ALBERT

Description: The del(5q) is the most commonly reported deletion in de novo MDS and is found in 10–15% of all patients. Our group demonstrated haploinsufficiency for the ribosomal gene RPS14, which is required for the maturation of 40S ribosomal subunits and maps to the commonly deleted region in patients with the 5q- syndrome (Boultwood et al, Br J Haematol2007, 139:578–89). Haploinsufficiency of RPS14 has been shown to be the mechanism underlying the erythroid defect in this disorder (Ebert et al, Nature2008, 451:335–9). We have recently shown that haploinsufficiency of RPS14 in patients with the 5q- syndrome is associated with deregulated expression of ribosomal- and translation-related genes, suggesting that the 5q- syndrome represents a disorder of aberrant ribosome biogenesis (Pellagatti et al, Br J Haematol2008, 142:57–64). The del(5q) in the 5q-syndrome is cytogenetically indistinguishable from the del(5q) found in other MDS and in the vast majority of these patients the CDR of the 5q- syndrome will be deleted (and therefore one allele of RPS14 will be lost). We are investigating the hypothesis that haploinsufficiency of RPS14 and consequent deregulated ribosome biogenesis may also play a role in the pathogenesis of non-5q- syndrome MDS patients with del(5q). Using Affymetrix U133 Plus2.0 arrays, we have studied the expression profiles of a group of 579 ribosomal- and translation-related genes in the CD34+ cells of 21 non-5q- syndrome MDS patients with del(5q) and 95 MDS patients without del(5q). 168 of 579 ribosomal-and translation-related probe sets were found to be significantly differentially expressed between these two groups, with approximately 90% of these showing lower expression levels in patients with del(5q). Hierarchical clustering using this set of 168 genes gave a good separation between patients with and without the del(5q). RPS14 was one of the most significant differentially expressed genes, with lower expression levels in patients with del(5q) confirming its haploinsufficient status in these patients. Other significant differentially expressed genes include the ribosomal protein RPL22L1, and the translation initiation factors EIF4EBP3 and EIF4B. Interestingly, when samples from 16 patients with 5q- syndrome were included in the analysis, hierarchical clustering using significantly differentially expressed ribosomal- and translation-related genes showed that most patients with 5q- syndrome and most patients with del(5q) clustered together. We are currently using polysome profile analysis on bone marrow cells to examine the levels of the 40S ribosomal subunit in patients with del(5q) and without del(5q). Our results support the hypothesis that haploinsufficiency of RPS14 and deregulation of ribosomal- and translation-related genes contribute to disease pathogenesis in MDS patients with del(5q). An exciting possibility is that other MDS with the del(5q) and the 5q- syndrome share a related molecular basis in that they are all disorders of defective ribosomal biogenesis.

Description: Abstract 298 The myelodysplastic syndromes (MDS) are a heterogeneous group of clonal hematopoietic stem cell malignancies that are characterized by ineffective hematopoiesis resulting in peripheral cytopenias and a hypercellular bone marrow. Approximately 40% of patients with MDS will develop an acute myeloid leukemia. It is important to establish prognosis of MDS patients since the treatment options vary from supportive care to bone marrow transplantation. In order to determine the relationship of gene expression levels to prognosis and so identify new molecular markers, we have used gene expression profiling to study the transcriptome of the hematopoietic stem cells of 125 MDS patients with a minimum 12 month follow up. The CD34+ cells obtained from MDS patients and healthy individuals were analyzed using Affymetrix U133 Plus2.0 arrays. The patients were split randomly in a training set (n=84) and a test set (n=41). Supervised principal components analysis was used to identify genes correlated with survival. Using the 84 patients in the training set, the Cox scores were computed for each gene, and the principal components calculated on the genes with the highest Cox scores. The first of the principal components was then used to generate a regression model to predict the survival in the test set. Finally, for each probe set an importance score was calculated equal to its correlation with the supervised principal component predictor. This approach returned a list of 150 top ranked probe sets correlated with survival. Patients in the training set were split into tertiles based on the predictor (low, medium and high score) and patients in the test set were assigned to their predicted class, and Kaplan-Meier plots were generated for both training and test set. The differences in survival for both training and test set were statistically significant (Figure 1). Top ranked genes showing lower expression levels in patients with shorter survival include CDH1, LEF1 and AKAP12/Gravin. Top ranked genes showing higher expression levels in patients with shorter survival include IL23A, WT1 and PTHR2. Figure 2 shows survival of patients divided into tertiles of expression for the individual genes CDH1, LEF1 and WT1. It is probable that the genes identified in this study will become the first validated molecular markers for MDS prognosis. Multivariate analysis is currently being performed. Figure 1 Figure 1. Figure 2 Figure 2. Disclosure: No relevant conflicts of interest to declare.

Description: Introduction: CMML is a clinically heterogeneous myeloid neoplasm hallmarked by the coexistence of dysplastic and proliferative patho-clinical features, which can include cytopenias, constitutional symptoms, splenomegaly, and leukocytosis. However, according to the FAB classification schema, CMML may be differentiated in dysplastic and proliferative subgroups only by the presence of leukocytosis in the latter (WBC ≥13 x 109/L). We hypothesize that incorporation of other clinically discriminating features may yield a more informative CMML stratification system. To address this, we propose three distinct CMML categories and explore their clinical relevance leveraging our existing international CMML database (Padron E et al. Blood Cancer J. 20151). Method: 1622 WHO-defined CMML cases diagnosed between 1973 and 2014 were collected from eight large cancer centres that include up to 80 discrete data elements as previously described1. Cases were placed into three clinically distinct groups and the Pearson Chi-Square test and the Kruskal-Wallis test were applied respectively to compare categorical and continuous characteristics. The Kaplan-Meier (KM) method was used to estimate median OS and the log rank test was used to compare survival curves.Cox models whereapplied to obtain univariate and adjusted hazard ratios. Identification of optimal cut-off values for continuous variable was supported by graphical inspection of martingale residuals from the null Cox model. Statistical analyses were done in SPSS v23 and R v.3.3.0. Results: We propose three categories to delineate clinically distinct CMML subtypes: (1) Myelodysplastic (MD)-CMML: WBC≤10 x 109/L, PB-immature myeloid cells (IMC) = 0%, no splenomegaly (2) MD/MP-CMML: WBC 10-20 x 109/L or WBC ≤10 x 109/L but PB-IMC〉0% and/or splenomegaly (3) Myeloproliferative (MP)-CMML: WBC 〉20 x 109/L. A recursive partitioning approach was used to identify the WBC cut points, with splenomegaly and IMC added to more accurately depict the MPN aspect of CMML. Numbers of patients included in the MD-, MD/MP-, and MP-CMML subcategories were 319 (19.7%), 789 (48.6%) and 514 (31.7%), respectively (Table 1). According to the FAB criteria, the MD/MP group included 521 (66%) MD- (WBC ≤13 x 109/L) and 268 (34%) MP-CMML (WBC〉13 x 109/L) patients suggesting that the proposed classification clinically reclassifies FAB-defined CMML. Within the MD/MP group, 344 patients (21.2%) had a WBC 0% and/or splenomegaly. Comparison of overall survival (OS) among proposed groups demonstrated that this classification schema was capable of discriminating the CMML natural history (Figure 1). In comparison to MD/MP-CMML, the unadjusted OS Hazard Ratio (HR) was 0.60 (95% CI 0.49-0.73) for MD-CMML and 1.57 (95% CI 1.36-1.81) for MP-CMML (p5%, RBC- and PLT-transfusion-dependence predicted poor OS only in the MD and MD/MP-subcategories (p

Description: The myelodysplastic syndromes (MDS) are a heterogeneous group of hematopoietic malignancies. We have used Affymetrix microarray technology to determine the gene expression profiles in CD34+ cells of 84 MDS patients (25 RA, 28 RARS and 31 RAEB) and 16 healthy controls. Twenty-five of 84 patients had a del(5q). CD34+ cells were isolated from bone marrow samples using MACS magnetic columns. Extracted total RNA was amplified using the Two-Cycle Target Labelling kit (Affymetrix) and samples were hybridized to Affymetrix U133 Plus2.0 chips (representing 39,000 human genes). Cell intensity calculation and scaling was performed using GeneChip Operating Software and data analysis using GeneSpring 7.3. The expression profiles of MDS CD34+ cells showed many similarities to reported interferon-γ induced gene expression in normal CD34+ cells. Indeed the two most up-regulated genes, IFIT1 and IFITM1, are interferon-stimulated genes. IFIT1 and IFITM1 were up-regulated by 〉2-fold in 58/84 and 53/84 MDS patients respectively. Genes down-regulated by 〉2-fold in the majority of MDS patients include the putative tumor suppressor gene Gravin/AKAP12, ARPP-21, CD24 and MME. The association of distinct gene expression profiles with specific FAB and cytogenetic groups was determined using data from 55 MDS patients as a training set. Hierarchical clustering performed using 457 significantly different genes between different FAB subtypes showed that MDS patients with RARS constitute a homogeneous group, while MDS patients with RA and RAEB show more overlap. CD34+ cells from patients with RARS showed up-regulation of mitochondrial-related genes, and in particular of those of heme synthesis (e.g. ALAS2). Statistical analysis showed that 889 probe-sets could discriminate MDS patients with a del(5q) from those without a del(5q). MDS patients with the del(5q) showed distinctive down-regulation of genes mapping to chromosome 5q, and up-regulation of the histone HIST1 gene cluster at chromosome 6p21 and of genes related to the actin cytoskeleton. In order to identify genes differentially expressed between early and advanced MDS, a comparison was made between the 18 patients with RA and the nine MDS patients with RAEBII. 762 significantly different probe sets were identified that could group together MDS patients with RAEBII. The most significant genes identified include CASP3 and FLT3, and represent potential prognostic markers or markers of disease progression. The remaining 29 MDS patients were used as a test set for class prediction using support vector machines. The FAB subtype was correctly predicted for 83% of the test samples. The presence or absence of a del(5q) was predicted correctly for 93% of the test samples. Finally, 94% of the test samples were predicted correctly as RA or RAEBII. This study provides important and new insights into the pathophysiology of MDS.

Description: Myelodysplasia (MDS) is a heterogeneous group of clonal disorders of hematopoietic stem cells characterised by ineffective hematopoiesis and a variable risk of transformation to acute myelogenous leukaemia. We have used Comparative Genomic Hybridisation (CGH) microarray analysis, a technology that represents a significant improvement in resolution over conventional cytogenetic analysis, to screen genomic DNA from MDS patients for the identification of genome-wide Copy-Number Changes (CNCs). We have studied genomic DNA obtained from the neutrophil population of 48 MDS patients and 40 normal controls. Of the 48 MDS patients 10 had the 5q- syndrome, 32 were assigned normal karyotype and 6 had complex karyotypes. Comparative Genomic Hybridisation (CGH) microarray analysis was performed using microarrays containing 3500 BAC clones at 1Mb intervals over the whole human genome. Furthermore we used a whole genome tiling-path (27 000 overlapping BAC clones) array to profile 9 5q-syndrome patients and for 3 of those patients the T-cell DNA were also profiled to act as constitutional control. The patient DNA and a pool of normal reference DNA was labelled with different fluorochromes and cohybridised to the microarray. The normalised ratio of signal intensities was calculated and log2 ratios between −0.4 and 0.4 were considered normal. Ratios below or above the normal range were interpreted as loss or gain of genetic material, respectively. The deletions on chromosome 5q were precisely mapped by array-CGH in the patients with the 5q- syndrome but no additional CNCs were detected. One of the 5q deletions, however, displayed a discontiguous pattern with the tiling resolution array. Copy-number changes (CNCs) that escaped conventional cytogenetic detection were identified in the MDS patients originally reported with normal bone marrow karyotypes. 8 out of those 32 patients displayed CNCs that were not detected in the 40 normal controls and as such were considered as disease-related changes (non-polymorphic). Many of those CNCs were single-clone abberrations that were validated by dye-swap experiments and some were confirmed by quantitative PCR. Microarray CGH data confirmed all abnormalities reported by conventional cytogenetic analysis in the MDS patients with complex karyotypes and previously undetected abnormalities were uncovered. Several genes involved in either the initiation or progression of hematological malignancies are known to map within the cryptic abnormalities identified in the patients studied. For example, one patient with an apparently normal karyotype showed a small deletion at 17q11 which encompasses the NF1 gene. Further work will determine whether particular abnormalities detected by microarray CGH are recurrent and the nature of the genes involved. However, the promise of microarray CGH in the diagnostic work up of MDS particularly in those patients with normal karyotypes is clear.

Description: Abstract 171 The 5q- syndrome is the most distinct of all myelodysplastic syndromes with a clear genotype/phenotype relationship. Haploinsufficiency of the ribosomal protein gene RPS14 underlies the erythroid defect found in the 5q- syndrome. The 5q- syndrome is a disorder of aberrant ribosome biogenesis and we have recently demonstrated that erythrocytes obtained from patients with the 5q- syndrome show impaired translation. This defect in translation may represent a potential therapeutic target in the 5q- syndrome and other ribosomopathies, and there are some indications that the use of the translation enhancer L-leucine may have some efficacy. L-leucine is a branched chain amino acid that has been shown to improve haemoglobin levels and transfusion independence in patients with the ribosomopathy Diamond Blackfan Anemia (DBA). Moreover, the treatment of zebrafish models of DBA and the 5q- syndrome with L-leucine has recently been shown by others to result in partial reversal of the anemia. To model the RPS14 haploinsufficiency observed in the 5q- syndrome, we used lentivirally delivered shRNA sequences to reduce the expression of RPS14 in human bone marrow CD34+ cells from healthy controls. We have recently shown that treatment of cultured human erythroid cells derived from CD34+ cells of healthy controls with RPS14 knockdown and cultured erythroid cells derived from the CD34+ cells of patients with the 5q- syndrome with L-leucine results in an increase in cell proliferation, erythroid differentiation and mRNA translation. There is evidence to suggest that L-leucine activates the mTOR (mammalian target of rapamycin) signaling pathway that controls many cellular processes including cell growth and mRNA translation. In order to investigate the mechanism of action of L-leucine, we have studied the phosphorylation levels of S6K1 and 4EBP1, the key downstream targets of mTORC1 (mTOR Complex 1), by sandwich ELISA, Human Phospho-kinase Antibody Array and flow cytometry in RPS14-deficient human erythroblasts. We have shown a significant increase in the levels of phospho-S6K1 and phospho-4EBP1 following L-leucine treatment of cultured erythroid cells derived from CD34+ cells of healthy controls with RPS14 knockdown. The effects of L-leucine on phospho-S6K1 and phospho-4EBP1 were abrogated by rapamycin (an mTOR inhibitor), suggesting that L-leucine has a specific action on the mTOR signaling pathway. Consistent to the results observed in the RPS14 knockdown model, treatment with L-leucine also increased the level of phospho-S6K1 in cultured erythroid cells derived from the bone marrow cells of 5q- MDS patients. These data suggest that L-leucine activates the mTOR pathway in RPS14-deficient human erythroblasts. Our studies support the evaluation of L-leucine as a potential therapeutic agent in the treatment of the 5q- syndrome, and provide evidence on its mode of action through activation of the mTOR signaling pathway. Disclosures: No relevant conflicts of interest to declare.

Description: Approximately 30-40% of patients with myelodysplastic syndromes (MDS) develop acute myeloid leukemia (AML). Several recurrent mutations have been identified in MDS using next-generation sequencing (NGS) technology and recent studies have greatly illuminated the molecular landscape of this disorder. However, the molecular events driving MDS progression to AML remain poorly understood. In order to investigate the genetic basis of leukemic transformation in MDS during disease progression, we evaluated the frequency and chronology of the acquisition of mutations using a targeted NGS myeloid gene panel on serial (paired) samples from 41 MDS patients before (pre-progression) and after disease progression (post-progression) to a more advanced subtype (n=7) or to AML (n=34). The mutational profile was characterized using a TruSeq Custom Amplicon panel (Illumina) targeting the hotspots of 31 recurrently (〉1%) mutated genes in myeloid malignancies. Samples were run on an Illumina MiSeq and variants were annotated and filtered using Illumina VariantStudio v2.1.36, and interpreted according to the ACMG recommendations. The proportion of sequencing reads reporting a given mutation (variant allele frequency, VAF) was used to estimate the fraction of tumor cells carrying that mutation, and to determine whether mutations are clonal (in all tumor cells) or subclonal (in a fraction of tumor cells). A total of 100 and 123 mutations across 23 genes were identified in pre- and post-progression samples, respectively. The number of mutations was generally higher in the post-progression samples: the number of cases with one or two mutations was 24 in pre-progression samples and 16 in post-progression samples, while the number of cases with three or four mutations was 12 in pre-progression samples and 18 in post-progression samples. Several cases showed ≥5 mutations. The most frequently mutated genes (in 〉15% of samples) were ASXL1, TET2, SRSF2, U2AF1, RUNX1 and TP53; ASXL1 was the top ranking mutated gene with a frequency of 44% in pre-progression samples and 46% in post-progression samples. SF3B1, the most frequently mutated gene in MDS, was mutated in only two cases in our cohort. This finding is consistent with the strong association of SF3B1 mutation with the low-risk MDS subtype RARS, and its status as a good prognostic marker. Our patient cohort is highly selected, comprised only of patients whose disease has progressed and our data thus indicate that ASXL1 mutations are strongly associated with MDS cases that show disease progression and conversely that SF3B1 mutations are rarely associated with MDS disease progression. Mutations of genes involved in splicing (U2AF1, SRSF2), chromatin modification (EZH2, ASXL1) and DNA methylation (TET2, IDH1/2) were present in the pre-progression samples for almost all cases with mutations of these genes; these mutations often occur in founding clones (VAF 〉40%) and may play a role in disease initiation. Mutations of genes involved in transcriptional regulation (RUNX1, ETV6, PHF6) and signal transduction (NRAS, KRAS) were found in many cases in the post-progression sample only, suggesting that these are often late events that may co-operate with early events to drive disease progression. Interestingly, co-occurrence of NRAS and ASXL1 mutations was a frequent event in post-progression samples (n=5) in our cohort. It has been reported that NRas mutation and Asxl1 loss co-operate to drive myeloid proliferation and myeloid leukemia in mice, and our data support this observation. The average VAF of some mutations changed markedly during disease progression, with NRAS showing the largest VAF fold increase among genes mutated in 〉5 cases. The majority of subclones containing mutations in RUNX1 or ASXL1 expanded with disease progression. EZH2 mutations were mainly in the founding clone, while TP53 mutations were mainly in a subclone. For six cases we sequenced an additional serial sample, thus giving more precise information on the mutational profile evolution during disease progression. This is the first study to investigate the mutation status of a large group of MDS patients showing disease progression by the study of serial samples using a NGS myeloid gene panel. This study informs the timing of mutation acquisition during disease initiation and progression in MDS and closely related conditions, illuminating the genetic basis of leukemic transformation in these disorders. Disclosures No relevant conflicts of interest to declare.

Description: Lack of progress in curing AML is likely, in part, to be due to the genetic and functional heterogeneity of AML. ~13 Tier 1 mutations occur per patient sample arrayed in 2-5 clones (CGARN, N Engl J Med, 2013). Not all AML cell populations may be equally chemosensitive; for example, leukemia-propagating leukemic stem cells (LSC) are more chemoresistant. (Ishikawa et al., Nat Biotechnol, 2007). Additionally, the impact of genetic heterogeneity on LSC function is unclear. In ~ 70% of primary human AML with 〉2% CD34+ cells, LSCs exist within both CD34+CD38- and CD34+CD38+ compartments (Taussig et al., Blood, 2008), and have progenitor-like transcriptional programmes (Goardon et al., Cancer Cell, 2011). ~30% of AML with

Description: Rabbit antithymocyte globulin (rATG; thymoglobulin, Genzyme) in combination with cyclosporine, as first-line immunosuppressive therapy, was evaluated prospectively in a multicenter, European, phase 2 pilot study, in 35 patients with aplastic anemia. Results were compared with 105 age- and disease severity–matched patients from the European Blood and Marrow Transplant registry, treated with horse ATG (hATG; lymphoglobulin) and cyclosporine. The primary end point was response at 6 months. At 3 months, no patients had achieved a complete response to rATG. Partial response occurred in 11 (34%). At 6 months, complete response rate was 3% and partial response rate 37%. There were 10 deaths after rATG (28.5%) and 1 after subsequent HSCT. Infections were the main cause of death in 9 of 10 patients. The best response rate was 60% for rATG and 67% for hATG. For rATG, overall survival at 2 years was 68%, compared with 86% for hATG (P = .009). Transplant-free survival was 52% for rATG and 76% for hATG (P = .002). On multivariate analysis, rATG (hazard ratio = 3.9, P = .003) and age more than 37 years (hazard ratio = 4.7, P = .0008) were independent adverse risk factors for survival. This study was registered at www.clinicaltrials.gov as NCT00471848.

Description: Key Points RNA-seq analysis of CD34+ cells identifies novel aberrantly spliced genes and dysregulated pathways in splicing factor mutant MDS. Aberrantly spliced isoforms predict MDS survival and implicate dysregulation of focal adhesion and exosomes as drivers of poor survival.