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MicroRNAs are key regulators of many biological processes, including cell differentiation. These small RNAs exert their function assembled in the RNA-induced silencing complexes (RISCs), where members of Argonaute (Ago) family of proteins provide a unique platform for target recognition and gene silencing. Here, by using myeloid cell lines and primary blasts, we show that Ago2 has a key role in human monocytic cell fate determination and in LPS-induced inflammatory response of 1,25-dihydroxyvitamin D3 (D3)-treated myeloid cells. The silencing of Ago2 impairs the D3-dependent miR-17-5p/20a/106a, miR-125b and miR-155 downregulation, the accumulation of their translational targets AML1, VDR and C/EBPβ and monocytic cell differentiation. Moreover, we show that Ago2 is recruited on miR-155 host gene promoter and on the upstream region of an overlapping antisense lncRNA, determining their epigenetic silencing, and miR-155 downregulation. These findings highlight Ago2 as a new factor in myeloid cell fate determination in acute myeloid leukemia cells.

Therapy-related acute promyelocytic leukemia (t-APL) has been reported as a late complication of exposure to radiotherapy and/or chemotherapeutic agents targeting DNA topoisomerase II. We have analyzed in t-APL novel gene mutations recently associated with myeloid disorders. Unlike previous reports in acute myeloid leukemia (AML), our results showed neither IDHs nor TET2 mutations in t-APL. However we found an R882H mutation in the DNMT3A gene in a patient with t-APL suggesting a possible role of this alteration in the pathogenesis of t-APL.

Background: Single nucleotide polymorphisms (SNPs) in double-strand break repair genes may alter DNA repair capacity and, in turn, confer predisposition to leukemia. We analyzed polymorphic variants of DNA repair and detoxification genes in patients with multiple sclerosis (MS) who developed secondary acute promyelocytic leukemia (sAPL), in most cases after treatment with mitoxantrone (MTZ). Methods: Using MassARRAY high-throughput DNA analysis with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, we genotyped patients with sAPL (n = 20) developed after treatment of MS (18 out 20 treated with MTZ) for the presence of 210 SNPs of 22 genes mostly involved in DNA repair and drug detoxification. Patients with MS who did not develop sAPL including 41 treated with MTZ (n = 253 and 41, respectively) and healthy blood donors (n = 310) were also genotyped as controls. Results: We observed risk allele frequency between MS and sAPL for BRCA2 (rs1801406): 6% and 26%, p = 0.007; XRCC5 (rs207906): 2.5% and 15%, p = 0.016; CYP3A4 (rs2740574): 4.5% and 25%, p = 0.0035. The association of homozygous variants of BRCA2 and XRCC5 yielded higher risk of sAPL (MS vs sAPL: 0.4% and 18%, p = 0.001). We also observed a significant association between a SNP in the promoter region (rs2740574) of CYP3A4, an enzyme involved in the metabolism of chemotherapeutic agents and development of sAPL. Conclusions: Increased susceptibility to develop sAPL in patients with MS receiving MTZ may be linked to genetic variants in DNA repair and drug-metabolizing enzymes that result in impaired detoxification of chemotherapy or inefficient repair of drug-induced genetic damage.

The deletion of 5q (5q-) is a frequent clonal chromosomal abnormality detected in patients with myelodysplastic syndromes (MDS). MDS with 5q- as a sole chromosome alteration is characterized by a more favorable prognosis when compared to other forms of MDS.[1][1] By contrast, when detected in

Objective: As a better understanding of the molecular basis of carcinogenesis has emerged, oncogene-specific cell-signaling pathways have been successfully targeted to treat human malignances. Despite impressive advances in oncogene-directed therapeutics, genetic instability in cancer cells often manifest acquired resistance. This is particularly noted in the use of tyrosine kinase inhibitors therapies and not more evident than for chronic myeloid leukemia. Therefore, it is of great importance to understand the molecular mechanisms affecting cancer cell sensitivity and resistance to tyrosine kinase inhibitors. Materials and Methods: In this study, we used continuous exposure to stepwise increasing concentrations of imatinib (0.6-1 μM) to select imatinib-resistant K562 cells. Results: Expression of BCR-ABL increased both at RNA and protein levels in imatinib-resistant cell lines. Furthermore, expression levels of sphingosine kinase 1 (SphK1) were increased significantly in resistant cells, channeling sphingoid bases to the SphK1 pathway and activating sphingosine-1-phosphate-dependent tyrosine phosphorylation pathways that include the adaptor protein Crk. The partial inhibition of SphK1 activity by N,N-dimethylsphingosine or expression by small interfering RNA increased sensitivity to imatinib-induced apoptosis in resistant cells and returned BCR-ABL to baseline levels. To determine the resistance mechanism-induced SphK1 upregulation, we used pharmacological inhibitors of the phosphoinositide 3-kinase/AKT/mammalian target of rapamycin signaling pathway and observed robust downmodulation of SphK1 expression and activity when AKT2, but not AKT1 or AKT3, was suppressed. Conclusions: These results demonstrate that SphK1 is upregulated in imatinib-resistant K562 cells by a pathway contingent on a phosphoinositide 3-kinase/AKT2/mammalian target of rapamycin signaling pathway. We propose that SphK1 plays an important role in development of acquired resistance to imatinib in chronic myeloid leukemia cell lines. © 2011 ISEH - Society for Hematology and Stem Cells.

The translocation t(16;21) involving RUNX1 (AML1) and resulting in the RUNX1-CBFA2T3 fusion is a rare but recurrent abnormality mostly found in therapy-related acute myeloid leukemia (t-AML) associated with agents targeting topoisomerase II (topo II). We characterized, at the genomic level, the t(16;21) translocation in a patient who developed t-AML after treatment of multiple sclerosis with mitoxantrone (MTZ). Long template nested PCR of genomic DNA followed by direct sequencing enabled the localization of RUNX1 and CBFA2T3 (ETO2) breakpoints in introns 5 and 3, respectively. Sequencing of the cDNA with specific primers showed the presence of the expected RUNX1-CBFA2T3 fusion transcript in leukemic cells. The RUNX1 intron 5 breakpoint was located at nucleotide position 24,785. This region contained an ATGCCCCAG nucleotide sequence showing approximately 90% homology to a "hotspot" DNA region ATGCCCTAG present in intron 6 of PML previously identified in therapy-related acute promyelocytic leukemia cases arising following treatment with MTZ. This study suggests a wider distribution in the human genome, and particularly at genes involved in chromosome translocations observed in t-AML, of DNA regions (hotspot) targeted by specific topo II drugs.

The common beta chain subunit (beta(c)), also known as CDw131, shared by the interleukin-3 (IL-3), granulocytic macrophage colony-stimulating factor (GM-CSF) and IL-5 receptors, is required for high-affinity ligand binding and signal transduction. The present study explored the expression of CDw131 in 105 de novo cases of acute myeloid leukaemia (AML). The levels of CDw131 expression were used to identify two AML subgroups characterized by low (75/105) and high (30/105) expression of this receptor chain. It was observed that (i) the level of CDw131 expression strictly correlated with the level of CD116 (GM-CSFalpha receptor chain) and CD123 (IL-3Ralpha chain); (ii) AMLs with high CDw131 expression were characterized by low CD34 expression and usually high CD11b, CD14 expression; (iii) AMLs with high CDw131 expression frequently co-expressed receptors for angiogenic growth factors (vascular endothelial growth factor R2, Tie-2); (iv) AMLs with high CDw131 expression were more cycling than those with low CDw131 expression; (v) AMLs with high CDw131 frequently displayed Feline Murine Sarcoma (FMS-related) tyrosine kinase 3 (FLT3) internal tandem duplication and constitutively activated Signal Transducer and Activator of Transcription-5 (STAT5). In conclusion, the analysis of the level of CDw131 expression enabled the identification of a subset of AMLs characterized by a high cycling status, the expression of myelo-monocytic markers, mutated FLT3 and the co-expression of receptors for angiogenic growth factors. These findings are of value for the development of new therapeutic strategies for the treatment of these AMLs.

Objectives: Mutations in the C-terminal region of the nucleophosmin (NPM1) gene occur in approximately 60% of acute myeloid leukemia (AML) cases with normal karyotype and represent the most common genetic lesion presently known in this disease. Because of their frequency and favorable impact on prognostic outcome, screening for this aberration is currently recommended in routine diagnostic characterization of AML. Several techniques enabling to detect NPM1 mutation have been reported, but all require sophisticated equipment, which represent an obstacle particularly in countries with limited resources. Methods: We designed an RT-PCR strategy to amplify NPM1 exon 12 followed by electrophoresis and fragment visualization on polyacrylamide gels to discriminate a 4–5 bp size difference resulting from mutations in this gene. A hemi-nested method was designed to increase sensitivity for the study of minimal residual disease (MRD). Results: The assay enabled specific detection of NPM1 mutations in 12/36 patients. A 10−2 sensitivity level was obtained using one amplification round, while the hemi-nested PCR approach yielded a 10−5 sensitivity level, therefore proving useful to assess MRD in patients carrying the mutation. The results were independently validated in 24 AML cases by sequencing analysis. Conclusions: This simple and low-cost assay may integrate diagnostic work-up of AML and could be used for assessment of response to therapy in patients with NPM1 mutations.

Nucleophosmin-1 (NPM1) mutations represent the most frequent gene alteration in acute myeloid leukemia (AML). The most common NPM1 mutation type, accounting for 75 to 80% of cases, is referred to as mutation A (NPM1-mutA). These NPM1 alterations have been shown to possess prognostic significance because they appear to identify patients who will benefit from chemotherapy. Given the high prevalence and stability of these mutations over the course of disease, NPM1 mutations may serve as ideal targets for minimal residual disease (MRD) assessment in AML. Current detection methods are costly, require sophisticated equipment, and are often not sufficiently sensitive. We report here an allele-specific (ASO)-RT-PCR assay that enables rapid and sensitive detection of NPM1-mutA. A semi-nested ASO-PCR method was also designed to increase the sensitivity of our assay for the monitoring of MRD. We analyzed bone marrow cells collected from 52 patients with AML at presentation. NPM1-mutA was detected in leukemic cells from 21 patients. Assay specificity was confirmed by capillary electrophoresis and DNA sequencing. ASO-RT-PCR and semi-nested ASO-PCR assays could detect NPM1-mutA with sensitivities of 10(-2) and 10(-5), respectively. Results obtained here verify that our ASO-RT-PCR assay is a specific and sensitive method for the routine screening of NPM1-mutA, as well as for MRD monitoring of AML patients with this alteration. This method is convenient and easily applicable in countries with limited resources and no access to real-time quantitative PCR-based technologies.

Therapy-related acute promyelocytic leukemia (t-APL) with t(15;17) translocation is a well-recognized complication of cancer treatment with agents targeting topoisomerase II. However, cases are emerging after mitoxantrone therapy for multiple sclerosis (MS). Analysis of 12 cases of mitoxantrone-related t-APL in MS patients revealed an altered distribution of chromosome 15 breakpoints versus de novo APL, biased toward disruption within PML intron 6 (11 of 12, 92% vs 622 of 1022, 61%: P = .035). Despite this intron spanning approximately 1 kb, breakpoints in 5 mitoxantrone-treated patients fell within an 8-bp region (1482-9) corresponding to the “hotspot” previously reported in t-APL, complicating mitoxantrone-containing breast cancer therapy. Another shared breakpoint was identified within the approximately 17-kb RARA intron 2 involving 2 t-APL cases arising after mitoxantrone treatment for MS and breast cancer, respectively. Analysis of PML and RARA genomic breakpoints in functional assays in 4 cases, including the shared RARA intron 2 breakpoint at 14 446-49, confirmed each to be preferential sites of topoisomerase IIα-mediated DNA cleavage in the presence of mitoxantrone. This study further supports the presence of preferential sites of DNA damage induced by mitoxantrone in PML and RARA genes that may underlie the propensity to develop this subtype of leukemia after exposure to this agent.

We present an investigation on theoretically possible protein structures which have not been selected by evolution and are, therefore, not present on our Earth ('Never Born Proteins' (NBP)). In particular, we attempt to assess whether and to what extent such polypeptides might be folded, thus acquiring a globular protein status. A library (ca. 10(9) clones) of totally random polypeptides, with a length of 50 amino acids, has been produced by phage display. The only structural bias in these sequences is a tripeptide substrate for thrombin: PRG, chosen according to the criteria described in the preceding Part I of this series. The presence of this substrate in an otherwise totally random sequence forms the basis for a qualitative experimental criterion which distinguishes unfolded from folded proteins, as folded proteins are more protected from protease digestion than unfolded ones. The investigation of 79 sequences, randomly selected from the initially large library, shows that over 20% of this population is thrombin-resistant, likely due to folding. Analysis of the amino acid sequences of these clones shows no significant homology to extant proteins, which indicates that they are indeed totally de novo. A few of these sequences have been expressed, and here we describe the structural properties of two thrombin-resistant randomly selected ones. These two de novo proteins have been characterized by spectroscopic methods and, in particular, by circular dichroism. The data show a stable three-dimensional folding, which is temperature-resistant and can be reversibly denatured by urea. The consequences of this finding within a library of 'Never Born Proteins' are discussed in terms of molecular evolution.

Detection of genetic markers improves diagnostic refinement of chronic myeloproliferative disorders (CMDs) and is helpful in discriminating reactive conditions mimicking CMDs such as reactive erythrocytosis and thrombocytosis. We set-up a multiplex real-time polymerase chain reaction assay followed by capillary electrophoresis, designed to simultaneously screen the two main genetic lesions associated with CMDs, i.e. the BCR-ABL fusion characteristic of chronic myeloid leukemia and the JAK2 V617F mutation that characterises polycythaemia vera and a proportion of cases of essential thrombocythemia and idiopathic myelofibrosis. The test was used in the diagnostic work-up of 50 patients with elevation of >or=2 myeloid cell types in their blood count at presentation and in 42 patients with isolated, non-reactive thrombocytosis. This approach refined diagnosis in 44 of 50 cases in the first series and in 22 of 42 cases with isolated thrombocytosis. We conclude that this non-isotopic and rapid assay amenable to automation may be adopted in routine genetic diagnosis of CMDs as well as for initial screening of thrombocytosis of unknown nature.

Background: The invention of Next Generation Sequencing (NGS) has spurred research into human diseases, especially in the field of malignancy. In acute myeloid leukemia (AML), a plethora of novel alterations have been identified, including mutations in epigenetic regulator genes (e.g. IDH1, IDH2, DNMT3A), genes coding for proteins of the cohesin complex (e.g. SMC1A, SMC3, STAG2) and spliceosome genes (e.g. SF3B1, U2AF1). Although the diagnostic and prognostic implications of many of these alterations are not yet clear, there is increasing evidence that several of them might have major implications for understanding the disease biology or for patient-treatment. Thus, there is increasing need to reliably detect these mutations in large patient groups in clinically relevant time-frames and at an affordable cost. Due to the large number of genes to be screened, amplicon-based NGS represents an attractive detection method. Although, several assays have been reported, integrating different numbers of genes, it is currently unclear whether they really allow reliable detection of alterations in a reproducible way. Here we report our results from a round robin comparison of the detection of known AML-variants using a highly multiplexed, single tube assay coamplifying a total of 568 amplicons covering 54 entire genes or hot spot gene regions involved in leukemia (TruSight Myeloid sequencing panel; Illumina), with respect to the sensitivity, reproducibility and quantitative accuracy. Material and Methods: Ten European laboratories routinely involved in molecular AML diagnostics participated in this study. All groups performed two sequencing runs, each containing 8 samples. These samples were centrally aliquoted and distributed, the analyses were done in a blinded fashion. Six out of the 8 samples on each run were derived from a set of 9 samples composed of DNA isolated from the blasts of 18 different newly diagnosed AML patients mixed at a 1:1 ratio, with 50 ng of DNA being used for the library preparation. Three of these 9 samples were analyzed in replicate in separate runs by each group. The remaining two samples were a commercial test DNA containing 10 known single nucleotide variants (SNV) or insertion/deletion (InDel) alterations with defined variant allele frequencies (VAF) between 4 and 25% and DNA derived from the OCI-AML3 AML cell line (mutant for DNMT3A and NPM1). Sequencing was performed on MiSeq NGS systems (Illumina) using 2x151 bp-runs. Sequencing data were analyzed by all laboratories using the VariantStudio software (Illumina), with the threshold for mutation calling set at 3%. Results: Analysis of data quality indicated that 85% of the samples met the predefined acceptance criteria (>=95% amplicons with at least 500 reads/amplicon), the median coverage was 7379 reads/amplicon (range 0-47403 reads). Of the 9 mutations present in the positive control, 7 were called at least once in the two replicates by all labs, two mutations with a VAF of 5% were missed by 1 and 4 participants, respectively. Overall, the VAF calls for this sample showed a high level of accuracy across the participants (median coefficient of variation 5%, range 0-22.5%) as well as excellent intra- and inter-laboratory reproducibility (Fig.1). In total, the 9 primary leukemic samples contained 43 known variants in 19 genes, including all commonly mutated genes in AML, i.e. CEBPA, DNMT3A,RUNX1, NPM1, FLT3, WT1. For these samples, the sensitivity was 95.7%. Based on the entire data set (positive control and leukemic samples), the calculated sensitivity of the assay for known variants with an expected VAF>=5% was 93.3%. The rate of non-calls was slightly higher for InDels (14/179; 7.8%) than for SNVs (25/407; 6.1%; P=.47). Two 57-bp long insertions in FLT3 exons 14/15 were not called, which is expected due to the specifications of the assay (max. detectable InDel length Conclusions: This inter-laboratory comparison shows a high sensitivity and impressive quantitative accuracy of NGS-based characterization for known variants down to a minor VAF of 5%. Although additional optimization in individual parameters might be necessary, these initial results clearly indicate that rapid comprehensive molecular characterization of patient samples appears feasible, even in the clinical setting. Figure 1 Figure 1. Disclosures Thiede: AgenDix GmbH: Equity Ownership, Research Funding; Illumina: Research Support, Research Support Other. Bullinger:Illumina: Research Support Other. Hernández-Rivas:Illumina: Research Support Other. Heuser:Illumina: Research Support Other. Preudhomme:Illumina: Research Support Other. Lo Coco:Illumina: Research Support Other. Martinelli:Illumina: Research Support Other. Schuh:Illumina: Research Support Other. Enjuanes:Illumina: Research Support Other. Lea:Illumina: Research Support Other. Schlesinger:Illumina: Employment.

Correction to: Blood Cancer Journal (2013) 3, e147; doi: 10.1038/bcj.2013.46; published online 13 September 2013

Nucleophosmin gene mutations (NPM1-Mt) are the hallmark of a large adult acute myeloid leukemia (AML) subgroup with normal karyotype and interact with p53 and its regulatory molecules (Arf, Hdm2/Mdm2), thus lowering cell proliferation and increasing apoptosis (Falini, 2007). Moreover, AML pts show co-existing NPM1-Mt and internal tandem duplications of FLT3 (FLT3-ITD) which increase potential for cell proliferation. Furthermore, genes and proteins involved in apoptosis, such as bcl-2 and bax, have been demonstrated to be relevant in response to treatment and outcome (Del Poeta, 2003). Therefore, we analysed NPM1-Mt, FLT3-ITD and apoptosis proteins (bcl-2 and bax) in 222 pts, affected by de novo non-M3 AML, median age 60 years, treated with intensive chemotherapy regimens according to GIMEMA-EORTC protocols. The aims of our study were: to correlate NPM1-Mt or FLT3-ITD with bax/bcl-2 ratio levels, as a measure of spontaneous apoptosis; to assess the independent prognostic significance of NPM1-Mt and FLT3-ITD. Bcl-2 and bax proteins were determined by multicolor flow cytometry and bax/bcl-2 ratio was obtained by dividing mean fluorescence intensity (MFI) of bax/MFI bcl-2. The threshold of positivity was set at the median value >0.35 (range 0.01–9.1). NPM1 mutations and FLT3-ITD were detected by multiplex PCR and capillary gel electrophoresis. One hundred-twenty-one/222 (54.5%) pts were bax/bcl-2 ratio positive, 54/222 (24.3%) were NPM1-Mt and 52/222 (23.4%) presented FLT3-ITD; 17/222 (7.6%) pts carried both FLT3-ITD and NPM1-Mt. There was a strong correlation between higher WBC counts (>100x109/L) and FLT3-ITD (P0.35) and NPM1-Mt without FLT3-ITD were significantly associated (30/37; P=0.0001), demonstrating that NPM1-Mt alone express high amount of spontaneous apoptosis. Moreover, NPM1-Mt cases were significantly related to FAB M4 or M5 AML (P=0.03). A normal karyotype was found in 37/45 (82%) NPM1-Mt pts (P=0.00001) and almost all NPM1-Mt cases were CD34 negative (47/54; P