METTL3 Dysregulates RNA Splicing by Translational Control of Splicing Factors via m 6A Modification in CLL

Abstract RNA splicing dysregulation is a hallmark of chronic lymphocytic leukemia (CLL). Although somatic mutations in SF3B1 or U1 snRNA present in >20% of CLL patients, general splicing defects cannot be fully explained by genetic alterations of spliceosome alone. We reported that splicing factors are upregulated at protein, but not RNA, level in CLL compared to normal B cells by an integrated transcriptomic and proteomic analysis. This highlights a post-transcriptional layer of regulation that controls the abundance of splicing factors and contributes to RNA splicing dysregulation in CLL, with mechanism that has yet to be elucidated. To discover these regulators, we performed weighted correlation network analysis and found expression of many splicing factors strongly correlated with the abundance of METTL3. METTL3 is an RNA methyltransferase that modifies N 6-methyladenosine (m 6A) on mRNA and regulates the translation of m 6A-installed transcripts. Primary CLL cells have consistent upregulated protein expression of METTL3 and exhibit an increased m 6A level on mRNA. To identify m 6A modification sites in normal and CLL B cells, we performed m 6A sensitive RNase sequencing and found transcripts with differential m 6A modification are highly enriched in the RNA splicing pathway (q=1.8E-4). Consistent with this, these transcripts appear to have a higher m 6A density. These results raised up a possibility that METTL3 translationally controls the expression of splicing factors through m 6A modification. To examine whether METTL3 impacts splicing factor expression, we performed an integrated ribosome profiling (Ribo-seq) and RNA sequencing using CLL cell line HG3 with or without METTL3. Knockout (KO) of METTL3 decreased overall translation efficiency with RNA splicing as the most significantly affected pathway (q=2.1E-52). We further confirmed that KO of METTL3 or treatment with METTL3 inhibitor STM2457 decreases the expression of many splicing factors in HG3 cells. However, we detected no protein changes in known METTL3 targets (BCL2, MYC), highlighting splicing factors as the preferred targets of METTL3 in CLL. Moreover, overexpression of wildtype but not catalytic mutant METTL3 restored splicing factor expression defects in METTL3 KO cells, demonstrating that the regulation of splicing factor expression is methyltransferase activity dependent. To dissect the mechanism of how METTL3 preferentially influences the expression of splicing factors via m 6A modification, we mapped out METTL3 responding m 6A sites using methylated RNA immunoprecipitation sequencing (MeRIP-seq). Consistent with its role as an methyltransferase, we detected 5875 hypomethylated and 1409 hypermethylated sites upon METTL3 KO. Most downregulated splicing factors harbored hypomethylation around the stop codon region, including SF3B1, SF3A2 and SR proteins, indicating they are direct targets of METTL3. To validate this association, we utilized m 6A editing platform dCasRx-METTL3 to install m 6A at the stop codon region of endogenous SF3B1 transcripts, leading to increased SF3B1 protein expression. These results provided evidence that METTL3 directly regulates splicing factor protein expression via m 6A mediated translational control. Unexpectedly, we also discovered that hypermethylated transcripts are highly enriched in RNA splicing with most affected sites localized at the CDS regions. The hypermethylation of these transcripts can be caused by a combined upregulation of m 6A writer (METTL16) and eraser (ALKBH5) protein upon KO of METTL3. To determine how hypermethylation affects expression of splicing factors, we conducted an integrated MeRIP-seq and Ribo-seq analysis and observed a convergence of increased ribosomal density and hypermethylated adenosines. Harnessing dCasRx-METTL3 platform, we installed m 6A at the CDS region of SF3A3 and confirmed the downregulation of protein by immunoblot. This implicates that, as an alternative mechanism, METTL3 regulates the translation of splicing factors via m 6A mediated decoding process. Altogether, our results uncovered a novel regulatory axis of METTL3 as a regulator for splicing dysregulation in CLL. We propose that METTL3 regulates splicing factor expression through m 6A-mediated translational control. Our study highlights a post-transcriptional layer of m 6A modification as a major contributor to genetic lesion-independent splicing defects in CLL. Disclosures Brown: Gilead, Loxo/Lilly, SecuraBio, Sun, TG Therapeutics: Research Funding; Invectys: Other: Data Safety Monitoring Committee Service; Abbvie, Acerta/Astra-Zeneca, Beigene, Bristol-Myers Squibb/Juno/Celgene, Catapult, Eli Lilly, Genentech/Roche, Janssen, MEI Pharma, Morphosys AG, Nextcea, Novartis, Pfizer, Rigel: Consultancy. Danilov: Abbvie: Consultancy, Honoraria; Takeda Oncology: Research Funding; TG Therapeutics: Consultancy, Research Funding; Beigene: Consultancy, Honoraria; Pharmacyclics: Consultancy, Honoraria; Gilead Sciences: Research Funding; Rigel Pharm: Honoraria; Genentech: Consultancy, Honoraria, Research Funding; Bayer Oncology: Consultancy, Honoraria, Research Funding; SecuraBio: Research Funding; Astra Zeneca: Consultancy, Honoraria, Research Funding; Bristol-Meyers-Squibb: Honoraria, Research Funding. Siddiqi: Celgene: Membership on an entity's Board of Directors or advisory committees; Janssen: Speakers Bureau; Kite Pharma: Membership on an entity's Board of Directors or advisory committees, Research Funding; BMS: Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; AstraZeneca: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; BeiGene: Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Juno Therapeutics: Membership on an entity's Board of Directors or advisory committees, Research Funding; Pharmacyclics LLC, an AbbVie Company: Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Oncternal: Research Funding; TG Therapeutics: Research Funding.

Download Full-text

Dysregulation of Splicing in Multiple Myeloma: The Splicing Factor SRSF1 Supports MM Cell Proliferation Via Splicing Control

Blood ◽

10.1182/blood-2018-99-118845 ◽

2018 ◽

Vol 132 (Supplement 1) ◽

pp. 4500-4500

Author(s):

Mariateresa Fulciniti ◽

Michael A Lopez ◽

Anil Aktas Samur ◽

Eugenio Morelli ◽

Hervé Avet-Loiseau ◽

...

Keyword(s):

Gene Expression ◽

Multiple Myeloma ◽

Alternative Splicing ◽

Board Of Directors ◽

Research Funding ◽

Splicing Factor ◽

Splicing Factors ◽

Rna Seq ◽

Advisory Committees ◽

Disease Biology

Abstract Gene expression profile has provided interesting insights into the disease biology, helped develop new risk stratification, and identify novel druggable targets in multiple myeloma (MM). However, there is significant impact of alternative pre-mRNA splicing (AS) as one of the key transcriptome modifier. These spliced variants increases the transcriptomic complexity and its misregulation affect disease behavior impacting therapeutic consideration in various disease processes including cancer. Our large well annotated deep RNA sequencing data from purified MM cells data from 420 newly-diagnosed patients treated homogeneously have identified 1534 genes with one or more splicing events observed in at least 10% or more patients. Median alternative splicing event per patient was 595 (range 223 - 2735). These observed global alternative splicing events in MM involves aberrant splicing of critical growth and survival genes affects the disease biology as well as overall survival. Moreover, the decrease of cell viability observed in a large panel of MM cell lines after inhibition of splicing at the pre-mRNA complex and stalling at the A complex confirmed that MM cells are exquisitely sensitive to pharmacological inhibition of splicing. Based on these data, we further focused on understanding the molecular mechanisms driving aberrant alternative splicing in MM. An increasing body of evidence indicates that altered expression of regulatory splicing factors (SF) can have oncogenic properties by impacting AS of cancer-associated genes. We used our large RNA-seq dataset to create a genome wide global alterations map of SF and identified several splicing factors significantly dysregulated in MM compared to normal plasma cells with impact on clinical outcome. The splicing factor Serine and Arginine Rich Splicing Factor 1 (SRSF1), regulating initiation of spliceosome assembly, was selected for further evaluation, as its impact on clinical outcome was confirmed in two additional independent myeloma datasets. In gain-of (GOF) studies enforced expression of SRSF1 in MM cells significantly increased proliferation, especially in the presence of bone marrow stromal cells; and conversely, in loss-of function (LOF) studies, downregulation of SRSF1, using stable or doxy-inducible shRNA systems significantly inhibited MM cell proliferation and survival over time. We utilized SRSF1 mutants to dissect the mechanisms involved in the SRSF1-mediated MM growth induction, and observed that the growth promoting effect of SRSF1 in MM cells was mainly due to its splicing activity. We next investigated the impact of SRSF1 on allelic isoforms of specific gene targets by RNA-seq in LOF and confirmed in GOF studies. Splicing profiles showed widespread changes in AS induced by SRSF1 knock down. The most recurrent splicing events were skipped exon (SE) and alternative first (AF) exon splicing as compared to control cells. SE splice events were primarily upregulated and AF splice events were evenly upregulated and downregulated. Genes in which splicing events in these categories occurred mostly did not show significant difference in overall gene expression level when compared to control, following SRSF1 depletion. When analyzing cellular functions of SRSF1-regulated splicing events, we found that SRSF1 knock down affects genes in the RNA processing pathway as well as genes involved in cancer-related functions such as mTOR and MYC-related pathways. Splicing analysis was corroborated with immunoprecipitation (IP) followed by mass spectrometry (MS) analysis of T7-tagged SRSF1 MM cells. We have observed increased levels of SRSF phosphorylation, which regulates it's subcellular localization and activity, in MM cell lines and primary patient MM cells compared to normal donor PBMCs. Moreover, we evaluated the chemical compound TG003, an inhibitor of Cdc2-like kinase (CLK) 1 and 4 that regulate splicing by fine-tuning the phosphorylation of SR proteins. Treatment with TG003 decreased SRSF1 phosphorylation preventing the spliceosome assembly and inducing a dose dependent inhibition of MM cell viability. In conclusions, here we provide mechanistic insights into myeloma-related splicing dysregulation and establish SRSF1 as a tumor promoting gene with therapeutic potential. Disclosures Avet-Loiseau: Janssen: Consultancy, Membership on an entity's Board of Directors or advisory committees; Celgene: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Sanofi: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Abbvie: Membership on an entity's Board of Directors or advisory committees; Amgen: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Takeda: Membership on an entity's Board of Directors or advisory committees, Research Funding. Munshi:OncoPep: Other: Board of director.

Download Full-text

Identification of Recurrent Alternative RNA Splicing in Adverse-Risk Acute Myeloid Leukemia

Blood ◽

10.1182/blood-2019-129537 ◽

2019 ◽

Vol 134 (Supplement_1) ◽

pp. 457-457

Author(s):

Govardhan Anande ◽

Ashwin Unnikrishnan ◽

Nandan Deshpande ◽

Sylvain Mareschal ◽

Aarif M. N. Batcha ◽

...

Keyword(s):

Alternative Splicing ◽

Board Of Directors ◽

Rna Splicing ◽

Myeloid Leukemia ◽

Research Funding ◽

Splicing Factor ◽

Rna Seq ◽

Advisory Committees ◽

Alternatively Spliced ◽

Acute Myeloid

RNA splicing is a fundamental biological process that generates protein diversity from a finite set of genes. Recurrent somatic mutations of genes involved in RNA splicing are present at high frequency in Myelodysplasia (up to 70%) but less so in Acute Myeloid Leukemia (AML; less than 20%). To investigate whether there were aberrant and recurrent RNA splicing events in the AML transcriptome that were associated with poor prognosis in the absence of splicing factor mutations, we developed a bioinformatics pipeline to systematically annotate and quantify alternative splicing events from RNA-sequencing data (Fig A). We first analysed publicly available RNA-seq data from The Cancer Genome Atlas (TCGA, n=170). We focussed on non-M3 AML patients with no splicing factor mutations (based on reported genomic sequencing and verified by re-analysis of RNA-seq data from all patients) who had received intensive chemotherapy. We segregated these patients based on their European Leukaemia Net (ELN) risk classification and identified 1290 alternatively spliced events impacting 910 genes that were significantly different (FDR<0.05) between all ELNAdv (n=41) versus all ELNFav patients (n=21, Fig B). The majority were exon skipping events (716 events, 62%, Fig B-C), followed by intron retention (201 events, 15.6%, Fig B). We next used RNA-seq data from a second non-M3 AML patient cohort (ClinSeq- Sweden; ELNAdv, n=75 and ELNFav, n=47), detecting 2507 events mapping to 1566 genes. Comparing across the two cohorts, 222 shared genes were detected to be affected by alternative splicing (Fig D). Ingenuity pathway analysis associated these genes with pathways related to protein translation. In order to prioritise those alternatively spliced events most likely to have a deleterious function, we developed an analytical framework to predict their impact on protein structure (Fig E). 87 alternatively spliced events, 25.81% of the commonly shared splicing events, relating to 78 genes (35.13% of all genes) were predicted to directly alter highly conserved protein domains within the affected genes, leading to either a complete (~25%, Fig E) or a partial loss of a domain (20%, Fig E). These in silico predictions are likely to be an underestimate of the true impact, as splicing alterations mapping to poorly annotated domains or affecting the tertiary structure of proteins would be missed. A number of splicing factors themselves were differentially spliced, with the alternative splicing predicted to have functional consequences. This was exemplified by hnRNPA1, a factor with well-established roles in splicing, is itself alternatively spliced in patients and predicted to be deleterious. Consistent with this, motif scanning analyses indicated that a number of mis-spliced transcripts had hnRNPA1 binding motifs (Fig F). To assess the impact of these alternatively spliced events (that were predicted to also disrupt highly conserved protein domains) on the transcriptome, we simultaneously quantified differential gene expression. IPA analysis of the 602 genes that were differentially expressed between ELNAdv and ELNFav patients and shared between both TCGA and ClinSeq cohorts indicated that they were associated with pathways (Fig G) that were distinct from those associated with aberrantly spliced genes (Fig D). A number of pathways related to inflammation were enriched amongst the genes observed to be upregulated in ELNAdv patients (Fig G). Network analyses integrating the alternatively spliced genes with differentially expressed genes revealed strong interactions (Fig H), indicating functional associations between these biological events. Given these strong network interactions, we investigated the potential prognostic significance of these alternatively spliced events. To this end, we utilised machine-learning methods to derive a "splicing signature" of four mis-spliced genes with a predictive capacity equivalent to the ELN (Fig I). The splicing signature further refined existing risk prediction algorithms to improve the classification of patients (Fig J). Taken together, we report the presence of extensive deregulation of RNA splicing in AML patients even in the absence of splicing factor mutations. Many of these events were shared in patients with adverse outcomes and their impact on the AML transcriptome points towards vulnerabilities that could be targeted. Figure Disclosures Unnikrishnan: Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding. Lehmann:TEVA: Consultancy, Membership on an entity's Board of Directors or advisory committees; Pfizer: Membership on an entity's Board of Directors or advisory committees; Abbive: Membership on an entity's Board of Directors or advisory committees. Pimanda:Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding.

Download Full-text

LUC7L2 Is a Novel RNA-Splicing Regulatory Factor Mutated in Myelodysplastic Syndromes

Blood ◽

10.1182/blood-2018-99-112838 ◽

2018 ◽

Vol 132 (Supplement 1) ◽

pp. 3073-3073

Author(s):

Courtney Hershberger ◽

James Hiznay ◽

Rosemary Dietrich ◽

Xiaorong Gu ◽

Cassandra M. Hirsch ◽

...

Keyword(s):

Board Of Directors ◽

Binding Sites ◽

Rna Splicing ◽

K562 Cells ◽

Splicing Factor ◽

Splicing Factors ◽

Rna Seq ◽

Advisory Committees ◽

Splicing Efficiency ◽

Low Expression

Abstract Myelodysplastic syndromes (MDS) are unique among cancers because of the frequent occurrence of somatic mutations impacting spliceosome machinery. At least 65% of MDS patients harbor a mutation in one of several splicing factors including U2AF1, SF3B1 and SRSF2. Whole exome sequencing of MDS bone marrow uncovered somatic frameshift mutations in LUC7L2, the mammalian ortholog of a yeast splicing factor. LUC7L2 is located in the most commonly deleted region of chromosome 7. Deletions and frameshifts lead to haploinsufficient expression and therefore it can be approximated that a combined 14% of MDS patients have low expression of LUC7L2. Restoring expression of LUC7L2 in del(7q)-iPSCs partially rescues the differentiation of iPSCs into CD45+ myeloid progenitors. Although perhaps partly due to associated losses of other genes on chromosome 7, low expression of LUC7L2 correlates with a poorer patient prognosis, so its haploinsufficiency may play an important role in bone marrow failure. While U2AF1, SF3B1, and SRSF2 are well-characterized splicing factors, the function of LUC7L2 in pre-mRNA splicing is unexamined and its role in the MDS pathogenesis is undefined. We hypothesize that low expression of LUC7L2 results in the aberrant splicing of oncogenes and tumor suppressor gene transcripts thus reducing expression or altering function and contributing to the pathogenesis of MDS. We have characterized LUC7L2 as an alternative splicing regulatory protein that plays a repressive role in the regulation of alternative RNA splicing. We generated HEK-293 cells overexpressing V5-tagged LUC7L2 for immunoprecipitation-mass spectrometry, to ascertain protein interactions with LUC7L2. LUC7L2 co-immunoprecipitated with splicing regulators which are involved in splice site recognition. We performed cross-linking-IP-high-throughput-sequencing (CLIP-seq) to identify LUC7L2 binding sites on RNA. We identified 301 LUC7L2 RNA-binding sites as well as binding sites on U1 and U2 which is common for splicing regulatory proteins. Metagene analysis of these binding sites showed that LUC7L2 bound near splice sites in exonic sequences. We knocked down LUC7L2 expression in HEK293 and K562 cells to phenocopy the frameshifts and deletions observed in MDS patients. We used a PCR-based assay to measure the splicing efficiency of introns near LUC7L2-binding sites. Knockdown of LUC7L2 increased the splicing efficiency of 8/13 selected introns; this suggests that LUC7L2 represses selective splice site usage. We also performed RNA-seq to characterize global mis-splicing events. Analysis of RNA transcripts revealed a multitude of splicing changes, including enhanced exclusion of alternative introns. Knockdown LUC7L2 cells exhibited-altered expression of other splicing factors; this could have further contributed to the vast number of splicing changes observed. To identify specific splicing changes that could contribute to the pathogenesis of MDS, we compared the splicing profiles of LUC7L2-knockdown in K562 cells with RNA-seq data from K562 cells expressing U2AF1S34F, SRSF2P95H or SF3B1K700E. This analysis yielded several exon-skipping splicing patterns in cancer-relevant transcripts, such as oncogene PRC1, splicing factor PTBP1 and MRPL33. Additionally, we noticed commonly mis-spliced transcripts among the four datasets in which the missplicing events occurred in the functional domain, potentially conferring a functional change. Surprisingly, we observed missplicing of U2AF1 in LUC7L2-knockdown, SRSF2P95H, and SF3B1K700E K562 cells, which altered the length of the RNA-recognition UHM domain by inclusion of a mutually exclusive exon or retention of an intron. In this way, low expression of LUC7L2, or point mutants U2AF1S34F, SRSF2P95H, and SF3B1K700E,could alter U2AF1 function as a distal convergence point. In summary, we identified a novel splicing factor implicated in the pathogenesis of MDS. We characterized LUC7L2 as a splicing repressor and discovered many splicing changes caused by low expression of LUC7L2. Several genes were also mis-spliced in U2AF1S34F, SRSF2P95H and SF3B1K700E K562 cells targeting these for further study. Commonly mis-spliced targets such as U2AF1 may indicate that some of the novel therapeutics may have spliceosome mutation agnostic effects. If this applies to the LUC7L2 mutations, then they may also be effective in del7/del7q cases. Disclosures Carraway: Celgene: Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; FibroGen: Consultancy; Jazz: Speakers Bureau; Novartis: Speakers Bureau; Amgen: Membership on an entity's Board of Directors or advisory committees; Balaxa: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Agios: Consultancy, Speakers Bureau. Sekeres:Opsona: Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees; Opsona: Membership on an entity's Board of Directors or advisory committees. Saunthararajah:Novo Nordisk, A/S: Patents & Royalties; EpiDestiny, LLC: Patents & Royalties. Maciejewski:Alexion Pharmaceuticals, Inc.: Consultancy, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Alexion Pharmaceuticals, Inc.: Consultancy, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Apellis Pharmaceuticals: Consultancy; Ra Pharmaceuticals, Inc: Consultancy; Apellis Pharmaceuticals: Consultancy; Ra Pharmaceuticals, Inc: Consultancy.

Download Full-text

U2AF1 and Other Splicing Factor Gene Mutations in Telomere Biology Disorders Are Associated with Hematologic Neoplasia and Worse Overall Survival

Blood ◽

10.1182/blood-2021-146946 ◽

2021 ◽

Vol 138 (Supplement 1) ◽

pp. 862-862

Author(s):

Emma M. Groarke ◽

Fernanda Gutierrez-Rodrigues ◽

Xiaoyang Ma ◽

Bhavisha A. Patel ◽

Nina Spitofsky ◽

...

Keyword(s):

Board Of Directors ◽

Research Funding ◽

Hematologic Malignancy ◽

Telomere Maintenance ◽

Splicing Factor ◽

Splicing Factors ◽

Cancer Genes ◽

Advisory Committees ◽

Factor Gene ◽

Telomere Biology

Abstract Introduction: Telomere Biology Disorders (TBD) are due to germline variants in telomere maintenance and repair genes. Clinical manifestations include bone marrow failure (BMF), liver and lung fibrosis, and risk of cancer, especially myeloid neoplasia. We characterized clinical phenotype, pathology, and clonal landscape of patients with TBD and myelodysplastic syndrome (MDS) or acute leukemia (AL). We assessed if somatic variants in myeloid cancer genes are associated with MDS/AL or overall survival (OS). Methods: Patients (n=109) from the National Institutes of Health and University of São Paulo (NIH/USP) (n=91) or MD Anderson (MDA) (n=18) met TBD clinical criteria or had a pathogenic/likely pathogenic germline variant in a telomere maintenance/repair gene. All patients gave informed consent. Clinical characteristics and details of hematologic malignancy were collected. MDS was defined using WHO 2016 criteria. In the NIH/USP cohort, somatic variants in myeloid cancer genes were assessed in peripheral blood using error-corrected DNA sequencing (ECS; minimum variant allele frequency [VAF] of 0.5%) and in the MDA cohort patients were screened by targeted amplicon-based next-generation sequencing (minimum VAF of 2%). Serial samples were available in 31 (41%) patients. Results: Eighteen out of 109 (17%) patients from both the NIH/USP and MDA cohorts had a diagnosis of MDS/AL, developing in patients with TERC (n=8/31; 25%), TERT (n=8/48; 16%), RTEL1 (n=1/5; 20%), and DKC1 (n=1/2; 50%). Karyotypes were normal diploid (n=6), chromosome 1 abnormality (n=5), trisomy 8 (n=2), deletion 20q (n=1), complex (n=2), monosomy 7 (n=1) and deletion 7q (n=1). Six patients had >5% blasts. Four patients had concurrent liver fibrosis and 9 had pulmonary fibrosis. Somatic mutation data at time of MDS/AL was available for 16/18 patients; splicing factor genes (n=14) were most frequent, seen in 11 (69%) patients, with U2AF1 predominating (n=7; 44% of patients) (Figure 1A). More than 1 mutation was present in 12/16 (75%) of patients. One patient developed AML 6 years after MDS diagnosis . U2AF1 variants were also present in 8 patients without MDS/AL; 5 had no sequential samples and 3 had stable mutations over 2 (n=2) and 4 (n=1) years. Recurrent variants in U2AF1 were present at p.S34 (n=12) and p.Q157 (n=2). Median U2AF1 variant allele fraction (measured in NIH/USP cohort only) was 23% in patients with MDS/AL compared to 7% in those without. Variant association analysis was confined to NIH/USP cohort due to DNA sequencing assay differences; data were available in 75 patients. Patients were divided into groups defined by specific variants at any time of sampling; "Clonal-hematopoiesis of indeterminate potential / aplastic anemia (CHIP/AA) associated" (DNMT3A, TET2, ASXLI, or BCOR/L1), "MDS-associated" (containing splicing factor genes, RUNX1, SETBP1, ETV1, KRAS, STAG2, GATA2/1, TP53), "PPM1D" (containing PPM1D), and a subgroup, "Splicing factors" (U2AF1, ZRSR2, SF3B1, SRSF2). Patients with MDS-associated variants (Figure 1A; p=0.02), particularly splicing factors (Figure 1B; p=0.007) more likely had or later developed MDS/AL, compared to patients without somatic variants or in other variant groups. MDS/AL was not associated with PPM1D or CHIP/AA-associated variants. OS from time of first detected somatic variant was lower in the MDS-associated variant group (Figure 1C p=0.013) compared to those without variants at time of first assessment; this was not the case for CHIP/AA-associated variants or PPM1D. Patients with somatic variants (median ages 36, 41, and 42 for PPM1D, CHIP/AA-associated, and MDS-associated respectively) were significantly older than patients without variants (median age 24) though ages were similar within variant groups. Conclusion: Splicing factor gene variants predominate the clonal landscape of TBD-associated hematologic malignancy; U2AF1 p.S34 is recurrent and can occur in the absence of neoplasia. Splicing factor gene variants such as U2AF1 in the peripheral blood may be potential biomarkers for hematologic malignancy in TBD patients. PPM1D, previously associated with therapy-related MDS, is commonly mutated in TBD but does not associate with MDS/AL. OS was decreased in patients with MDS-associated variants but not with PPM1D or CHIP/AA-associated variants. Further study of U2AF1 variants in TBD patients may give insight to the underlying drivers of MDS/AL. Figure 1 Figure 1. Disclosures DiNardo: Agios/Servier: Consultancy, Honoraria, Research Funding; Notable Labs: Current holder of stock options in a privately-held company, Membership on an entity's Board of Directors or advisory committees; ImmuneOnc: Honoraria, Research Funding; Bristol Myers Squibb: Honoraria, Research Funding; AbbVie: Consultancy, Research Funding; Forma: Honoraria, Research Funding; GlaxoSmithKline: Membership on an entity's Board of Directors or advisory committees; Novartis: Honoraria; Takeda: Honoraria; Foghorn: Honoraria, Research Funding; Celgene, a Bristol Myers Squibb company: Honoraria, Research Funding. Calado: Novartis Brasil: Honoraria; Instituto Butantan: Consultancy; AA&MDS International Foundation: Research Funding; Alexion Brasil: Consultancy; Agios: Membership on an entity's Board of Directors or advisory committees; Team Telomere, Inc.: Membership on an entity's Board of Directors or advisory committees. Young: Novartis: Research Funding.

Download Full-text

A Prognostic Human Splicing Signature That Precurses Leukemia

Blood ◽

10.1182/blood-2018-99-115000 ◽

2018 ◽

Vol 132 (Supplement 1) ◽

pp. 877-877 ◽

Cited By ~ 1

Author(s):

Meenakshi Venkatasubramanian ◽

Xiaoting Chen ◽

Kashish Chetal ◽

Aishwarya Kulkarni ◽

Kasiani C. Myers ◽

...

Keyword(s):

Bone Marrow ◽

Alternative Splicing ◽

Board Of Directors ◽

Protein Isoforms ◽

Splicing Factor ◽

Healthy Population ◽

Rna Seq ◽

Advisory Committees ◽

Factor Expression ◽

Pediatric Aml

Abstract Alternative splicing is a primary mechanism used to achieve mRNA transcript and proteomic diversity in higher-order eukaryotes. While alternative splicing is a recognized oncogenic driver in a small percentage of adult acute myeloid leukemia (AML) cases (~10-15%), splicing factor mutations are rarely found in pediatric AML. To discover splicing heterogeneity within diverse cancers in the absence of known causal mutations we developed a new computational workflow called OncoSplice. This workflow incorporates unsupervised splicing pattern analysis to iteratively identify novel patient splicing-defined subtypes (splice-ICGS algorithm), in conjunction with new integrative methods for cis-regulatory motif, CLIP-Seq binding and splicing factor expression data analysis (Fig. 1a). Analysis of RNA-Seq data from over 800 AML diagnosis samples identified subtypes associated with nearly all known splicing factor mutations in addition to over a dozen novel splicing-defined subtypes. Novel splicing subtypes were confirmed in independent patient cohorts and were associated with the expression or mutation of oncogenes (MYC, TP53, NPM1), oncofusions (CBFB-MYH11, MLL, PML-RAR, RUNX1), or the regulation of diverse splicing factors (U2AF1, SRSF2, HNRNPK). Both adult and pediatric AML are most frequently characterized by a single predominant splicing signature which divides the majority of AML patients into subtypes with splicing events overlapping those found in patients with mutations in U2AF1 or SRSF2 (Figure 1b). These "U2AF1-covarying" or "SRSF2-covarying" (CV) occur independently of splicing-factor mutations and were principally linked to mis-splicing rather than differential gene expression. Unlike patients with U2AF1-S3F mutations, U2AF1-CV splicing events are associated with canonical rather than altered U2AF1 binding specificity (Fig. 1c). In both adult and pediatric AML, U2AF1-CV splice events result in a shift towards longer protein isoforms associated with stem and progenitor programs, have significantly worse outcomes (poor survival and increased relapse) and are persistent during relapse in adults (Fig. 1d). Survival correlated U2AF1-CV splicing events were statistically enriched in genes required for leukemic growth based on a published CRISPR dropout screen. U2AF1-CV splicing was not associated with prior described epigenetic AML subtypes, but appears to be dependent on the expression of MYC and downstream splicing regulators (WDR77 and PRMT5). Surprisingly, RNA-Seq analysis of CD34+ bone marrow progenitors in healthy donors finds the same overall skewing in a subset of U2AF1-CV or SRSF2-CV splicing events as those found in AML. Distinct sorted progenitor populations (HSC, Multi-Lin, CMP, GMP, MEP) further show consistent U2AF1-CV or SRSF2-CV skewing within progenitors from the same donors, indicating that this is not a cell-type associated splicing difference. Hence, our data suggest that healthy bone marrow is skewed in the healthy population towards either U2AF1 or SRSF2 splicing pathways and that these splicing profiles impact future oncogenic transformation and patient survival in AML. These data further suggest a paradigm shifting model, in which widespread coordinated pathogenic splicing occurs across cancers, likely via imbalances in splicing factor expression, regulation or mutation. Figure 1. a) Steps implemented in the OncoSplice splicing subtype discovery workflow for splicing event quantification (MultiPath-PSI), iterative unsupervised splicing subtype discovery (splice-ICGS), supervised splicing subtype discovery (Bridger) and RNA-regulatory splicing subtype prediction (RBP-Finder). b) Comparison of splicing events enriched in adult AML with splicing factor mutations identifies their coincidence with U2AF1-CV and SRSF2-CV splicing events. c) Analysis of U2AF1 binding-site preferences at the e-3 splice-site position for cassette-exon splicing events (U2AF1-S34-specific but not U2AF1-CV; occurring in U2AF1-S34; occurring in U2AF1-CV; U2AF1-CV-specific but not U2AF1-S34). d) Kaplan-Meier curves for overall survival in patients from TCGA (top) and TARGET (bottom) with associated coxph p-values (all splice-ICGS stringently classified U2AF1-CV versus all other considered AMLs). Analysis of TCGA was restricted to cytogenetically normal AMLs with no splicing factor mutations and under 60 years of age. Figure 1. Figure 1. Disclosures Myers: Bellicum Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees; Novartis: Membership on an entity's Board of Directors or advisory committees.

Download Full-text

Characterizing Specificities of Chronic Lymphoid Leukemia Harboring a BCL2 rearrangement

Blood ◽

10.1182/blood-2020-139210 ◽

2020 ◽

Vol 136 (Supplement 1) ◽

pp. 29-30

Author(s):

Charles Herbaux ◽

Imelda Raczkiewicz ◽

Kamel Laribi ◽

Loic Ysebaert ◽

Agnes Daudignon ◽

...

Keyword(s):

Protein Expression ◽

Board Of Directors ◽

Research Funding ◽

Limit Of Detection ◽

B Cell Lymphoma ◽

Advisory Board ◽

Advisory Committees ◽

Ras Pathway ◽

Trisomy 12 ◽

A Cell

Introduction: Although survival dependence on Bcl2 is a well-known aspect of the pathophysiology of chronic lymphocytic leukemia (CLL), the mechanisms of Bcl-2 dysregulation are incompletely understood. Recurrent translocations involving BCL2 and immunoglobulin genes, including t(14;18)(q32;q21) and variants such as t(2;18) or t(18;22), are classically observed in follicular lymphoma or germinal center diffuse large B-cell lymphoma (GC DLBCL), but are uncommon (<5%) in CLL and usually associated with an indolent clinical course. Here, we characterize the mutational landscape and the functional Bcl-2 family dependencies of BH3 proteins in BCL-2-rearranged (BCL2-R) CLL. We used a functional approach known as BH3 profiling which measures the proximity of a cell to the threshold of apoptosis ("priming") and identifies which anti-apoptotic proteins a cell depends on for survival. Methods: Clinically annotated primary samples from BCL2-R CLL patients identified by karyotype were obtained from the French Innovative Leukemia Organization network and Dana-Farber Cancer Institute. Primary samples from CLL without BCL2 rearrangement were used as a control (ctrl CLL). Next generation sequencing (NGS) was performed using a custom-designed panel of 29 genes, including among others: BIRC3, NOTCH1, FBXW7, MLL2, RAS pathway, SF3B1 and TP53. The mean coverage obtained was 2000X (limit of detection (LOD): 1%). Digital droplet PCR (ddPCR) was used to quantify NOTCH1 c.7544_7545delCT (LOD: 0.025%). Protein expression (Bcl2, Mcl1, Bim) was assessed by Western blot. Baseline BH3 profiling was performed as per Ryan et al., Bio Chem 2016. To mimic the lymph node microenvironment, viability assays were performed in co-culture with the stromal cell line NK.tert. Viability was assessed by AnnexinV/Hoechst staining. Ex vivo drug treatments included: BCL2i (inhibitor): venetoclax; MCL-1i: AZD5991, S63845 and BCLXLi: A133. Statistical analyses were by unpaired and paired t-test with a two-tailed nominal p ≤ 0.05 considered as significant. Results: In our cohort of 110 patients, the median age was 70 years old, and 79% were male. BCL2-R were t(14;18) in 77.2%, t(18;22) in 16.3% and t(2;18) in 6.3% of patients. The translocation involving BCL2 gene was isolated in 23.6% of cases, and was associated with trisomy 12 in 45.4% of patients. The most frequently mutated genes in this cohort were in the NOTCH pathway (NOTCH1 mutation: 43.6 %, mostly subclonal (mean of variant allelic frequency: 6.1%) and FBXW7: 4.5%)) and RAS pathway (KRAS, NRAS, BRAF: 9.1%). BCL2 mutations were observed in 22.8% of the 57 examined cases. No mutation previously described in venetoclax resistant CLL, such as F104L or G101V variant, were observed. Furthermore, MLL2 mutations were observed in 14.5% cases and were significantly associated with complex karyotype (p=0.01) and trisomy 12 (p=0.04). Others mutated genes were: BIRC3 (5.4%), TP53 (3.6%), SF3B1 (1%) and MYD88 L265P(1%). No mutations in EZH2, CREBBP or EP300 were found. In 15 CLL representative samples from each group (BCL2-R and ctrl), Bcl2 protein expression was significantly higher in BCL2-R CLL (ratio Bcl2/actin 0.94 vs 0.74, p=0.009) as was expression of the pro-apoptotic protein Bim (ratio Bim/actin: 2.059 vs 1.524, p=0.007). BH3 profiling demonstrated that BCL2-R CLL and ctrl CLL samples (n=23 in each group) had comparable overall priming (cyto-C release 66.1% vs 63.3%, ns) and Bcl-2 dependence (cyto-C release 75.4% vs 76.3%, ns). Both also had low dependence on Bcl-xL (cyto-C release 8.2% vs 8.8%, ns). In contrast, Mcl-1 dependence was found to be significantly lower in BCL2-R CLL (cyto-C release 15.6% vs 37.4%, p<0.0001). Consistent with our BH3 profiling results, the activity of venetoclax and the Bcl-xLi (A133) did not differ significantly between the 2 groups (n=15). In contrast, both Mcl-1i were less active in the BCL2-R group: average viabilities after 24h treatment with AZD5991 were 76.4% vs 56.3% (p=0.006) and with S63845 77.3% vs 62.9% (p=0.02) in the BCL2-R vs ctrl group, respectively. Conclusion: The genomic landscape of BCL2-R CLL is characterized by a high frequency of trisomy 12, subclonal NOTCH and RAS pathway mutations, as well as BCL2 and MLL2 mutations. Protein expression, BH3 profiling and viability assays data are consistent with nearly exclusive dependence on Bcl-2. Our data suggest that Bcl-2 inhibition should be favored over Mcl-1 inhibition in BCL2-R CLL. Disclosures Herbaux: Roche: Consultancy, Honoraria, Research Funding. Laribi:abbvie: Honoraria, Research Funding; amgen: Research Funding; novartis: Honoraria, Research Funding; takeda: Research Funding. Ysebaert:Roche: Consultancy; Janssen: Consultancy; AbbVie: Consultancy. Morel:Janssen: Honoraria. Guieze:abbvie: Honoraria, Other: advisory board, travel funds; janssen cilag: Honoraria, Other: advisory board, travel funds; roche: Other: travle funds; gilead: Honoraria, Other: travel funds; astrazanecka: Honoraria, Other: advisory board. Brown:Sun: Research Funding; Acerta: Consultancy; Pharmacyclics: Consultancy; Genentech: Consultancy; Morphosys: Consultancy, Membership on an entity's Board of Directors or advisory committees, Other; Invectys: Membership on an entity's Board of Directors or advisory committees, Other: DSMC; Gilead: Consultancy, Research Funding; BeiGene: Consultancy; Catapult: Consultancy; Dynamo Therapeutics: Consultancy; Eli Lilly and Company: Consultancy; Juno/Celgene: Consultancy; Kite: Consultancy; MEI Pharma: Consultancy; Nextcea: Consultancy; Novartis: Consultancy; Octapharma: Consultancy; Pfizer: Consultancy; Rigel Pharmaceuticals: Consultancy; Sunesis: Consultancy; TG Therapeutics: Consultancy; Verastem: Consultancy, Research Funding; Loxo: Consultancy, Research Funding; Astra-Zeneca: Consultancy; Janssen: Honoraria; AbbVie: Consultancy.

Download Full-text

Hotspot U2AF1 Mutations Determine Missplicing Selectivity: Novel Mechanisms Altering Splicing Factors

Blood ◽

10.1182/blood-2019-129367 ◽

2019 ◽

Vol 134 (Supplement_1) ◽

pp. 2985-2985

Author(s):

Vera Adema ◽

Courtney E Hershberger ◽

Wencke Walter ◽

Cassandra M Kerr ◽

Stephan Hutter ◽

...

Keyword(s):

Board Of Directors ◽

Growth Regulation ◽

Data Monitoring Committee ◽

Splicing Factor ◽

Splicing Factors ◽

Cell Cycle Regulators ◽

Bioinformatics Pipeline ◽

Advisory Committees ◽

Dismal Prognosis ◽

Increased Risk

Mutations in splicing factor genes (SF3B1, SRSF2, U2AF1, and ZRSR2) are identified in over 50% of patients diagnosed with myelodysplastic syndrome (MDS). U2AF1 is a U2 auxiliary factor that forms a heterodimer with U2AF2 for the recognition of the 3' splice site (SS) and results in the subsequent recruitment of U2snRNPs during pre mRNA splicing. U2AF1 mutations are present in 11% of MDS and its presence is correlated with an increased risk of progression to AML. Non-canonical mutations are rarely seen in U2AF1 but two highly conserved hotspots (S34, Q157) are frequently seen and result in distinct downstream effects. We performed NGS analysis of a large cohort of patients with myeloid neoplasms (MN; n=3,328) and identified 238 patients with U2AF1 mutations (7%). We analyzed the somatic mutational profile, clonal hierarchy, and splicing profile of patients with U2AF1S34 (n=99), U2AF1Q157 (n=119), and others (n=20; M1/*, A26T/V, R35Q, R118C, E124K, F150L, E152G, C154S, R156H, M172L). The mutational spectrum of U2AF1S34 and U2AF1Q157 was equally dismal but pretty distinct. U2AF1 S34 cases were mostly co-mutated for DNMT3A (5%), TET2 (4%), RUNX1 (2%), ASXL1, CBL, ETV6, KRAS, NRAS (1.3%), STAG2 (1%), CUX1, and TP53 (<1%) while U2AF1Q157 had higher numbers of mutations in ASXL1 (10%), SETBP1, TET2 (3%), NRAS (2%), DNMT3A, PHF6 (2%), JAK2 (2%), CBL, EZH2, TP53 (2%), IDH2, RUNX1, STAG2 (2%), KRAS (1%), and IDH1 (<1%). Mutational rank showed: U2AF1S34 was ancestral in 38% of the cases followed by secondary DNMT3A and NRAS (5%, both). Ancestral U2AF1Q157 was found in 35%, with ASXL1 (19%) being the most common secondary hit. Subclonal U2AF1S34 (44%) was most commonly preceded by DNMT3A (21%), while secondary U2AF1Q157 (40%) had ASXL1 (28%) as the most common first hit. U2AF1S34 and U2AF1Q157 were co-dominant to a miscellanea of mutations. U2AF1S34 cases had a shorter OS than U2AF1Q157 cases (n=82 vs. n=101; 20 vs. 25 mo.; P=.002). Ancestral U2AF1S34 or U2AF1Q157 defined a dismal prognosis compared to secondary U2AF1S34 or U2AF1Q157 (OS: n=63 vs. n=86; 29 vs. 37 mo.; P=.03). To investigate the effects of both mutations on splicing patterns, we analyzed RNA-Seq profiles, followed by the rMATS bioinformatics pipeline to determine alternative splicing (AS) events that were classified as skipping exon (SE), retained intron (RI), and 3' or 5' alternative SS (A3SS, A5SS) (Hershberger, ASH 2019). Overall, 675 AS events in 430 genes were scored significant (pFDR<.05) when the splicing inclusion/exclusion difference was ±10%. U2AF1S34 and U2AF1Q157 caused an equal fraction of SE (79% U2AF1S34; 72% U2AF1Q157). Only 4% of the genes were commonly misspliced by both mutations, while the rest of the genes were uniquely spliced according to each mutation. Some exemplary genes misspliced by both mutations were DDX3X (an RNA helicase) showing a consistent SE at exon 5 and an RI 3-5a and CCNG1 (cell growth regulation) which was enriched for RI 7-7. Among others, U2AF1S34 uniquely affected the splicing of TET2 (SE e3); cell cycle regulators, CDC37L1 (SE), CCNC (SE e8), and HDAC3 (SE e6). We then investigated whether U2AF1 mutations might affect the splicing of other RNA splicing components. This mechanism would lead to the loss of regulation of the spliceosome complex. U2AF1S34 produces selective RIs in SRSF2 (4-4a) and A5SS in SRSF6 (7a and 7). Tumor suppressors and proto-oncogenes were also found to be misspliced by U2AF1S34 including PTEN (RI 3-Ua), CTNNB1 (RI 15-19; 3'SS (19 and 19a), and CCNL1 (RI 4-U). Major regulators of splicing factor activity are phosphatases like PP1R12A and PPP1R12B, which showed an RI 8-7 and an A3SS, respectively. Among genes exclusively misspliced by U2AF1Q157, we identified DEAD-Box helicases [DDX17 (RI), DDX59 (SE e8), DHX29 (RI)], ALAS family members (ALAS1, SE e6; ALAS2, SE e5) and UTX (KDM6A; SE e16). U2AF1Q157 affected the missplicing of DYRK1A (SE e7), a kinase known to phosphorylate SF3B1 at T434 site. In sum, our study suggests that while concurrent mutations in splicing factors lead to lethality, the presence of mutations (as the case of U2AF1S34 and U2AF1Q157) and consequent missplicing of other splicing factors are permissive events in MN and might represent novel mechanisms of disease pathogenesis. Disclosures Walter: MLL Munich Leukemia Laboratory: Employment. Hutter:MLL Munich Leukemia Laboratory: Employment. Meggendorfer:MLL Munich Leukemia Laboratory: Employment. Nazha:Abbvie: Consultancy; Daiichi Sankyo: Consultancy; Jazz Pharmacutical: Research Funding; Incyte: Speakers Bureau; Novartis: Speakers Bureau; Tolero, Karyopharma: Honoraria; MEI: Other: Data monitoring Committee. Sekeres:Syros: Membership on an entity's Board of Directors or advisory committees; Millenium: Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Maciejewski:Alexion: Consultancy; Novartis: Consultancy.

Download Full-text

A New Therapeutic Hypothesis: Nonsense-Mediated Decay Is an Exploitable Target in Multiple Myeloma

Blood ◽

10.1182/blood-2018-99-114801 ◽

2018 ◽

Vol 132 (Supplement 1) ◽

pp. 1937-1937

Author(s):

Alexander Leeksma ◽

Ingrid A.M. Derks ◽

Brett Garrick ◽

Torsten Trowe ◽

Aldo Jongejan ◽

...

Keyword(s):

Multiple Myeloma ◽

Cell Death ◽

Er Stress ◽

Board Of Directors ◽

Cell Lines ◽

Research Funding ◽

Protein Production ◽

Splicing Factors ◽

Advisory Committees ◽

Nonsense Mediated Decay

Abstract Background Nonsense-mediated decay (NMD) is a cellular quality control system that degrades mRNAs containing premature termination codons (PTCs) as well as ~10% of normal mRNAs (Kurosaki and Maquat, 2016). NMD thus prevents translation of misfolded proteins, and potential activation of the unfolded protein response (UPR). Mutations in splicing factors such as SF3B1, SRSF2, U2AF1 and ZRSR2 found in hematological as well as solid tumors, can lead to generation of aberrant mRNAs that contain PTCs. Aberrant splicing patterns in cancer cells can possibly result in increased pressure on the NMD machinery. CC-115, a potent inhibitor of mTOR kinase (TORK) and of DNA-dependent protein kinase, (DNA-PK; Mortensen et al., 2015; Tsuji et al., 2017), is in clinical development for the treatment of solid and hematologic malignancies (Thijssen et al., 2016). Preclinical data revealed an additional target of CC-115 and its differential effect on NMD. Our hypothesis was that a subset of tumor cells, especially hematologic tumors with high protein production and/or splicing factor mutations, would be susceptible to NMD inhibition by CC-115. Methods In total, 141 cell lines were screened for sensitivity to CC-115-mediated inhibition of proliferation and induction of cell death, in comparison to specific inhibition of TORK (CC-223). Isogenic DNA-PK knockout cell lines HCT116/HCT116 DNA-PK-/- and M059K/M059J DNA-PK-/- were treated with CC-115 and CC-223. Activity on NMD in vivo was tested using HCT-116 xenograft tumors treated with Vehicle or CC-115. Dependence on CC-115 sensitivity was determined using CRISPR/Cas9 technology of apoptosis or UPR genes in various MM cell lines. RNA sequencing was used for identification of potential targets in sensitive and resistant cell lines. Results A subset of cancer cell lines underwent cell death at sub-micromolar concentrations of CC-115 due to inhibition of NMD, but this was independent of mutations in splicing factors such as SF3B1. We next focused on MM cells as these generally produce high levels of (immunoglobulin) proteins and are prone to ER stress, and therefore potentially susceptible to NMD inhibition. Indeed, treatment with CC-115 resulted in activation of the UPR independent of TORK and DNA-PK inhibition, and cell death in 11/12 MM cell lines. Activity of CC-115 correlated strongly with cell death by the known ER-stress inducer, thapsigargin. Cell death by CC-115 occurred by the mitochondrial pathway of apoptosis, as it depended on caspase activity and the presence of Bax-Bak. Analysis of RNA sequencing data is ongoing and has indicated potential targets dictating sensitivity to CC-115-mediated cell death. Conclusions We describe that hematologic tumors with high protein production are specifically sensitive to CC-115, a novel and clinically exploitable inhibitor of NMD. This might lead to application in malignancies that depend on NMD to avoid excessive protein stress, such as multiple myeloma. Disclosures Garrick: Celgene: Employment. Trowe:Celgene: Employment. Kater:Acerta: Membership on an entity's Board of Directors or advisory committees, Research Funding; Abbvie: Membership on an entity's Board of Directors or advisory committees, Research Funding; Roche/Genentech: Membership on an entity's Board of Directors or advisory committees, Research Funding; Celgene: Research Funding; Janssen: Membership on an entity's Board of Directors or advisory committees, Research Funding. Eldering:Celgene: Research Funding. Filvaroff:Celgene: Employment.

Download Full-text

The Spliceosome As a New Therapeutic Target in Cytarabine-Resistant Acute Myeloid Leukemia

Blood ◽

10.1182/blood-2021-150879 ◽

2021 ◽

Vol 138 (Supplement 1) ◽

pp. 3334-3334

Author(s):

María Luz Morales ◽

Roberto Garcia-Vicente ◽

Alba Rodríguez García ◽

Noemí Álvarez Sánchez-Redondo ◽

Alejandra Ortiz-Ruiz ◽

...

Keyword(s):

Gene Expression ◽

Board Of Directors ◽

Rna Splicing ◽

Ex Vivo ◽

Sr Proteins ◽

Splicing Factors ◽

Advisory Committees ◽

Paired Samples

Abstract Introduction. Despite the recent approval of several drugs for the treatment of AML, the 3 + 7 regimens remain as the standard of care for many patients. Its lack of efficacy represents the main cause of death, since only 10% of patients who show refractoriness/relapse overcome the disease. Therefore, there is still an urgent need for seeking more effective treatments. Aberrant RNA splicing has been described in AML, but its relevance as mechanism of resistance is unclear. In this study, we deepen the mechanism of resistance to cytarabine and the role of splicing factors SR proteins, involved in the spliceosome functionality, to seek more effective therapies for AML. Methods. First, the expression levels of genes encoding SR proteins were analyzed with the GEPIA2 platform, comparing the data from the TCGA-LAML (AML patients) and GTEx (healthy) projects. Then, the gene expression of one of the most overexpressed genes, SRRM2, was validated by qPCR in samples of AML patients compared to controls and other myeloid disorders, as MDS and MPN (n=54). The resistance-associated phospho-proteomic profile was analyzed by LC-MS / MS after IMAC enrichment in paired samples from 3 AML patients. The expression of SR proteins and their phosphorylated forms was studied by immunohistochemistry (IHC) before and after resistance in paired bone marrow samples from 3 AML patients. We also analyzed by IHC the prognostic value of phospho-SR proteins at the moment of diagnosis in 64 patients with different responses to cytarabine (non-responders and responders). In order to validate an altered function of SR proteins, the analysis of the differential use of exons of paired samples from 25 AML patients was performed using RNAseq. Then, we evaluated in vitro the efficacy of some splicing modulators, and its combination with other approved drugs, in cytarabine-sensitive and resistant cells. The combination of H3B-8800, a spliceosome inhibitor, with venetoclax was tested in ex vivo samples from AML patients and healthy donors. Results. We found that the gene expression levels of SRSF9, SRSF12 and SRRM2 were altered in AML (Fig 1A-B). Immunohistochemical studies revealed that, although at the protein level no differences were found in SR proteins expression between the diagnosis and relapse moment, an increase in the levels of phosphorylated SR proteins was associated at the time of relapse (Fig 1C). Indeed, the phosphorylation levels of SRRM2, among other SR proteins, were found to be increased during cytarabine resistance by phospho-proteomics (Fig 1D). Moreover, the phosphorylation levels of SR proteins predicted the response to cytarabine treatment, as AML patients that were non-responders presented significantly higher levels compared to responders ones (Fig 1E). The observed alterations in the phosphorylation of these proteins were correlated with a differential use of exons in some of their known targets, when comparing the diagnostic condition and drug resistance moment. Based on this evidence, the efficacy of combining different therapeutic options was evaluated in vitro using sensitive or cytarabine-resistant cell models (Fig 1F). The combination of H3B-8800 together with venetoclax was the most effective in vitro and also presented synergic effects ex vivo in AML patients samples (Fig 1G). Furthermore, this combination did not show toxicity over healthy hematopoietic progenitors, since the same doses that were effective in AML did not show toxicity in a healthy context (Fig 1H). Conclusions. The results of this work shed light on the role of the RNA splicing process in cytarabine resistance in AML. Interestingly, the high levels of phosphorylated splicing factors SR proteins at diagnosis in refractory patients, would allow us to use them as a predictive biomarker of response to cytarabine treatment. Otherwise, due to the need to search effective and safe treatments in this disease, we have found that the combination of splicing inhibitors with venetoclax should be a good strategy for the treatment of AML. Acknowledgment. This work has been possible thanks to the granting of the project PI19/01518 from the Carlos III Health Institute and the CRIS Against Cancer Foundation. ML.M. enjoys a research grant from the Spanish Society of Hematology and Hemotherapy and R.GV. a FPU grant from the Ministry of Science, Innovation and Universities. Figure 1 Figure 1. Disclosures Sanchez: Altum sequencing: Current Employment. Ayala: Incyte Corporation: Membership on an entity's Board of Directors or advisory committees; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees; Astellas: Honoraria; Celgene: Honoraria.

Download Full-text

Characteristics of Different Splicing Factor Mutation Hotspots in Myelofibrosis

Blood ◽

10.1182/blood-2020-140145 ◽

2020 ◽

Vol 136 (Supplement 1) ◽

pp. 37-37

Author(s):

Franco Castillo Tokumori ◽

Chetasi Talati ◽

Najla E. Al Ali ◽

David A. Sallman ◽

Seongseok Yun ◽

...

Keyword(s):

High Risk ◽

Board Of Directors ◽

Research Funding ◽

Splicing Factor ◽

World Health ◽

Severe Thrombocytopenia ◽

Leukemic Transformation ◽

Advisory Committees ◽

Splicing Mutations ◽

The Impact

CONTEXT: Splicing factor mutations (SRSF2, U2AF1, SF3B1, and ZRSR2) are present in ~50% of myelofibrosis (MF) patients. SRSF2 and U2AF1 Q157 are considered to be high-risk mutations, while the prognostic significance of ZRSR2 and SF3B1 has not been well established. As a group, splicing mutations are associated with cytopenias, the management of which is an area of unmet clinical need in MF. OBJECTIVE: To describe the clinical characteristics, treatment approaches, and outcomes in MF patients with splicing mutations. DESIGN: This is a single-institution, retrospective analysis of 133 MF patients with splicing mutations who presented to our institution between 2006 and 2019. PMF, post-ET MF, and post-PV MF were defined according to the World Health Organization and International Working Group criteria, respectively. Baseline variables were compared between patients harboring different splicing factor mutations and different mutations within the same splicing gene. Median overall survival (OS) was measured from time of diagnosis to date of death or censored at last follow up or date of transplant. Kaplan-Meier plots were created to compare LFS and OS among treatment cohorts, and differences were assessed using Log-rank tests. RESULTS: Among 133 MF patients with a splicing mutation, SRSF2 mutations were most common (n = 48), followed by U2AF1 (n = 36), SF3B1 (n = 27) and ZRSR2 mutations (n = 24). Most SRSF2 mutations occurred at P95 (90%). Thirty (83%) U2AF1 mutations occurred at Q157, with 5 (14%) at S34. Fourteen (63%) SF3B1 mutations occurred K666, with 9 (33%) at K700. Thirteen (54%) ZRSR2 mutations were in-frame insertions/deletions, 4 (17%) frameshift mutations, 3 (13%) nonsense mutations and 4 (17%) missense. All frameshift/nonsense ZRSR2 mutations occurred in males. Spliceosome mutations were mutually exclusive but for 2 cases (one had U2AF1 and SRSF2 mutations and the other had SF3B1 and ZRSR2 mutations). Baseline characteristics were similar between splicing mutations. The presence of a U2AF1 mutation correlated with lower hemoglobin (p 0.018) and U2AF1 Q157 mutations were associated with thrombocytopenia p=0.051) and higher DIPSS-plus scores (p=0.006). Severe thrombocytopenia (platelets < 50 x 109/L) was present in 20 (17%) patients and enriched in those with U2AF1 mutations (n = 9). ASXL1 mutations rarely occurred in conjunction with SF3B1 mutations (p = 0.007). Among all patients with splicing mutations, median OS was 60.6 months. Median OS was decreased in patients with SRSF2 mutations (33 vs 106 months, p=0.001) compared to those with other splicing mutations. Median OS was increased in patients with SF3B1 mutations compared to patients with other splicing mutations (181 mo vs 42 mo, p = 0.002). Median OS for patients with U2AF1 and ZRSR2 mutations was 44 and 106 months, respectively. Among patients with U2AF1 mutations, the presence of severe thrombocytopenia was associated with inferior survival (13.9 mo vs not reached, p = 0.045). The presence of an SRSF2 mutation was associated with an increased risk of leukemic transformation (24% vs 3%, p = 0.002). Among patients with SRSF2 mutations, median OS in those with documented leukemic transformation was 32.9 mo compared to 48.7 mo in those without (p = 0.17). CONCLUSIONS: Splicing mutations in MF have unique phenotypic and prognostic correlations. While SRSF2 mutations appear detrimental, SF3B1 mutations correlate with favorable outcomes. While U2AF1 and SRSF2 mutations are considered high-risk in MF, the impact appears driven by cytopenias in the former and leukemic transformation in the latter. This may hold relevance when considering therapeutic approaches in these patients. Disclosures Talati: AbbVie: Honoraria; Jazz: Speakers Bureau; Astellas: Speakers Bureau; BMS: Honoraria; Pfizer: Honoraria. Sallman:Celgene, Jazz Pharma: Research Funding; Agios, Bristol Myers Squibb, Celyad Oncology, Incyte, Intellia Therapeutics, Kite Pharma, Novartis, Syndax: Consultancy. Sweet:Takeda: Membership on an entity's Board of Directors or advisory committees; BMS: Membership on an entity's Board of Directors or advisory committees; Novartis: Membership on an entity's Board of Directors or advisory committees; Incyte: Research Funding; Stemline: Honoraria; Agios: Membership on an entity's Board of Directors or advisory committees; Astellas: Honoraria. Padron:Incyte: Research Funding; Kura: Research Funding; BMS: Research Funding; Novartis: Honoraria. Lancet:Abbvie: Consultancy; Agios Pharmaceuticals: Consultancy, Honoraria; Astellas Pharma: Consultancy; Celgene: Consultancy, Research Funding; Daiichi Sankyo: Consultancy; ElevateBio Management: Consultancy; Jazz Pharmaceuticals: Consultancy; Pfizer: Consultancy. Komrokji:Geron: Honoraria; Novartis: Honoraria; Acceleron: Honoraria; Incyte: Honoraria; Abbvie: Honoraria; Agios: Speakers Bureau; BMS: Honoraria, Speakers Bureau; Jazz: Honoraria, Speakers Bureau. Kuykendall:Blueprint Medicines: Research Funding; BMS: Research Funding; Incyte: Research Funding; Novartis: Research Funding.

Download Full-text