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The t(9;22)(q34;q11) is evident in more than 90% of patients with chronic myelocytic leukemia (CML) and gives rise to the Philadelphia chromosome (Ph). Approximately 5%-10% of CML patients show variant translocations involving other chromosomes in addition to chromosomes 9 and 22. In some variant translocations, additional material is transferred on der(22), resulting in a masked Ph chromosome. In this paper, we report two apparently Ph-negative (Ph-) CML cases showing a t(7;9;22)(q22;q34;q11) and a t(8;9;22)(q12;q34;q11), respectively. A detailed molecular cytogenetic characterization was performed by fluorescence in situ hybridization (FISH), which disclosed the presence of the 5'BCR/3'ABL fusion gene on the der(7) and der(8) chromosomes, respectively. Derivative (22) appeared as a masked Ph chromosome in both cases. FISH analysis with appropriate BAC/PAC clones allowed us to precisely characterize the complex chromosomal rearrangements that were not detected by conventional cytogenetic analysis.

The EVI1 proto-oncogene encodes a nuclear zinc finger protein that acts as a transcription repressor factor. In myeloid leukemia it is often activated by chromosomal rearrangements involving band 3q26, where the gene has been mapped. Here we report two leukemia cases [a chronic myeloid leukemia blast crisis (CML-BC) and an acute myeloid leukemia (AML) M4] showing a t(3;7)(q26;q21) translocation in a balanced and unbalanced form, respectively. Fluorescent in situ hybridization (FISH) analysis revealed that both patients showed a breakpoint on chromosome 3 inside the clone RP11-33A1 containing the EVI1 oncogene and, on chromosome 7, inside the clone RP11-322M5, partially containing the CDK6 oncogene which is a D cyclin-dependent kinase gene, observed to be overexpressed and disrupted in many hematological malignancies. Reverse transcriptase polymerase chain reaction (RT-PCR) analysis showed overexpression of EVI1 in both cases, but excluded the presence of any CDK6/ EVI1 fusion transcript. CDK6 expression was also detected. Together, these data indicate that EVI1 activation is likely due not to the generation of a novel fusion gene with CDK6 but to a position effect dysregulating its transcriptional pattern.

The t(9;22)(q34;q11), generating the Philadelphia chromosome (Ph), is found in more than 90% of patients with chronic myeloid leukemia (CML) and in 15-30% of adults with acute lymphoblastic leukemia (ALL). Different groups have recently described the presence of large genomic deletions adjacent to the translocation breakpoint on the derivative chromosome 9 in 9-16% of CML patients. In the present paper, we report a FISH study of 45 Ph+ adult ALL patients with the aim of investigating the presence of deletions on derivative chromosome 9. In four (9%) of 45 cases, all showing an M-bcr, we detected deletions on der(9). The frequency of deletions we observed is similar to that reported in CML patients. The association of an M-bcr breakpoint and deletions appears significant (P=0.03). Some authors have suggested a very low incidence of der(9) deletions in ALL. This discrepancy can be explained by taking into account the low percentage of M-bcr ALL patients in the latter study (18%) compared to the present one (44%).

The "golden path", produced by the Human Genome Project effort, is composed of a collection of overlapping and fully sequenced BAC/PAC clones covering almost completely the human genome. These clones can be advantageously exploited as fluorescence in situ hybridization (FISH) probes for the characterization of rearrangements frequently found in tumors. Breakpoint characterization can be further refined by generating additional smaller FISH probes through LONG-PCR amplification of specific DNA segments, 5-10 kb in size, using appropriate BAC/PAC probes as template. We report here an example of this approach that has been used to characterize a complex Ph-negative chronic myeloid leukemia (CML Ph-) case in which the BCR/ABL fusion gene was found located on chromosome 9.

A patient with a typical form of chronic myeloid leukemia was found to carry a large deletion on the derivative chromosome 9q+ and an unusual BCR-ABL transcript characterized by the insertion, between BCR exon 14 and ABL exon 2, of 126 bp derived from a region located on chromosome 9, 1.4 Mb 5′ to ABL. This sequence was contained in the bacterial artificial chromosome RP11-65J3, which in fluorescence in situ hybridization experiments on normal metaphases was found to detect, in addition to the predicted clear signal at 9q34, a faint but distinct signal at 22q11.2, where the BCR gene is located, suggesting the presence of a large region of homology between the two chromosomal regions. Indeed, blast analysis of the RP11-65J3 sequence against the entire human genome revealed the presence of a stretch of homology, about 76 kb long, located approximately 150 kb 3′ to the BCR gene, and containing the 126-bp insertion sequence. Evolutionary studies using fluorescence in situ hybridization identified the region as a duplicon, which transposed from the region orthologous to human 9q34 to chromosome 22 after the divergence of orangutan from the human-chimpanzee-gorilla common ancestor about 14 million years ago. Recent sequence analyses have disclosed an unpredicted extensive segmental duplication of our genome, and the impact of duplicons in triggering genomic disorders is becoming more and more apparent. The discovery of a large duplicon relatively close to the ABL and BCR genes and the finding that the 126-bp insertion is very close to the duplicon at 9q34 open the question of the possible involvement of the duplicon in the formation of the Philadelphia chromosome translocation.

Introduction Lymphoid enhancer-binding factor 1 (LEF1) is a downstream effector of the Wnt/ β-catenin signaling pathway, which controls cell growth and differentiation. In normal hematopoiesis, LEF1 plays a pivotal role in the development of B- and T-lymphocytes as well as granulocyte progenitor cells. High LEF1 expression has been reported as a favorable prognostic marker in cytogenetically normal acute myeloid leukemia whereas it is associated with poor prognosis in adult B precursor acute lymphoblastic leukemia and in chronic lymphocytic leukemia. Moreover, marked downregulation of LEF1 is associated with disease progression in myelodysplastic syndromes. Given the functional role of LEF1 in hematopoiesis and its putative prognostic impact in several hematological malignancies, we evaluated the prognostic significance of LEF1 expression in adult acute promyelocytic leukemia (APL). Methods One hundred and three consecutive patients with newly diagnosed APL were observed and treated with ATRA-based regimens (AIDA04937 and AIDA2000 GIMEMA protocols), between January 1996 and December 2012. LEF1 expression was measured by real-time qPCR in 78 patients (median age 45 years, range 16 to 88 years) with sufficient available material from the primary cohort. Advanced relative quantification analysis was performed using LightCycler 480 Software 1.5.1, based on the ΔΔCt method. APL samples were dichotomized at the median value and divided into two expression groups: low LEF1 (39 patients) with LEF1 values below the median value (LEF1low) and high LEF1 (39 patients) with LEF1 values above the median value (LEF1high). Clinical and biological features of the two groups were compared. A p value Results Patients with LEF1high expression had lower white blood cell counts at baseline (1.8 vs 12.0 x109/L; p < 0 .0001), and were less likely to carry a FLT3-ITD than LEF1low patients (12.8% vs 35.9%, respectively, p=0.02). The association between LEF1low and the presence of FLT3-ITD was also confirmed when the 11 patients with FLT3-TKD were included among patients with FLT3 mutations (p=0.03), or the group of FLT3 wild type patients, as compared to those bearing FLT3-ITD (p=0.03). Early death (defined as death during induction treatment) occurred in nine cases (23%) of the LEF1low group versus no case in the LEF1high group (OR = 0.04; p= 0.002). LEF1low expression was associated with a high relapse risk score (53.9% vs 7.7%, OR=0.07; p < 0.0001). The LEF1high group showed a trend toward a statistically significant association with a lower median age (p = 0.08). No significant differences were observed regarding CD34, CD2, bcr3 positivity and LEF1 expression. Survival analysis of 61 APL patients < 60 years revealed that the LEF1high group had significantly longer overall survival (OS) (p = 0.03), whereas no differences were observed between the two groups in terms of relapse-free survival. Cox analysis for OS confirmed only LEF1 expression as an independent prognostic factor (HR=5.4; 95% CI, 1.0 – 27.5, p =0.04). Among the 17 patients over the age of 60, those with LEF1high expression showed a higher median survival than those in the LEF1low group (6.5 vs 0.04 y.rs, p = 0.05). In silico analysis of the differential expression of LEF1 in APL identified 9 differentially expressed, up-modulated genes associated with a high expression of LEF1 (ETS1, FAIM3, CCR7, IL7R, LCK, IL2RB, ITK, RASGRP1, TRBC1); the majority of these genes is involved in the regulation of apoptosis Conclusions Our study provides, for the first time, evidence that LEF1 expression is an independent prognostic factor in APL and that it could be used in patients risk stratification. The observation provided by in silico gene expression analysis that LEF1 expression in APL is associated with biologic changes, mostly in terms of apoptosis regulation, will need to be confirmed experimentally. Disclosures: No relevant conflicts of interest to declare.

Background The t(9;22)(q34;q11) generating the BCR/ABL1 fusion gene represents the cytogenetic hallmark of chronic myeloid leukemia (CML). About 5–10% of CML cases show variant translocations with the involvement of other chromosomes in addition to chromosomes 9 and 22. The molecular bases of biological differences between CML patients with classic and variant t(9;22) have never been clarified. Findings In this study, we performed gene expression microarray analysis to compare CML patients bearing variant rearrangements and those with classic t(9;22)(q34;q11). We identified 59 differentially expressed genes significantly associated with the two analyzed groups. The role of specific candidate genes such as TRIB1 (tribbles homolog 1), PTK2B (protein tyrosine kinase 2 beta), and C5AR1 (complement component 5a receptor 1) is discussed. Conclusions Our results reveal that in CML cases with variant t(9;22) there is an enhancement of the MAPK pathway deregulation and show that kinases are a common target of molecular alterations in hematological disorders.

Abstract 5058 Leukemic transformation has been reported in 15–30% of primary myelofibrosis (PMF). However, very little is known about the molecular bases responsible for acute myeloid leukemia (AML) transformation. JAK2 status analysis of paired chronic myeloproliferative neoplasms (MPN) and AML samples showed that during AML transformation the JAK2 mutation could be lost. Two probable models have been proposed to explain the MPN evolution to AML: a) JAK2-mutated AML usually arose from PMF or myelofibrotic transformation of ET/PV as a consequence of genetic instability conferred by the presence of JAK2 mutations; b) JAK2 wild-type AML generally developed in patients with chronic-phase ET or PV, frequently as a consequence of a clone selection driven by the therapy (Thoennissen NH et al. Blood 2010, 115:2882; Beer PA et al., Blood 2010, 115:2891; Spivak JL, Blood 2010, 115:2727). In this report we describe two PMF cases with the JAK2V617F mutation associated with molecular/cytogenetic abnormalities who developed JAK2-wild type AML characterized by a leukemic clone bearing a new cytogenetic aberration. At the PMF diagnosis, Case #1 showed a normal karyotype 46, XY[20] and resulted JAK2V617F positive. Molecular analyses performed at the time of AML transformation revealed the presence of a JAK2V617F negative clone bearing a novel t(12;18)(p13;q12) rearrangement. As the t(12;18) breakpoints were located centromerically to SETBP1 (18q12. 3), quantitative real-time PCR (qRT-PCR) experiments were made, showing SETBP1 overexpression. To investigate the occurrence of SETBP1 dysregulation and the presence of t(12;18) at PMF onset, qRT-PCR and Fluorescence in situ hybridization were performed, revealing gene overexpression and absence of the chromosomal translocation, respectively. At PMF onset, Case #2 harbored a novel t(3;5)(q27. 1;q31. 1) in addition to the JAK2V617F mutation. At the time of AML evolution, disappearance of the t(3;5)(q27. 1;q31. 1) and leukemic clone expansion of t(3;3)(q21. 3;q26. 2) was associated with disappearance of the JAK2V617F mutation. In contrast to literature data showing that JAK2 mutation loss is commonly associated with AML transformation after PV and ET, our findings suggest that evolution to JAK2-wild type AML could also occur in JAK2V617F PMF patients. The presence of different cytogenetic abnormalities associated with PMF and AML allowed us to follow the sequence of molecular events that lead to JAK2V617F disappearance, indicating that MPN and AML are clonally unrelated and probably generated by the transformation of different stem cell levels. Moreover, the well-documented clonal heterogeneity landscape in our cases demonstrated that the genomic instability responsible for AML transformation already existed at PMF onset and was not generated either by JAK2V617F mutation expression or by the therapy. Disclosures: No relevant conflicts of interest to declare.

Abstract 1674 The t(9;22)(q34;q11) generating the Philadelphia chromosome and the BCR/ABL1 fusion gene represents the cytogenetic hallmark of chronic myeloid leukemia (CML). About 5–10% of CML cases show variant translocations with the involvement of other chromosomes in addition to chromosomes 9 and 22. The greater frequency of occurrence of genomic microdeletions proximally to ABL1 or distally to BCR has been reported in CML cases with variant translocations (30–40%) than in cases with a classic t(9;22) (10–18%). The prognostic significance of variant t(9;22) was unclear and debated in the pre-imatinib era, whereas recent studies of large CML series showed that the presence of variant translocations has no impact on the cytogenetic and molecular response or on prognosis (Marzocchi et al. Blood 2011,117:6793-800). However, the molecular bases of differences between CML patients with classic and variant t(9;22) have never been elucidated. Here we report a gene expression profile analysis of 8 CML cases with variant t(9;22) and 12 patients with a classic t(9;22). RNA samples were extracted from bone marrow cells and hybridized on the Agilent SurePrint G3 Human GE 8×60K Microarray slide (Agilent Technologies). Ingenuity Pathways Analysis (IPA, www.ingenuity.com) software was used to provide an accurate biological and statistical analysis of microarray experimental data revealing functional relationships among the identified genes. Gene expression analysis identified a 59 gene set able to distinguish the two CML subsets. These genes are mostly involved in the development of the hematological system and in the occurrence of hematological diseases. Forty-five out of 59 (76%) genes were up-regulated, causing the probable activation of different molecular mechanisms such as cellular responses to stimuli, protein degradation, DNA repair, cell cycle progression. IPA analysis revealed that most of the dysregulated genes are included in a network where they are functionally linked to MAPK p38, AKT, and NFKB. Moreover, several genes play a role in cytoskeleton organization (WIPF1), in signal transduction and cell cycle progression (TRIB1, PDE4B, PTK2B, PLK3), in regulation of apoptosis (ZFAND5, STK17B), and in protein degradation (ZFAND5, SNRPG). On the contrary, among the downregulated genes, 5 (BCDIN3D, TMEM68, HILPDA, TMEM68, and C17orf61) establish direct interactions with ubiquitin C (UBC), a crucial gene involved in different intracellular mechanisms such as protein degradation, DNA repair, cell cycle regulation, and the regulation of other signaling pathways. In conclusion, gene expression profiling in cases with variant t(9;22) revealed biological differences in this CML subset. Our data show an overall deregulation of genes involved in hematological system development and in cell proliferation signaling pathway. Disclosures: No relevant conflicts of interest to declare.

Abstract 4628 Background. Tribbles homolog gene 2 (TRIB2) is a pseudokinase gene belonging to a three member gene family. Tribbles gene was first identified in Drosophila melanogaster where is involved in the regulation of morphogenesis and mitosis. Likewise, mammalian homologous genes of Tribbles (TRIB1, TRIB2, TRIB3) promotes the degradation of specific transcription factors and interacts with several cell signaling mediators and modulators. Recently it has been demonstrated that TRIB2 was able to induce AML in bone marrow transplanted mouse by inducing C/EBPα proteasome-dependent degradation. Moreover, gene expression profiles data from AML patients revealed that patients carrying C/EBPα mutations clustered with those patients with up-regulated TRIB2.Aims. To test the hypothesis that TRIB2 expression was related to a differentiation degree in AML, we evaluated several AML cases based on FAB cytotype. Patients and Methods. We performed quantitative Real Time-PCR (qRT-PCR) analysis on AML patients (15 AML-M0, 14 AML-M2, 5 AML-M3, 2 M4 and 3 M5b bone marrow aspirate samples) to measure the expression level of TRIB2 in different FAB AML subtype. Four healthy bone marrows were used as reference samples. qRT-PCR was conduct using SYBR green chemistry and specific primers for TRIB2 transcript and for two housekeeping genes (B2M and IPO8) previously tested for their stability and efficiency. All AML sample were tested by conventional cytogenetic analysis and by FISH with TRIB2 specific probe. We performed, also, methylation analysis of a CpG island located in the TRIB2 promoter region by methylation sensitive restriction enzyme (MSRE) and qPCR. Briefly, DNA samples were digested with MSRE and were quantified by qPCR using specific primer pairs surrounding restriction enzymes recognition sites. Results. qRT-PCR experiments revealed that TRIB2 expression was higher (from 3 to 20 fold) in AML-M0 respect to the AML-M2 (p= 0.02), AML-M3 (p=0.01), AML-M5 (p=0.006) FAB subtypes, and references (p=0.003), respectively. Moreover, the AML-M0 cases showed a TRIB2 overexpression compared to that observed in the two AML-M4 cases (about 4 fold changes) but this difference there was not statistically significant probably because of M4 cases paucity in our series. Therefore qRT-PCR displayed a progressive decreasing TRIB2 expression along FAB subtypes. Conventional cytogenetic and FISH analysis did not show any kind of rearrangement involving TRIB2 gene. MSRE experiments revealed an higher methylation degree of a CpG island located in the TRIB2 promoter region in AML-M0 cases respect to the others FAB subtypes; moreover, methylation was significantly correlated with TRIB2 expression (r = 0.9; p = 0.0002). Conclusions. Our data showed that the TRIB2 gene overexpression was associated to AML-M0. In our cases TRIB2 dysregulation was not due to gene amplification as in other cancers. Surprisingly we observed that AML-M0 samples showed an higher methylation degree in the TRIB2 promoter region. Usually methylation cause gene silencing but our results showed that TRIB2 promoter region methylation was associated to the overexpression of the gene. Maybe methylation inhibits binding of some unknown transcriptional repressor as already seen for hTERT gene in others tumors cells. In conclusion, our data revealed that TRIB2 dysregulation seems to be linked to AML-M0 phenotype. Further studies are needed to clarify the reasons for this association. Disclosures: No relevant conflicts of interest to declare.

Background The t(9;22)(q34;q11), generating the Philadelphia (Ph) chromosome, is found in more than 90% of patients with chronic myeloid leukemia (CML). As a result of the translocation, the 3' portion of the ABL1 oncogene is transposed from 9q34 to the 5' portion of the BCR gene on chromosome 22 to form the BCR/ABL1 fusion gene. At diagnosis, in 5-10% of CML patients the Ph chromosome is derived from variant translocations other than the standard t(9;22). Results We report a molecular cytogenetic study of 452 consecutive CML patients at diagnosis, that revealed 50 cases identifying three main subgroups: i) cases with variant chromosomal rearrangements other than the classic t(9;22)(q34;q11) (9.5%); ii) cases with cryptic insertions of ABL1 into BCR, or vice versa (1.3%); iii) cases bearing additional chromosomal rearrangements concomitant to the t(9;22) (1.1%). For each cytogenetic group, the mechanism at the basis of the rearrangement is discussed. All breakpoints on other chromosomes involved in variant t(9;22) and in additional rearrangements have been characterized for the first time by Fluorescence In Situ Hybridization (FISH) experiments and bioinformatic analyses. This study revealed a high content of Alu repeats, genes density, GC frequency, and miRNAs in the great majority of the analyzed breakpoints. Conclusions Taken together with literature data about CML with variant t(9;22), our findings identified several new cytogenetic breakpoints as hotspots for recombination, demonstrating that the involvement of chromosomes other than 9 and 22 is not a random event but could depend on specific genomic features. The presence of several genes and/or miRNAs at the identified breakpoints suggests their potential involvement in the CML pathogenesis.

Abstract 3261 Poster Board III-1 A crucial role of segmental duplications (SDs) of the human genome has been demonstrated in chromosomal rearrangements associated with several genomic disorders. Limited knowledge is yet available on the molecular processes resulting in chromosomal rearrangements in tumors. The t(9;22)(q34;q11) causing the 5'BCR/3'ABL gene formation has been detected in more than 90% of chronic myeloid leukemia (CML) cases. Some years ago, a 76-kb duplicon was reported, closely located to both ABL and BCR genes which are involved in the t(9;22)(q34;q11) translocation associated with CML. However, the exact role of this duplicon in mediating the t(9;22) rearrangement remained mostly speculative. In 10–18% of CML patients genomic deletions were detected on der(9) chromosome next to translocation breakpoints. The molecular mechanism triggering the t(9;22) and deletions on der(9) is still unknown. Our study presents an experimental evidence of the involvement of SDs in the genesis of the t(9;22) translocation in CML and in the occurrence of genomic deletions on der(9) chromosome. We identified 71 (17%) cases with der(9) deletions by FISH screening of 416 CML patients at diagnosis. Fine-mapping of deletions was performed using appropriate bacterial and Phage P1-derived artificial chromosome clones. The deletions sizes were heterogeneous, ranging from 230 Kb to 12.9 Mb on chromosome 22 and from 260 Kb to 41.8 Mb on chromosome 9. The mapping of all breakpoints revealed an evident breakpoints clustering, on both chromosomes 9 and 22, in two regions of about 2 Mb in size. Indeed, these regions contained the breakpoints detected in 54 out of 60 (90%) patients bearing chromosome 9 deletions and in all patients with chromosome 22 sequences loss. Bioinformatic analysis of chromosome 9 and chromosome 22 genomic regions involved in the deletions was performed to search for features that could correlate with the breakpoints clustering. To this aim, the breakpoint regions were subdivided into 250 Kb intervals. The most striking result was the fact that both clusters contain the above reported 76-kb duplicon, shared by chromosome 9 and 22 (SD_9/22). The SD_9/22 is the only duplication located inside the breakpoints clustering region on chromosome 9, whereas the chromosome 22 clustering region harbors several duplications. A remarkable feature of the chromosome 9 clustering region was the high frequency of Alu repeats. The mean Alu frequency overall on chromosome 9 is 10.8%, whereas the average Alu content on this cluster is 31.3%. Accordingly, as expected, the content in LINE sequences of the region was relatively low (average overall on chromosome 9: 21.2%, as opposed to 8.7% on the cluster region). Gene distribution analysis of chromosome 9 and 22 showed that both SD_9/22 map inside gene-poor regions, of about 460 Kb and 250 Kb in size, respectively. To corroborate the observations on the distribution of SDs and Alu/LINE repeats, the chromosome 9 and 22 regions surrounding the SD_9/22 were once more divided into 250 Kb segments, positioning the SD_9 and SD_22 as landmarks. A statistically significant negative association was observed between the number of breaks and the distance from SD_9/22, on both chromosomes 9 (p=0.01) and 22 (p=0.006), respectively. The relationship between the breaks and the interspersed repeats revealed, on chromosome 9, a positive linear regression with Alu repeats (p=0.04), and a negative one with LINEs (p=0.04). Very similar conclusions were obtained by comparing the distance from the SD_9 and the Alu (p= 0.03, positive) and LINE distribution (p=0.02, negative). No statistically significant relationship was observed on chromosome 22. In our study the involvement of SDs was proposed to explain the recurrent t(9;22) translocation in CML and the genomic deletions that could accompany the rearrangement. Although the chromosomes 9 and 22 breakpoints clustering regions are quite large, the strong non-randomness of SD_9/22 location and the genomic features identified in our work suggest that the chromosomal segments near the ABL and BCR genes are brought together by an active process, facilitating recombination. At the light of these findings, the analysis of secondary non-recurrent events could represent a new methodological approach able to identify architectural elements involved in the occurrence of recurrent primary rearrangements in human neoplasia. Disclosures: No relevant conflicts of interest to declare.

MicroRNAs (miRNAs) are small, single stranded non-coding RNAs, 19–24 nucleotides long, involved in crucial biological processes, including differentiation, apoptosis and proliferation. Recent evidence indicates that miRNAs may play an important role in tumorigenesis; changes in miRNAs expression level were identified in many types of human hematological and solid malignancies. To date, several papers have reported the occurrence of genomic deletions flanking the breakpoint on der(9)t(9;22) in 10%–18% of patients with chronic myeloid leukemia (CML). The most probable consequence of der(9) deletions is the loss of tumour suppressor genes, conferring a proliferative advantage to the Philadelphia-positive clone. On the other hand, two miRNAs, namely miR219-2 and miR-199b, are found to map centromeric to the ABL gene within the chromosomal region at 9q34 that is frequently lost in CML patients with der(9) deletions. In this study, we investigated the loss of miR-219-2 and miR-199b by fluorescence in situ hybridization (FISH) analysis with specific bacterial artificial chromosome (BAC) probes in 68 CML cases bearing der(9) deletions. We further evaluated miR-219-2 and miR- 199b expression levels by quantitative real-time polymerase chain reaction (qRT-PCR) experiments in cases showing deletions of at least one of these miRNAs. Depending on RNA sample availability, miRNAs expression level was evaluated in 7 and in 5 CML cases with miR-219-2 and miR-199b deletions, respectively. Statistical analysis of the relative expression results was performed by the Relative Expression Software Tool (REST). To explore the predicted miR-199b target genes, the miRGen targets database (http:// www.diana.pcbi.upenn.edu/cgi-bin/miRGen/v3/Targets.cgi) was queried; this interface provides integrated data of four widely used target prediction programs (miRanda, PicTar, TargetScan, DIANA-microT). FISH experiments revealed the loss of miR-219-2 and miR-199b in 17 (25%) and 10 (15%) out of 68 patients. The miR-199b expression study showed a downregulation in the analyzed group of 5 CML cases with miR-199b deletion as compared to a pool of 10 patients without deletions. The expression level of the miR-199b was 0.279 and the difference between the two groups was statistically significant (p= 0.028). On the contrary, the miR- 219-2 analysis did not reveal a detectable expression level in the examined patients. There were 26 predicted miR-199b target genes, involved in several biological processes such as signal transduction (Protein phosphatase inhibitor 2, PPP1R2), regulation of transcription (Hepatic leukaemia factor, HLF), chromosome organization and biogenesis (Zinc finger protein 238, ZNF238), cell proliferation (Mitogen-activated protein kinase 11, MAP3K11) and DNA repair (UV excision repair protein RAD23 homologue B, RAD23B). Among the CML patients evaluable for the response to the treatment, all cases with the miR-199b deletion were resistant to IFN-a and imatinib therapy. In conclusion, our data demonstrate a crucial role for miR-199b in CML cases bearing der(9) deletions. This miR-199b downregulation could influence the expression level of different target genes modifying important cellular pathways. Further analysis of miR-199b target genes will be needed to shed light on the link between miRNAs and CML.

Deletions on der(9) are associated with chronic myeloid leukemia(CML) in 15–18% of cases. To date, the biological significance of this genomic loss in the pathogenesis of CML is unknown. The most plausible hypothesis is that the loss of a tumor suppressor gene may confer a proliferative advantage to the Philadelphia-positive clone. On the other hand, it has now become evident that microRNAs (miRNAs) play an important regulatory role in some hematological malignancies. To investigate the presence of miRNAs within the genomic regions lost on der(9) we analyzed 60 CML patients with der(9) deletions. Methods. Genomic characterization of the deleted sequences was performed by fluorescence in situ hybridization (FISH) using a contig of DNA clones; the miRBase (http://microrna.sanger.ac.uk/) was queried to assess the presence of miRNAs in the der(9) deleted genomic regions. FISH experiments showed that the genomic loss on der(9) of the 9 (centromeric to ABL) and 22 (telomeric to BCR) chromosome sequences ranged from 260 Kb to 54 Mb and from 230 Kb to 12.9 Mb, respectively. Consultation of the miRBase revealed that in 16 (27%) patients there was loss of miRNAs mapping on chromosome 9 whereas no known miRNAs were mapped on the deleted genomic sequences belonging to chromosome 22. Moreover, 4 cases with a complex t(9;22) rearrangement and der(9) deletions showed loss of the miRNAs sequence also on the third derivative chromosome (4p16, 7p14, 13q14, and 11q13, respectively); among them, only in one case the loss of miRNAs on the third derivative was not associated with the miRNAs deletion mapped on chromosome 9. The most recurrent miRNAs deleted on der(9) were mir-219–2 (deleted in 100% of cases) and mir-199-b (lost in 67% of cases). It is noteworthy that mir-219–2 neighbors and overlaps CpG-islands, suggesting a potential role of this miRNA in CpG-island methylation. Experimental studies indicate that miRNAs can function as tumor suppressor genes or as oncogenes. In fact, in chronic lymphocytic leukemia associated with del(13)(q14) it has been demonstrated that the miRNAs loss can induce downregulation of the antiapoptotic BCL-2 protein. The novel evidence that deletions on der(9) in CML are associated with miRNAs loss may shed new light on the significance of genomic sequences loss. Further studies are needed since it is known that some microRNAs may have as many as a few thousand targets, so prediction algorithms and strategies allowing large-scale screening of multiple target genes are required.

It is known that the receptor activator of nuclear factor kB (RANK) is only identified on progenitor and mature osteoclasts and in dendritic cells. A recent report (Blood107:4334, 2006) described a dose-dependent decrease of RANK expression in osteoclasts when cultured in the presence of imatinib; these data were confirmed in adult mice treated with imatinib, in which a decrease in osteoclasts activity was demonstrated. Therefore, it is speculated that imatinib may have a potential antiresorptive effect. We evaluated bone marrow RANK molecular expression in patients affected by chronic myeloid leukemia (CML) receiving imatinib therapy, to verify the effect of the tyrosine kinases inhibitor on RANK expression. The study included 13 CML patients (7 males, 6 females, median age 37 yrs). Six were treated with Imatinib at standard dosage (400 mg) and the remaining 7 at higher doses (> 400 mg). The median duration of imatinib therapy was 28 months (range 13 – 44 months). The RANK gene expression level was determined by Real-Time PCR using 1X Platinum SYBR Green qPCR SuperMix-UDG. The RANK gene expression level variation was estimated by comparing the values of 2−Δ Δ Ct obtained in CML patients at diagnosis and during imatinib treatment. For each of the tested cases the sample at diagnosis was utilized as calibrator and 28S rRNA was used as reference gene. Eleven (85%) patients showed an upregulation of RANK, the gene expression fold increase ranging from 1.17 to 15.88 as compared to the value at diagnosis; all patients treated with high-dose imatinib showed a RANK overexpression, the fold increase ranging from 1.57 to 15.88. Although the median RANK expression fold increase observed in the group of patients treated with high-dose imatinib was higher than in the cases taking standard dosage (2.47 versus 1.34 fold increase, respectively), this difference was not statistically significant. There was no association between the RANK expression level and the duration of imatinib treatment. Our study reveals that imatinib mesylate is accountable for the molecular overexpression of the RANK gene in CML patients. These data seem to be in conflict with those previously reported (Blood2006;107: 4334). It is possible that the RANK overexpression which we observed was related to the immune (i.e. dendritic cells) and not the bone cells (i.e. osteoclasts). In this regard, a new type of cell has recently been described in mice, that may account for the immune effect of imatinib; the new cell, which seems to be a cross between a dendritic cell and a natural killer cell, has been called an “interferon-producing killer dendritic cell” (Nat Med2:214, 2006; Nat Med2:207, 2006). These studies suggest a new mechanism by which imatinib might exert an antitumor effect, apart from its direct action on chronic myeloid leukemia cells. Therefore, in this context, the RANK upregulation observed in our study could be an expression of the immune effect of imatinib. Further studies are needed to verify if the RANK gene overexpression mediated by imatinib could affect the molecular and cytogenetic response in CML patients.

The receptor activator of the nuclear factor kB ligand (RANKL) is a key molecule in the pathogenesis of malignant osteolytic lesions in multiple myeloma or bone metastases in prostate and breast cancer. Inhibition of RANKL is therefore a promising new therapy for controlling bone loss and pain in bone tumors and associated osteolysis. Changes in bone and mineral metabolism developing in a proportion of patients taking imatinib for either chronic myeloid leukemia (CML) or gastrointestinal stromal tumors have previously been described. The aim of our study was to verify in CML patients the effect of imatinib on RANKL bone marrow molecular expression. The study included 13 CML patients (7 males, 6 females, median age 37 yrs). Six were treated with imatinib at standard dosage (400 mg) and the remaining 7 at higher doses (> 400 mg). The median duration of imatinib therapy was 28 months (range 13 – 44 months). The RANKL gene expression level was determined by Real-Time PCR using 1X Platinum SYBR Green qPCR SuperMix-UDG. Variations in RANKL gene expression level were estimated by comparing the values of 2−Δ Δ Ct obtained in CML patients at diagnosis and during imatinib treatment. For each of the tested cases the sample at diagnosis was utilized as calibrator and 28S rRNA was used as reference gene. Eight (62%) patients showed a downregulation of RANKL gene expression, the fold decrease ranging from 0.01 to 0.47 as compared to the value at diagnosis; among these 8 patients, 6 (75%) were treated with imatinib at standard dosage. Instead, 5 (38%) patients showed an upregulation of RANKL, the gene expression fold increase ranging from 1.43 to 4.94 as compared to the gene level observed at CML onset; all these 5 patients were treated with high doses of imatinib. There was no association between RANKL expression and the duration of imatinib treatment. These findings suggest that imatinib mesylate could control RANKL expression. At standard dosage, imatinib can downregulate RANKL production. The RANKL upregulation observed in CML patients treated with high doses of imatinib could be explained by the possible activation of the immune system cells, such as T and B cells, induced by the tyrosine kinases inhibitor. Further studies are needed to verify the minimal effective dose of imatinib on RANKL expression, with the aim of administering it as an antiosteolytic agent in such diseases as osteoporosis, metastatic bone disease, and multiple myeloma.

Chronic myeloid leukemia (CML) is characterized by a reciprocal translocation t(9;22)(q34;q11) that generates a BCR-ABL fusion gene on the Philadelphia (Ph) chromosome. Large deletions adjacent to the t(9;22) breakpoint on the derivative 9 chromosome have now been found, which result in genomic loss at both sides of the translocation breakpoint. We report a FISH study in CML cases bearing deletions on the der(9) chromosome. FISH analysis with specific BAC/PAC clones for the ABL1 and BCR genes was performed on bone marrow cells of 305 CML patients at diagnosis. A set of BAC/PAC probes, belonging to chromosomes 9, 22 was selected according to the University of Santa Cruz (UCSC) database and employed in FISH experiments. We detected der(9) deletions in 56 (18.4%) CML cases. Deletions of chromosome 9 sequences on the der(9) were found in 47 (84%) cases; they ranged from 350 Kb to 41.6 Mb. Chromosome 22 deletions on der(9) were found in 49 (87.5%) of the analysed cases; the deleted chromosome 22 sequences were shorter than the deleted chromosome 9 sequences (ranging from 400 Kb to 12.7 Mb). Although deletions size appeared to be heterogeneous, 2 main breakpoints cluster regions were identified proximally (at about 1.9 Mb) to the ABL and distally (at about 0.7 Mb) to the BCR genes, respectively. In fact, a cluster region of 1.1Mb, delimited by RP11-203J24 and RP11-247A12, was defined on chromosome 9 whereas a 0.8 Mb region, included between CTA-322B1 and RP5-930L11, was identified on chromosome 22. Bioinformatic analysis of breakpoints cluster regions was performed to identify sequence motifs that could mediate the chromosomal rearrangement. The presence of Matrix Association Regions (MARs) and the topoisomerase II consensus was investigated by MAR-Wiz software (http://www.futuresoft.org/modules/MarFinder/); the RepeatMasker program (http://www.repeatmasker.org/) was employed to detect interspersed repeats and low complexity DNA sequences (such as SINE, LINE, and LTR). Potential sequence similarities between breakpoints cluster regions were searched for using Genalyzer software. Sequence analysis revealed that the frequency distribution of MARs, topoisomerase II sites, and repeated elements was no different from the frequency observed in other genomic regions. Genalyzer software did not detect sequence similarities between the 2 clustering regions; however, a 76 Kb duplicon, previously reported in literature, was located at a distance of 500 kb and 550 Kb from the chromosomes 9 and 22 cluster regions, respectively. In conclusion, our analysis revealed that sequence motifs do not seem to be involved in the occurrence of der(9) deletions. We hypothesize that the presence of a duplicon could mediate the juxtaposition of ABL and BCR genes and that a probable open chromatin status of chromosomes 9 and 22 sequences could confer to DNA more vulnerability to double strand breaks, mediating the t(9;22) rearrangement and the occurrence of der(9) deletions.

Translocation t(8;21)(q22;q22) is a common karyotypic abnormality detected in about 15% of Acute Myeloid Leukemia (AML) cases. The rearrangement results in fusion of the RUNX1 (also known as AML1) and CBFA2T1 (also known as ETO) genes generating a 5′RUNX1/3′CBFA2T1 transcriptionally active fusion gene on derivative chromosome 8. In 1 to 8.5% of AML cases insertions events generating a 5′RUNX1/3′CBFA2T1 fusion gene have been reported, whereas the occurrence of inversions accompanying the t(8;21) has never been observed. We report a screening of 82 AML cases bearing the RUNX1/CBFA2T1 rearrangement detected by RT-PCR; all cases were tested by Fluorescence In Situ Hybridization (FISH) with BAC and PAC clones specific for CBFA2T1 and RUNX1 genes. This analysis allowed us to reveal five cases with ins(21;8), one with ins(8;21), and two with a pericentric chromosome 8 inversion followed by a t(8;21) translocation. A detailed molecular cytogenetic characterization of breakpoints has been performed in all cases. FISH co-hybridization experiments with CBFA2T1 and RUNX1 probes revealed the presence of a functional fusion gene on the der(21) instead of the der(8) chromosome in five cases with ins(21;8); a single fusion signal on the der(8) chromosome was detected in the case with ins(8;21). The use of the same clones in FISH studies showed the presence of a single unexpected fusion signal on the 8p derivative chromosome in addition to faint CBFA2T1 and RUNX1 signals on the long arm of der(8) and der(21) chromosomes, respectively. These results suggested that a pericentric chromosome 8 inversion involving CBFA2T1 gene occurred and that the chromosome 21 was rearranged with the 8p derivative chromosome. Appropriate chromosome 21 and 8 BAC clones were employed to precisely define the size of inserted regions in cases with insertions and the breakpoint on the 8p derivative chromosome in cases showing pericentric chromosome 8 inversion. The insertion size turned out to be very heterogeneous, ranging from a minimum of 2.4 Mb to a maximum of 44 Mb. In both cases with chromosome 8 inversion, the CBFA2T1 gene represents the breakpoint at the chromosome 8 long arm whereas the 8p breakpoint showed different mapping positions in 8p21.3 and 8p21.1, respectively. Our results illustrate that (1) heterogeneous mechanisms can lead to the generation of the 5′RUNX1/3′CBFA2T1 chimeric gene; (2) molecular cytogenetic techniques may identify cryptic chromosomal changes, not detected by conventional cytogenetic analysis; (3) the crucial role of the 5′RUNX1/3′CBFA2T1 fusion gene in leukemogenesis does not depend on its location.

// Francesco Albano 1 , Antonella Zagaria 1 , Luisa Anelli 1 , Paola Orsini 1 , Crescenzio Francesco Minervini 1 , Luciana Impera 1 , Paola Casieri 1 , Nicoletta Coccaro 1 , Giuseppina Tota 1 , Claudia Brunetti 1 , Angela Minervini 1 , Domenico Pastore 1 , Paola Carluccio 1 , Anna Mestice 1 , Angelo Cellamare 1 , and Giorgina Specchia 1 1 Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, Bari, Italy. Correspondence: Francesco Albano, email: // Keywords : acute promyelocytic leukemia, LEF1; prognosis; outcome. Received : November 20, 2013 Accepted : December 19, 2013 Published : December 19, 2013 Abstract Lymphoid enhancer-binding factor 1 ( LEF1 ) is a downstream effector of the Wnt/ β-catenin signaling pathway. High LEF1 expression has been reported as a prognostic marker in hematologic malignancies. We evaluated the prognostic significance of LEF1 expression in 78 adult acute promyelocytic leukemia (APL) patients. APL samples were dichotomized at the median value and divided into: LEF1 low and LEF1 high . LEF1 high patients had lower WBC counts at baseline and were less likely to carry a FLT3 -ITD than LEF1 low patients. Early death occurred only in the LEF1 low group. Moreover, LEF1 low expression was associated with a high Sanz score. Survival analysis of 61 APL patients < 60 years revealed that the LEF1 high group had a significantly longer overall survival (OS). Cox analysis for OS confirmed only LEF1 expression as an independent prognostic factor. Of the 17 patients over the age of 60, those in the LEF1 high group showed a higher median survival. In silico analysis identified 9 differentially expressed, up-modulated genes associated with a high expression of LEF1 ; the majority of these genes is involved in the regulation of apoptosis. Our study provides evidence that LEF1 expression is an independent prognostic factor in APL, and could be used in patients risk stratification.