ALBERT

Description: Next generation sequencing (NGS) and single nucleotide polymorphism arrays (SNP-A) contribute to more precise identification of the spectrum of somatic mutations and karyotypic abnormalities in myeloid neoplasms. The diversity of individual defects and their combinations corresponds to the tremendous clinical heterogeneity. Identification of key driver genes remains a fundamental component to understanding the immense data generated from this technology and the contributions to leukemogenesis. In this project, we evaluated 1200 cases of MDS and AML. Somatic mutations of AT rich interactive domain 2 (ARID2) were found in myelodysplastic syndrome (MDS), myeloproliferative neoplasms (MPN), primary acute myeloid leukemia (pAML) or secondary AML (sAML). All ARID2 mutations occurred in either frameshift (at p.S1489 and p.T1645) or nonsense (at p.E65, p.S154 and p.Q1637) configurations, consistent with loss of function. We have identified a total of 5 mutant cases, all of somatic origin. Study of clonal architecture elucidated that ARID2 mutations were ancestral events in 50% of mutant cases as defined by variant allelic frequencies. By SNP-A, a commonly deleted region on chr.12q was defined by mapping minimally affected lesions in 9 patients with MDS, MPN, sAML or pAML. Haploinsufficient expression of ARID2 was confirmed by expression array analysis in the cases with del(12q), which is compatible to the frequent incidence of heterozygous ARID2 loss-of-function mutations. Del(12q) was more frequent in high-risk phenotype with higher blast counts. In addition, significantly lower expression of ARID2 was also observed in 22 out of 183 patients with diploid 12q. Interestingly, amplification of locus was not found in any of the cases studied by SNP-A. Altogether, such lesions of defective ARID2 were pathogenic in more than 10% of cases with myeloid neoplasms. ARID2 is encoding one of the components of SWI/SNF complex and involved in chromatin remodeling. Therefore, we stipulate that other genes which function together with ARID2 might be affected with somatic mutations or deletions. Further analyses demonstrated the presence of other somatic mutations and deletions affecting SWI/SNF complex, including ACTL6B (N=53) and SMARCD3 (N=66). While SWI/SNF complex lesions were mutually exclusive, concomitant subclonal mutations in such affected cases were commonly observed in RAS pathway genes, including K/NRAS, NF1 and PTPN11. To the contrary, ARID1B, which negatively regulates chromatin remodeling, is predominantly activated in the cohort with similar phenotype. While germline mutations of multiple genes in SWI/SNF complex are reported to be associated with Coffin-Siris syndrome, no family or past history characteristic of this congenital disorder was observed in our cohort. Further clues into the function of ARID2 in myeloid neoplasms came from studying splicing dysfunction in U2AF1 mutant cases. Deep RNA sequencing in the cases with U2AF1 mutations (p.S43F and p.Q157P), showed a consistent loss of ARID2 exon 8 (predominantly noted in sAML). Two types (whole and partial) of exon skipping led to frameshift in the transcript creating a stop codon. Targeted RT-PCR confirmed the transcriptome sequencing results in primary bone marrow samples of the cases with U2AF1 but not in the corresponding wild-type cases. These results are compatible with the genetic finding that spliceosomal mutations were not concomitantly observed in the cases with SWI/SNF complex defects, suggesting misspliced transcript with nonsense decay consequences is enough pathogenic to preclude additional spliceosomal mutations. To validate functional consequences of ARID2 loss, knockdown experiment using ARID2-shRNA transduction in K562 and HL60 cell lines were performed. Knockdown of ARID2 generally demonstrated cell cycle arrest in G2 phase prior to entry into the S-phase, which was partly caused by decreased expression of CDKL3 and CCND3. Hb staining with Benzidine showed impairment of erythroid differentiation in ARID2 knockdown K562, which was confirmed by cytological examination. In sum, multiple mechanisms of defective ARID2 including somatic mutations, haploinsufficiency and phenocopy due to spliceosomal mutations can be involved in ARID2-mediated leukemogenesis. Together with the other components, novel lesions of SWI/SNF complex constitute a group of tumor suppressor genes in myeloid neoplasms. Disclosures No relevant conflicts of interest to declare.

Description: 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.

Description: Abstract 1698 Hypomethylating agents decitabine and azacitidine are standard treatments for myelodysplastic syndromes (MDS). In their use, one hopes to rectify cytopenias and prolong survival by retarding further disease progression. However, individual treatment responses vary from complete remission (CR) to complete refractoriness. In general, at least 4 cycles of therapy are administered prior to assessing response. Thus, patients may have prolonged exposure to ineffective therapy, suffering toxicities without clinical benefit, while alternative and potentially more effective treatments are delayed. Currently, there are no reliable phenotypic or mutational markers for predicting response to hypomethylating agents. Once whole exome sequencing (WES) became available for more routine analysis, we theorized that somatic mutational patterns may help identify patients who would most benefit from these drugs, thereby maximizing response rate by rational patient selection. To pursue this hypothesis, we screened a cohort of 168 patients with MDS who received either azacitidine or decitabine for the presence of somatic mutations. Only those who received sufficient therapy, i.e., completed at least 4 cycles, were selected for outcome analysis. Targeted Sanger sequencing, including a panel of up to 19 genes frequently affected by somatic mutations was performed. For a representative subset of 26 patients (this subset is expanding) of whom there were 15 responders and 11 non-responders, mutational analysis was performed by WES to select target genes for further analysis. WES utilizes paired DNA (tumor vs. CD3+ lymphocytes) to produce raw sequence reads aligned using Burrows-Wheeler Aligner (BWA). Variants are detected using the Broad Institute's Best Practice Variant Detection GATK toolkit. Median age was 68 years (range, 55–85), 50% were female, and MDS subtypes were as follows: RA/RCUD/RARS 13%, RCMD 16%, RAEB-1/2 20%, MDS/MPN & CMML-1/2 31%, and sAML 20%. Response was assessed using IWG 2006 criteria at 4 and 7 months after therapy initiation. Overall response was 48%; rate of CR (including marrow/cytogenetic CR) was 28%, any HI 20%, SD 22%, and no response 29%. The cohort was then dichotomized into “responders” and “non-responders,” with responders classified as those achieving CR or any HI. Baseline patient characteristics were similar between both groups, including average age at treatment initiation, disease subtypes, proportion of abnormal/complex karyotypes, and presence of common cytogenetic aberrations. Overall, the most frequently mutated genes include TET2/IDH1/IDH2, SRSF2, ASXL1, SF3B1, RUNX1, EZH2/EED/SUZ12, SETBP1, CBL, and PPIAF2. The highest rate of refractoriness was noted in mutants of TET2/IDH1/IDH2 (67%), SF3B1 (67%), U2AF1/2 (67%). We also identified several genes whose mutants were few but associated exclusively with refractory disease (100%), including KIT, ZRSR2, PRPF8, LUC7L2. We next applied a recursive partitioning algorithm to construct a decision tree for identifying the most pivotal mutations associated with response: we found mutant CBL and PPFIA2 to be strongly associated with response, whereas mutant U2AF1/2, SF3B1 and PRPF8 were strongly associated with refractoriness. Our final approach was to dichotomize the cohort by the presence/absence of each mutation/group of mutations, and response within mutant vs. wild type cases was compared. Among refractory cases, TET2/IDH1/IDH2 (26%) and SF3B1 (17%) were most frequently mutated; among responders, mutations in RUNX1 (19% vs. 4%]), CBL (14% vs. 0%), SRSF2 (23% vs. 9%), and SETBP1 (18% vs. 4%) were most frequent. When multiple genes were combined in “either-or” fashion, mutation in TET2, SF3B1, PRPF8, or LUCL71 was significantly associated with refractoriness (52%, p=.0287), whereas mutations of RUNX1, CBL, SRSF2, SETBP1, or PPFIA2 mutation was significantly associated with response (86%, p=.0001). Mutational patterns appear to predict response to standard hypomethylating agents. Identification of the most predictive genes could guide development of molecular maker-based selection of patients for hypomethylating agent therapy, but will require ongoing analysis and additional prospective testing for validation. Disclosures: Advani: Genzyme: Honoraria, Research Funding; Immunomedics: Research Funding. Maciejewski:NIH: Research Funding; Aplastic Anemia&MDS International Foundation: Research Funding.

Description: Introduction: The myelodysplastic syndromes (MDS) are a heterogeneous group of clonal hematopoietic stem cell disorders. Ringed sideroblasts (RS) are found in the following subclasses of MDS: refractory anemia with ringed sideroblasts (RARS), refractory cytopenia with multilineage dysplasia and ringed sideroblasts (RCMD-RS), and refractory anemia with ringed sideroblasts associated with marked thrombocytosis (RARS-T). The objective of this study was to evaluate the use of single nucleotide polymorphism (SNP) arrays (SNP-A) in patients with MDS and RS and specifically to compare chromosomal abnormalities detected by metaphase karyotyping (MC) with those detected using high-resolution SNP based karyotyping (which can detect unbalanced genomic lesions in addition to copy-neutral loss of heterozygozity) and to conduct a disease association analysis using the SNP-A. Methods: We reviewed the electronic records of patients with MDS and RS seen at our institution between 2002 and 2008. DNA was extracted using the Puregene DNA Purification Kit. Gene Chip Mapping 250K Assay Kit (Affymetrix) was used. Signal intensity and genotype calls were analyzed using CNAG v.3.0. For the disease association analysis, the Fisher’s p-value was used to compare SNPs found in patients with MDS and RS versus 150 normal controls. Results: 83 patients with MDS who have RS were identified. 40 (48%) had RARS, 25 (30%) had RCMD-RS, and 18 (22%) had RARS-T. The mean age of these patients was 70.7 years, 53 patients (64%) were males, and 70 (84%) were Caucasian. Of those 83 patients, 45 had available DNA for SNP analysis, 23 (51%) of whom had RARS, 11 (24%) had RCMD-RS, and 11 (24%) had RARS-T. The mean age of these 45 patients was 69.9 years, 29 (64%) were males, and 39 (87%) were Caucasian. By MC, 20/45 (44.5%) patients had abnormal karyotypes and 25/45 (55.5%) patients had normal karyotypes. Using SNP-A, chromosomal abnormalities including UPD were identified in 29/45 (64.5%) of patients. Of the 25 pts who had normal karyotypes by MC, 11 (44%) had abnormal karyotypes by SNP-A. The chromosomal distributions of the lesions detected by MC were as follows: chromosome 5 (18.4%), chromosome 7 (15.8%), chromosome 8 (13.1%), chromosome 17, 18, 19, 20, 21 (5.2% in each), and others (26.3 % in total). The distribution of chromosomal lesions detected by SNP-array analysis (excluding UPD) was as follows: chromosome 8 (18.7 %), chromosome 5 (14.6%), chromosome 7 (12.5%), chromosome 17 (10.4%), chromosome 20 (8.3%), chromosome 4 (6.2%), chromosomes 2, 3, 13, 22 (4.1% each), and others (12.5% in total). UPD was found in 12/45 (26.7%) patients mostly affecting chromosome 1 (27.8%). A large number of SNPs were found to be significantly more prevalent in patients with MDS with RS than in controls (with p-value 〈 0.0001). Genes within 50 kb from these SNPs were scrutinized. At least 11 of those genes (RP1, LIMD1, CHL1, ATP6V1F, TEAD2, SPTLC2, CDH13, DIAPH2, DLEU2, FAM10A4, TRPM8) are known to be related to cancer in the literature. Given that karyotypic abnormalities were more prevalent in chromosomes 8, 5, and 7, we looked specifically at the SNPs in those chromosomes which were significantly associated with disease (rs 409429, rs 446153, rs 453186 and rs 509273 in chromosome 8; rs6891109 in chromosome 5; and rs6970371 in chromosome 7). The genes within 50 kb of these SNPs that are known to be associated with cancer are: RP1 in chromosome 8 (colon cancer), and ATP6V1F in chromosome 7 (prostate cancer). Conclusion: This study shows that SNP-A based karyotyping is a useful tool for karyotyping and can detect more chromosomal abnormalities than MC (64.5 versus 44.5%, odds ratio 1.45). We also found that about half of the patients who had normal karyotypes by MC were found to have karyotypic abnormalities by SNP-A. In addition, we show multiple candidate genes that could be important in the pathogenesis of MDS with RS.

Description: Autophagy contributes to therapeutic resistance and malignant progression by generating alternative metabolic fuel to maintain cell survival under stress conditions including those imposed by hypoxia, radiation, chemotherapy, and targeted agents. The FDA approved anti-malarial drug hydroxychloroquine (HCQ) inhibits autophagy through the disruption of lysosomal function. Robust efforts to repurpose HCQ for cancer therapy based on these properties stimulated numerous clinical trials where HCQ was combined with an array of other anticancer regimens and ultimately produced modest clinical activity. However, it was unclear if the maximum tolerated dose of HCQ was sufficient to completely inhibit autophagy in tumors. New autophagy inhibitors with increased potency and more favorable therapeutic indices are clearly needed to rigorously investigate the potential benefit of this approach. Polyvalent molecules can yield nonlinear, multifold potency against their respective targets compared to their corresponding monomers. We generated a series of novel dimeric compounds containing modified core elements of HCQ, CQ and the anti-schistosomal drug lucanthone with the goal of developing new autophagy inhibitors with superior potency, tolerability, and anticancer efficacy. Initial screens that tested for drug-induced increased expression of p62, a protein that is specifically turned over by autophagy, and anticancer activity identified ROC-325 as a lead agent. The structure of ROC-325 was confirmed by NMR and MS analyses. Direct comparison of the in vitro activity of ROC-325 and HCQ in 13 different genetically and histologically diverse human cancer cell lines demonstrated that ROC-325 was approximately 10-fold more potent than HCQ based on IC50 analyses. Acute myeloid leukemia (AML) was selected as a primary malignancy for intensive investigation based on the high sensitivity of FLT3-ITD+ MV4-11 cells to this agent in preliminary studies. Transmission electron microscopy analyses demonstrated that treatment with ROC-325 triggered all of the hallmark features of autophagy inhibition including the accumulation of autophagosomes with undegraded cargo, an increase in lysosomal membrane permeability, deacidification of lysosomes, and elevated LC3B, p62, and cathepsin D expression. Bafilomycin A1 clamp experiments showed that ROC-325 potently inhibited autophagic flux. Genetic impairment of two different genes that are essential for functional autophagy, ATG5 and ATG7, using lentiviral shRNA approaches significantly diminished the anticancer effects of ROC-325, thus indicating that autophagy inhibition is a key component of its anticancer mechanism of action.RNA sequencing and gene level analyses demonstrated that treatment with ROC-325 (1 µM) in MV4-11 cells altered the levels of autophagy-dependent degradation pathways while preserving protein synthesis through the upregulation of post-translational ribosomal, methylation, and splicing components. In vitro treatment of a panel of human AML cell lines and normal human bone marrow progenitors demonstrated that ROC-325 diminished AML cell viability (IC50 range 0.7-2.2 µM), antagonized clonogenic survival, and induced apoptosis in a manner that was therapeutically selective. Analysis of primary blasts from patients with AML showed that its activity was not significantly affected by adverse cytogenetics or multi-drug resistance due to relapsed/refractory clinical status. Oral administration of 50 mg/kg ROC-325 (QDx5) to mice bearing disseminated MV4-11 human AML xenografts significantly increased lifespan (P

Description: NPM1 and DNMT3A mutations are highly recurrent (∼30% of cases) in de novo acute myeloid leukemia (AML). Besides aberrant cytoplasmic localization of mutated NPM1, and decreased DNA methyltransferase activity of mutated DNMT3A, the molecular mechanisms of pathogenesis are mysterious. Here, novel specific molecular mechanisms are demonstrated. These results build on and are separate from data presented (poster) at ASH 2012. LC-MSMS analysis of murine hematopoietic cells was used to analyze the protein interaction network of the key monocyte/macrophage differentiation-driving transcription factor Pu.1. Npm1 was noted to interact with Pu.1 in these analyses, confirmed by bidirectional co-immunoprecipitation-Western blot assays. This interaction suggested that PU.1 might be dragged into the cytoplasm by mutated NPM1 in AML. Accordingly, in the OCI-AML3 cell line that contains an NPM1 mutation, but not in OCI-AML2 cells with wild-type NPM1, PU.1 was co-dislocated into the cytoplasm together with NPM1, obvious by Western analysis of cellular fractions, and by immunofluorescence (IF) assays. IF analysis of primary AML cells from patients with NPM1 mutated AML confirmed this cytoplasmic dislocation of both NPM1 and PU.1 (n=3), with strong cytoplasmic instead of nuclear staining of both proteins. In contrast, primary AML cells with wild-type NPM1demonstrated the expected strong staining of these proteins in the nucleus but not in the cytoplasm (n=3). NPM1 movement into the cytoplasm is mediated by CRM1 (exportin). Thus, we hypothesized that antagonizing mutated NPM1 interaction with CRM1 would retain mutated NPM1 and PU.1 in the nucleus. Decoy peptides based on NPM1 C-terminal sequences, to hopefully minimize disruption to CRM1 interactions with other proteins, were designed to antagonize NPM1 binding to CRM1. These decoy peptides were combined with different nuclear delivery sequences including the TAT peptide, and with fluorescent tags for tracking. All six peptides entered AML-OCI3 cells (shown by IF), with the strongest signals observed for peptides fused to TAT and TAT-NES (nuclear export signal). The decoy peptides significantly and substantially inhibited cell growth of AML-OCI3 cells (〉3-fold reduction), accompanied by an increase in expression of the monocyte differentiation marker CD14 (quantified by flow-cytometry). In contrast, TAT peptide alone, as a control, did not inhibit cell growth or induce monocytic differentiation. Western and IF analyses was used to study PU.1 and NPM1 localization: decoy peptide treatment clearly increased nuclear presence of both PU.1 and NPM1, although these proteins remained detectable in cytoplasmic fractions also. At ASH 2012, we showed that OCI-AML3 cells have high nuclear CEBPA and retain granulocytic differentiation potential, readily induced by ATRA. Thus, we hypothesized that the NPM1-induced differentiation block, that is specific for the monocytic lineage, creates selective pressure for cooperative mutations that derepress monocyte-commitment. DNMT3A interacts with polycomb proteins that repress lineage-programs, and in NPM1/DNMT3A double mutant versus NPM1 mutant AML, double mutation was significantly associated with M4/M5 (14/23 [61%]) versus M1 morphology (4/13 [30%], p40-fold, p

Description: Abstract 2173 Poster Board II-150 Loss of heterozygosity (LOH) due to acquired uniparental disomy (UPD) is a commonly observed chromosomal lesion in myeloproliferative neoplasms (MPN) and myelodysplastic/myeloproliferative neoplasms (MDS/MPN) including chronic myelomonocytic leukemia (CMML). Most recurrent areas of LOH point towards genes harboring mutations. For example, UPD11q23.3 and UPD4q24 were found to be associated with c-Cbl and TET2 mutations, respectively. Cbl family mutations (c-Cbl and Cbl-b) have been associated with atypical MDS/MPN including CMML and juvenile myelomonocytic leukemia (JMML) as well as more advanced forms of MDS and secondary AML (sAML). Ring finger mutants of Cbl abrogate ubiquitination and thereby tumor suppressor function related to inactivation of phosphorylated receptor tyrosine kinases, Src and other phosphoproteins. TET2 mutations are present in a similar disease spectrum. The TET family of proteins is involved in conversion of methylcytosine to methylhydroxycytosine which cannot be recognized by DNMT1. Thereby, the proteins seem to counteract maintenance hypermethylation. In our screen of MDS/MPN, we found c-Cbl and Cbl-b ring finger mutations in 5/58 (9%) of CMML and AML derived from CMML, 2/39 (5%) MDS/MPNu, 4/21 (19%) JMML and 14/148 (9%) RAEB/sAML. In the same cohort, TET2 mutations were present in 37% and 14% of patients with MDS/MPN and MDS, respectively. Of note we did not find any TET2 mutations in JMML. We and others have also noted that TET2 and c-Cbl mutations were also detected in atypical chronic myeloid leukemia. While translocations resulting in BCR/ABL fusion characterize CML, we stipulated that in analogy to other chronic myeloproliferative diseases, TET2 and c-Cbl mutations may be also present in CML and contribute to phenotypic heterogeneity within BCR/ABL associated disorders. In particular, progression of CML to accelerated phase (AP) or blast crisis (BC) could be associated with acquisition of additional lesions. When 22 patients with CML chronic phase (CP) were screened, no TET2 and c-Cbl mutations were found. However, we identified 1 c-Cbl, 2 Cbl-b (6%) and 6 TET2 (12%) mutations in 51 patients with CML-AP (N=18) and CML-BC (N=33) with myeloid and lymphoid/mix 24 and 9 phenotype, respectively. These mutations were mutually exclusive. We also noted that TET2 mutations were present in 1/9 CML in BC with lymphoid phenotype. We subsequently screened Ph+ ALL cases (N=9) and found a TET2 mutation in 1 case but no Cbl family mutations. In contrast when 9 Ph- ALL cases were screened as controls, neither TET2 or Cbl mutations were found. SNP-A analysis revealed 2 cases of LOH involving chromosome 4 (UPD4q24 and del4) in a patient with lymphoid blast crisis and Ph+ ALL, respectively. However, UPD was not found in Cbl family gene regions (11q23.3 or 3q13.11). A homozygous deletion of Cbl-b region was seen in a CP patient. Cbl family mutations were associated with a more complex karyotype than TET2 mutations (67% vs. 17% cases with abnormal phenotype). Patients with Cbl family mutations were resistant to imatinib which was effective in only 2 out of 6 patients with TET2mutations. Dasatinib was effective in 2 patients with TET2 mutation. Median over all survival of progressed CML was 47, 49 and 48 months in patients with Cbl, TET2 or no mutations, respectively. In conclusion, our results indicate that Cbl family mutations can occur as secondary lesions in myeloid type aggressive CML (AP and myeloid BC), but not in lymphoid types. TET2 mutations were identified in both lymphoid BC and Ph1+ALL, as well as myeloid BC and AP. In contrast to CMML or JMML in which a vast majority of mutations are homozygous, all Cbl family mutations were heterozygous (no LOH). Similarly, all but two TET2 mutations were heterozygous (1 hemizygous in del4 and 1 homozygous case in UPD4q), suggesting that additional cooperating lesions affecting corresponding pathways may be present. These mutations likely represent secondary lesions which contribute to more either progression (CML) or more aggressive features (Ph+ ALL) and characterize disease refractory to therapy with imatinib. Disclosures: No relevant conflicts of interest to declare.

Description: Germ line mutations in growth factor independent-1 (GFI1) have been described in a small subset of patients (pts) with severe congenital neutropenia. Subsequently, the GFI136N polymorphism, present in 3-5% of controls, has been found overrepresented (11%) in pts with primary (p) acute myeloid leukemia (AML), conveying 1.6 fold risk of development of AML. Mutant GFI136S and N variants lack affinity to HOXA9 (overrepresented in corresponding AML cases), shows increased proliferative potential in vitro and accelerates RAS-driven myeloproliferative neoplasm (MPN) disease in mice. Whole exome next generation (WE NGS) technology facilitates comprehensive screens for the presence of both somatic and germ line genetic alteration. In this study, we used NGS to search for germline variants of the GFI1 gene. We screened 140 pts (mean age 66.8 years, range 44-85) with MDS and related disorders (MDS/MPN and secondary (s) AML) for the presence of GFI1 variants. We found non-synonymous variants in 11 cases (8%), including the previously described pathogenic p.S36N (n=8), p.P107A (n=2), or p.L400F (n=1), while the corresponding frequencies for these alterations were .04 and .001, .002 in the general population. This frequency appears comparable or higher to those previously reported for pAML, but our screen of the TCGA AML cohort, perhaps due to very low coverage for this gene, did not reveal any GFI1 polymorphisms. We next focused on the clinical features of altered GFI1 carriers. A significant proportion of GFI1 cases were younger (age

Description: Recurrent somatic nonsense PHF6 mutations have been reported in patients with T-acute lymphocytic leukemia, AML and chronic myeloid leukemia in blast crisis. Germ line (GL) PHF6 mutations are responsible for Borjeson−Forssman−Lehmann syndrome (BFLS), a hereditary X-linked disorder characterized by mental retardation and dysmorphic features. PHF6 is a highly conserved 41kDa protein with ubiquitous expression in hematopoietic cells, including CD34+ cells. We screened patients (N=1166) with myeloid neoplasms by targeted multi-amplicon deep NGS targeting all ORFs of PHF6 to determine the prevalence and distribution and molecular context of PHF6 gene alterations. In total, we identified and verified 52 cases with somatic PHF6 mutations, 32 of which were frameshift or nonsense mutations and with a strong male predominance (76%). Mutations were distributed almost equally between 2 DNA binding domains. Previously, PHF6 has been included in other screening panels (Haferlach et al. 2014 and Papaemmanuil 2013) with somatic mutations found in 24/944 and 21/738 MDS cases, respectively. SNP-array karyotyping showed that microdeletions involving the PHF6 locus were present in about 1.2% of myeloid neoplasms, but affected only female patients. The most frequent chromosomal aberration observed in conjunction with PHF6 mutations was trisomy-8 (P=.018). The most commonly associated somatic mutations included RUNX1 (P=.001) and IDH1 (P=.008) but not IDH2 (P〉.1). There was no impact on overall survival with respect to PHF6 mutant status in total or within individual risk groups (low risk (RA,RARS) vs. high-risk (RAEB1/2). Concomitant PHF6 and RUNX1 mutations were associated with particularly poor prognosis. RUNX1 mutational status correlated with PHF6 expression levels and PHF6 expression inversely correlated with RUNX1 mRNA levels. Subsequent analysis of clonal architecture using VAF calculations and serial samples for these cases suggested that PHF6 may function as a founder driver gene in 18% of cases. PHF6 variant allelic frequency (VAF) varied between disease subtypes, with the highest clonal burden found in AML patients (P

Description: TET2 is one of the most commonly mutated genes in myeloid neoplasia. The frequency of TET2 mutations (TET2MUT) increases with age and they have been found in aging healthy controls, in whom their presence was associated with a subsequent risk of developing a myeloid neoplasm. The TET2 gene product is an enzyme that uses alpha-ketoglutarate (αKG) and vitamin C to hydroxylate 5-methylcytosine (5MC), leading to both passive demethylation during cell replication and active demethylation via base excision DNA repair enzymes. Despite large studies, there is no consensus opinion as to the clinical impact of TET2 mutations and their mechanistic role in the pathogenesis of MDS. It is likely that the heterogeneity of TET2MUT, their configuration, sub-clonal context and co-associated variables result in biological heterogeneity that precludes proper assessment of clinical impact. To address these issues we analyzed a cohort of 4974 patients with myeloid neoplasms using targeted deep sequencing of a panel of 60 genes found to be most frequently affected by somatic mutations in myeloid neoplasms. A total of 1861 TET2 alterations were identified as somatic in 1238 cases using various bioanalytic algorithms and sequencing of germline DNA where possible. Of these mutations, 80% were frame shift/stop codons (fs/sc) likely leading to various truncations, while 20% were missense (ms) mutations. While no hotspots for mutations were found, 53% were located in the proximity of the catalytic domain. The most recurrent ms alteration was p.Ile1873Thr, found in 2% of all TET2MUT cases. Biallelic TE2MUT were present in 45% of mutant cases; of which fs/sc alteration combinations were the most common (333/557; 60%), and an additional 9% were homozygous fs/sc variants. Biallelic ms mutations were present in 5% of biallelic cases (3% of homozygous ms configurations). Clinically, TET2MUT were found in 17% of MDS patients, 65% of MDS/MPN, 12% of MPN, 21% of non-core binding factor pAML, and 26% of sAML, and were most frequently associated with normal cytogenetics (p