and International Prognostic Scoring System (IPSS) category at diagnosis. IPSS category was split into two groups (Low or Int-1 vs. Int-2 or High). Matching was performed using the R package by calculating a propensity score, which was then used to determine the two most similar WT SF3B1 patients for each SF3B1-mutated pt, without replacement. Additionally, to be included in the population, pts also had to have been treated with one of the following: ESAs, HMA, or lenalidomide. Response to treatment was evaluated by international Working Group criteria (IWG 2006) and classified as response if hematological improvement or better was achieved (HI+). Survival was calculated from date of treatment until date of death or last known follow-up, unless otherwise noted.Results:We identified 48 Pts with MT and 96 matched controls. Table 1 summarizes baseline characteristics comparing MT vs WT SF3B1 cohorts. SF3B1 MT was detected more often in association with RS, as expected. The majority of pts had lower-risk disease by IPSS and revised IPSS (IPSS-R). Pts with MT had higher platelets than controls. The most common concomitant somatic mutations observed were TET2 (30%), DNMT3A (21%), and ASXL1 (7%). Median follow-up time from diagnosis was 35 months (mo). Median overall survival (OS) from diagnosis was significantly longer for patients with SF3B1 MT (108.5 mo (68.8, NA)) than wild-type controls (28.3 mo (22.3, 36.4); p < 0.001). Patients with an SF3B1 MT had a decreased hazard of death (hazard ratio [HR]: 0.49 (95% confidence limits [95% CL]: 0.29, 0.84); p = 0.009)ESA was the first line therapy for 43 pts (88%) with MT and 55 WT Pts (56%). For ESA treated pts, 14 out 40 MT Pts responded (35%) compared to 9/56 among WT Pts (16%), p 0.032. Among those treated with HMA therapy, 5 out 21 (24%) MT pts responded compared to 11/46 (24%) WT Pts (p 0.99). Finally, for Pts treated with lenalidomide 4/16 (25%) and 4/21 (19%) responded among SF3B1 MT and WT Pts respectively, p 0.7.ConclusionsSF3B1 somatic mutation in MDS is commonly associated with RS, lower risk disease, and better OS. Pts with SF3B1 mutation had higher response to ESA compared WT SF3B1. No difference in response to HMA or lenalidomide was observed compared to WT patients. Response rates to lenalidomide and HMA were low in both MT patients and controls. Biologically rational therapies are needed that target this molecular disease subset.Table 1Baseline characteristicsSF3B1 MT (n=48)SF3B1 WT (n=96)P valueAgemedian65670.6Gendermale29 (60%)64(67%)0.5RaceWhite44/45 (98%)83/90 (92%)0.34WHO classificationRA RARS RCMD RARS-T Del5 q RAEB-I RAEB-II MDS-U MDS/MPN CMML3 24 8 4 1 3 3 2 0 06 9 17 2 6 10 9 3 11 9IPSSLow Int-1 Int-2 High29 (60%) 16 (33%) 3 (6%) 021 (22%) 69 (72%) 4 (4%) 2 (2%)< 0.001IPSS-RVery low Low Intermediate High Very High15 (31%) 26 (54%) 5 (10%) 2 (4%) 011 (11%) 37 (39%) 26 (27%) 18 (19%) 4 (4%)<0.001Lab values (mean)Hgb Platelets ANC myeloblasts9.7 274 2.63 19.6 108 1.92 20.46 <0.001 0.04 0.05 DisclosuresKomrokji:Novartis: Research Funding, Speakers Bureau; Celgene: Consultancy, Research Funding; Incyte: Consultancy; Pharmacylics: Speakers Bureau. Padron:Novartis: Speakers Bureau; Incyte: Research Funding. List:Celgene Corporation: Honoraria, Research Funding. Steensma:Incyte: Consultancy; Amgen: Consultancy; Celgene: Consultancy; Onconova: Consultancy. Sekeres:Celgene Corporation: Membership on an entity's Board of Directors or advisory committees; TetraLogic: Membership on an entity's Board of Directors or advisory committees; Amgen: Membership on an entity's Board of Directors or advisory committees.

Somatic Gene Mutations Serve As Molecular Biomarkers Predictive for Response to Immunosuppressive Therapy (IST) in Myelodysplastic Syndromes (MDS)

IntroductionImmunosuppressive therapy (IST) yields durable hematologic improvement (HI) in a subset of patients (pts) with lower risk MDS. Age, HLA-DR15+, and duration of transfusion dependence are the strongest independent clinical variables predictive for response. We investigated the impact of somatic gene mutations on response to IST in lower risk MDS pts.MethodsMDS pts who received ATG +/- CSA were identified at the Moffitt Cancer Center. The National Institutes of Health (NIH) IST response model was calculated for each pt. Next Generation sequencing (NGS) for somatic gene mutations was conducted using DNA extracted from archived BM prior to therapy. All pts underwent mutation analysis by a 49 myeloid gene panel. The library was generated with the ThunderBolt (RainDance Technologies, Billerica, MA) and sequenced on a MiSeq instrument (Illumina, San Diego, CA). Alignment and variant calling was performed with NextGene (Soft Genetics, State College, PA).ResultsSixty-six pts treated with ATG +/- CSA were identified. Median age was 61 and the majority of pts had IPSS lower risk disease with favorable risk karyotype. Median time to initiation of IST was 1 year. All pts received ATG (60% rabbit (r-ATG); 32% equine (e-ATG)), and CSA was used in 60% of pts. Overall frequency of HI was 42% with a trend favoring e-ATG vs. r-ATG (52% vs. 39%, p=0.09). Erythroid HI was evaluable in 30 pts with 60% responding, neutrophil improvement was evaluable in 15 pts and 39% responded, while platelet improvement was evaluable in 18 pts with 57% responding. Six of 18 (33%) pts with pancytopenia experienced trilineage response. Mean time from ATG to next therapy was 12 mo (median of 7.7 mo). Neither presence of an LGL clone, hypocellular BM or fibrosis, HLA DR15, trisomy 8, nor age influenced response to IST. Pts classified as IPSS-R Very high or high risk were unresponsive (n= 5), whereas 10 of 19 pts (53%) with intermediate risk responded. Poor risk IPSS karyotype was associated with a trend for lower response rate when compared to intermediate and good risk (25% vs. 41% vs. 44%; p=0.6). The response rate based on the NIH IST model was 38% for low response probability category pts and 45% for high probability category (p=0.5). Response rate to IST was higher if administered within 2 years from diagnosis, with an HI rate of 48% vs. 33% when treated after 2 years (p=0.04). Pts who received ATG as first line treatment or after lenalidomide had a trend for higher response rates than those treated after azacitidine (46%,75%, and 25% respectively). Addition of CSA significantly improved HI rate (51% vs. 27% for ATG alone, p=0.02). Transformation to AML occurred in 10 pts, 7% of responders and 24% of non-responders (p=0.08). Median OS was 67.2 mo with no significant difference based on IST response.Among 40 pts evaluated by NGS, 20 (50%) had at least one demonstrable somatic mutation (SM) and 9 pts (22.5%) had two or more SM. SF3B1 was the most common SM detected (n=9, 22.5%), followed by ASXL-1 (n=7, 17.5%), TET-2 (n= 5, 12.5%), and STAG2, EZH-2 and ZRSR2 (2 pts each, 5%), and 1 pt each with IDH-1, KDM6A, SETBP1, RAD2, GNAS or GATA-2. Absence of a SM was associated with a higher response to IST (70% vs. 40%, p=0.16), whereas number of SM (1 vs. 2+) did not influence response. The presence of an SF3B1 mutation was a significantly associated with IST nonresponse (1/9 SF3B1 SM, 11% vs. 21/31 WT, 68%; p=0.01). All pts with SF3B1 SM had ring sideroblasts >15% (RS) by morphology and the corresponding HI rate was 20% among pts with RS vs 50% for those without RS, p=0.09. Median OS in pts with an SF3B1 SM was 111 mo vs. 54 mo in SF3B1 WT (p=0.016). The two pts with EZH-2 and the single pt with WT-1 S achieved HI. Mean duration of response was 12 mo among pts with no SM vs. 9 mo in those harboring a SM (p=0.09). Rate of AML transformation among pts with a SM other than SF3B1 was higher in pts without SM (4/11 pts, 36%vs. 1/20, 5%; p =0.023, with a corresponding reduced median OS (52 mo vs. 96, p=0.24).ConclusionsThese findings support an improved response rate to ATG when administered in combination with CSA, and early in the disease course. The presence of an SF3B1 mutation adversely influences response to IST, suggesting a non-immunologic pathogenesis in this molecularly defined subset. The presence of non-SF3B1 somatic mutations adversely affects response duration and probability of AML transformation. SM should be considered in selection of IST in lower risk MDS patients. DisclosuresKomrokji:Pharmacylics: Speakers Bureau; Novartis: Research Funding, Speakers Bureau; Celgene: Consultancy, Research Funding; Incyte: Consultancy. Lancet:Seattle Genetics: Consultancy; Pfizer: Research Funding; Boehringer-Ingelheim: Consultancy; Kalo-Bios: Consultancy; Amgen: Consultancy; Celgene: Consultancy, Research Funding. List:Celgene Corporation: Honoraria, Research Funding. Padron:Incyte: Research Funding; Novartis: Speakers Bureau.

Splicing Inhibition By Spliceostatin_A Is a Promising Therapeutic Strategy in Chronic Lymphocytic Leukaemia

SF3B1 is a critical component of the RNA splicing machinery that achieves successful transcription and provides the functional diversity of protein species through alternative splicing. Recent studies have identified SF3B1 mutations in several tumours. In chronic lymphocytic leukemia (CLL) these mutations are associated with altered splicing, reduced survival and resistance to treatment. We therefore hypothesised that inhibition of the spliceosome may be an effective therapeutic strategy in SF3B1 mutated individuals.Initially, we utilized Spliceostatin A (SSA), an agent known to inhibit SF3B1 and alter gene splicing in various cell types. We showed that in CLL cells (SF3B1 WT and mutated samples), SSA treatment resulted in a dose-dependent increase in the un-spliced mRNA of DNAJB1 and RIOK3, two genes known to be regulated by SF3B1. We then assessed the ability of SSA to kill CLL cells with an SF3B1 mutant (n=12) or wild-type (n=28) genotype over a 24 hour period. CLL cells, regardless of SF3B1 mutational status, underwent apoptosis in a dose- (Figure A) and time-dependent manner (data not shown), with a mean IC50 of 5.1 nM. Interestingly, SSA induced more apoptosis in IGHV unmutated-CLL (U-CLL) compared to mutated-CLL samples (M-CLL) (p=0.037) and was active in 17p-deleted CLL (n=7), an aggressive disease sub-type that exhibits pronounced resistance to standard treatments. Normal B and T cells were significantly more resistant to SSA treatment than CLL samples purified from age-matched normal donors (B-cells p=0.006, T-cells p=0.001) and CLL derived T cells (p=0.003).SSA-induced apoptosis proceeded via a caspase-dependent mechanism (inhibited by ZVAD.FMK) coincident with elevations in Noxa. No changes in Bcl-2 or Bcl-xL were observed. Given the known ability of Noxa to interact with, and destabilise, Mcl-1, we next assessed the ability of SSA to modulate Mcl-1, and observed a substantial decrease in protein expression (Figure B, p=0.028). SSA treatment also altered the splicing of MCL-1; reducing the proportion of full length MCL-1L and increasing the amount of MCL-1s transcripts produced. The key role of Mcl-1 in regulating SSA-induced apoptosis was also observed in Ramos cells where over-expression of Mcl-1L, significantly protected them from SSA-induced apoptosis (p=0.001). Furthermore, in CLL cells exposed to CD40L and IL-4, factors known to induce Mcl-1 expression, SSA-induced apoptosis was significantly reduced (p=0.008). Taken together, these data implicate aberrant Mcl-1 splicing and Noxa upregulation in the apoptosis induced after SSA exposure. CD40L and IL-4 are proposed to be key factors preventing the apoptosis of CLL cells in the proliferative niche. Therefore, to explore possible strategies for overcoming this resistance, we investigated combining SSA with the Bcl-2/Bcl-xL inhibitor ABT-263 and showed that dual exposure to both inhibitors significantly increased apoptosis overcoming the protective effects of IL-4/CD40L (p=0.004; Figure C).In conclusion, our data shows that SSA induces apoptosis at nanomolar concentrations in CLL cells, independently of SF3B1 mutational status, through effects on Mcl-1. In combination with ABT-263, we show that SSA is particular active and can overcome the protective effects of CD40L and IL-4, suggesting promising clinical utility. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Abstract 2932: SF3B1 mutations induce aberrant mRNA splicing in cancer and confer sensitivity to spliceosome inhibition

Abstract Recurrent heterozygous mutations of the spliceosome protein SF3B1 have been identified in myelodysplastic syndromes, chronic lymphocytic leukemia (CLL), breast, pancreatic and skin cancers. SF3B1 is a component of the U2 snRNP complex which binds to the pre-mRNA branch point site and is involved in recognition and stabilization of the spliceosome at the 3′ splice site. To understand the impact of SF3B1 mutations, we compared RNAseq profiles from tumor samples with SF3B1 hotspot mutations (SF3B1-MUT) or wild-type SF3B1 (SF3B1-WT) in breast cancer, melanoma and CLL. This analysis revealed significant increases in the usage of novel alternative splice junctions in SF3B1-MUT samples including selection of alternative 3′ splice sites and less frequently exon skipping. These events induce expression of alternative mRNAs that are translated into novel proteins or aberrant mRNAs that are decayed by cells. A common alternative splicing profile was shared across different hotspot mutations and lineages (e.g. ZDHHC16 and COASY); however, unique alternative splicing profiles were also observed suggesting lineage specific effects. RNAseq analysis of several cell lines with endogenous SF3B1 hotspot mutations confirmed the presence of the same spliced isoforms as observed in tumor samples. To prove that SF3B1-MUT were inducing alternative splicing, transient transfection of several SF3B1 hotspot mutations in 293FT cells induced the expression of the common alternatively spliced genes suggesting functional similarity. Selective shRNA depletion of mutant SF3B1 allele in SF3B1-MUT cells resulted in downregulation of the same splice isoforms. Furthermore, isogenic B-cell lines (NALM-6) expressing the most frequent SF3B1 mutation (K700E) were generated and profiled by RNAseq. As expected, similar alternatively spliced genes were observed in NALM-6 SF3B1-K700E cells exclusively. To investigate the role of nonsense-mediated mRNA decay (NMD) in eliminating aberrant mRNAs induced by SF3B1-MUT, we treated NALM-6 SF3B1-K700E cells with cycloheximide, a translation inhibitor known to inhibit NMD. In the treated samples, expression of several aberrant mRNAs was revealed and some of these transcripts were shown to be downregulated in patient samples. Taken together, these results confirm the association between different SF3B1 hotspot mutations and the presence of novel splice isoforms. We demonstrated that E7107, a potent and selective inhibitor of wild-type SF3B1, also binds and inhibits SF3B1-MUT protein. In addition, E7107 represses the expression of several common aberrant splice mRNA products in SF3B1-MUT cells in vitro and in vivo. When tested in a NALM-6 mouse model, E7107 induced tumor regression and increased the overall survival of animals implanted with NALM-6 SF3B1-K700E cells. These data suggest splicing inhibitors as a promising therapeutic approach for cancer patients carrying SF3B1 mutations. Citation Format: Silvia Buonamici, Kian Huat Lim, Jacob Feala, Eunice Park, Laura Corson, Michelle Aicher, Daniel Aird, Betty Chan, Erik Corcoran, Rachel Darman, Peter Fekkes, Gregg Keaney, Pavan Kumar, Kaiko Kunii, Linda Lee, Xiaoling Puyang, Jose Rodrigues, Anand Selvaraj, Michael Thomas, John Wang, Markus Warmuth, Lihua Yu, Ping Zhu, Peter Smith, Yoshiharu Mizui. SF3B1 mutations induce aberrant mRNA splicing in cancer and confer sensitivity to spliceosome inhibition. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2932. doi:10.1158/1538-7445.AM2014-2932