Chronic myeloid leukemia (CML) is characterized by formation of the BCR-ABL fusion gene, usually as a consequence of the Philadelphia (Ph) translocation between chromosomes 9 and 22. Large deletions on the derivative chromosome 9 have recently been reported, but it was unclear whether deletions arose during disease progression or at the time of the Ph translocation. Fluorescence in situ hybridization (FISH) analysis was used to assess the deletion status of 253 patients with CML. The strength of deletion status as a prognostic indicator was then compared to the Sokal and Hasford scoring systems. The frequency of deletions was similar at diagnosis and after disease progression but was significantly increased in patients with variant Ph translocations. In patients with a deletion, all Ph ؉ metaphases carried the deletion. The median survival of patients with and without deletions was 38 months and 88 months, respectively (P ‫؍‬ .0001). By contrast the survival difference between Sokal or Hasford high-risk and non-high-risk patients was of only borderline significance (P ‫؍‬ .057 and P ‫؍‬ .034). The results indicate that deletions occur at the time of the Ph translocation. An apparently simple reciprocal translocation may therefore result in considerable genetic heterogeneity ab initio, a concept that is likely to apply to other malignancies associated with translocations. Deletion status is also a powerful and independent prognostic factor for patients with CML. IntroductionChronic myeloid leukemia (CML) is a clonal hematologic malignancy that results from transformation of a multipotent hemopoietic stem cell. [1][2][3] The molecular hallmark of CML is the formation of a BCR-ABL fusion gene, usually formed as a consequence of the Philadelphia (Ph) translocation involving chromosomes 9 and 22. 4-6 BCR-ABL plays a pivotal role in the pathogenesis of CML and its formation is likely to represent the initiating event. In support of this concept transgenic and retroviral transduction studies have demonstrated that expression of BCR-ABL in murine bone marrow cells resulted in leukemia, with some cases closely resembling CML. [7][8][9][10][11][12][13] In one recent transgenic model the leukemia could be reversed by down-regulating BCR-ABL. 14 Chronic myeloid leukemia is a biphasic disease with an initial chronic phase that is readily controlled. However, this is followed by an ill-defined accelerated phase, and then a terminal blastic phase that resembles an acute leukemia, which is usually refractory to therapy. Transformation to blast crisis is accompanied by secondary cytogenetic changes in about 85% of cases, 15 but the molecular basis for this transformation is poorly understood. A number of molecular changes have been identified in a minority of cases of blast crisis, including mutations or deletions of p53, p16 INKA , and the retinoblastoma protein, and mutation or overexpression of Ras and EVI-1. 1,2 However, none provide a method for prospectively distinguishing those patients who will progress rapidly to blast...

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We report the molecular and cytogenetic characterization of a novel variant of acute promyelocytic leukemia (APL IntroductionThe majority of acute promyelocytic leukemia (APL) cases are characterized by the PML-RARA fusion gene, usually as a consequence of the t(15;17)(q22;q21) translocation. 1 As a result, retinoid sensitivity of the retinoic acid receptor ␣ (RAR␣), which normally functions as a retinoid-inducible transcription factor, is reduced, causing a block in myeloid differentiation. 2 Prolonged disease-free survival can be achieved by combining all-trans retinoic acid (ATRA) and chemotherapy. 3 Arsenic trioxide (As 2 O 3 ) is of proven value in relapsed disease 4 and is also effective during initial induction or consolidation or both. 5 In a small number of APL variants, RARA (at chromosome 17q21) is fused with an alternative partner gene; promyelocytic leukemia zinc finger (PLZF, 11q13), 6 nucleophosmin (NPM, 5q35), 7 nuclear mitotic apparatus (NUMA, 11q23), 8 or signal transducer and activator of transcription 5b (STAT5B, 17q21). 9 RAR␣ fusions to PML, NPM, and NUMA are ATRA responsive, whereas PLZF-RAR␣ is ATRA resistant. 10,11 This report describes a new variant APL and identifies the RARA partner gene. Study designThe patient concerned in this report was originally registered in a multicenter national trial for acute promyelocytic leukemia that had institutional ethics approval at the hospital concerned. Informed consent was obtained in accordance with the Declaration of Helsinki. The patient was subsequently deemed ineligible for that trial because he failed to meet the required genetic inclusion criterion. This report is concerned with an in vitro characterization of the patient's leukemic cells and did not involve any direct patient experimentation.A 66-year-old man with a history of excessive alcohol consumption, clinical evidence of chronic liver disease, and a 14-month history of mild thrombocytopenia was investigated for lethargy, anorexia, and weight loss. A full blood count showed a hemoglobin level of 104 g/L, white cell count of 5.3 ϫ 10 9 /L, neutrophil count of 2.1 ϫ 10 9 /L, and platelet count of 93 ϫ 10 9 /L. The blood film was leukoerythroblastic with occasional hypergranular promyelocytes. Both creatinine (0.22 mmol/L) and ␥-glutamyltransferase (5.17 kat/L [310 U/L]) were mildly elevated. Coagulopathy was absent apart from mildly increased D-dimers (0.4 mg/L; normal, Ͻ 0.2 mg/L). A markedly hypercellular marrow contained 88% hypergranular promyelocytes, and most exhibited regular nuclear outlines ( Figure 1A). Auer rods and faggot cells were absent. Flow cytometric analysis revealed strong intracellular myeloperoxidase expression; however, expression of CD13, CD33, and CD11b was weak. The cells were negative for CD2, CD19, CD34, CD56, CD117, and HLA-DR. The karyotype was 47,XY,ϩ22[5]/46,XY [30], without the classic t(15;17) translocation. Fluorescence in situ hybridization (FISH) studies showed del(17)(q21)(5ЈRARA-,3ЈRARAϩ) ( Figure 1B) plus a split RARA signal ( Figure 1C) with ...

Purpose: Amplification of cyclin E1 (CCNE1) is associated with poor outcome in breast, lung, and other solid cancers, and is the most prominent structural variant associated with primary treatment failure in highgrade serous ovarian cancer (HGSC). We have previously shown that CCNE1-amplified tumors show amplicon-dependent sensitivity to CCNE1 suppression. Here, we explore targeting CDK2 as a novel therapeutic strategy in CCNE1-amplified cancers and mechanisms of resistance.Experimental Design: We examined the effect of CDK2 suppression using RNA interference and smallmolecule inhibitors in SK-OV-3, OVCAR-4, and OVCAR-3 ovarian cancer cell lines. To identify mechanisms of resistance, we derived multiple, independent resistant sublines of OVCAR-3 to CDK2 inhibitors. Resistant cells were extensively characterized by gene expression and copy number analysis, fluorescence-activated cell sorting profiling and conventional karyotyping. In addition, we explored the relationship between CCNE1 amplification and polyploidy using data from primary tumors.Results: We validate CDK2 as a therapeutic target in CCNE1-amplified cells by showing selective sensitivity to suppression, either by gene knockdown or using small-molecule inhibitors. In addition, we identified two resistance mechanisms, one involving upregulation of CDK2 and another novel mechanism involving selection of polyploid cells from the pretreatment tumor population. Our analysis of genomic data shows that polyploidy is a feature of cancer genomes with CCNE1 amplification.Conclusions: These findings suggest that cyclinE1/CDK2 is an important therapeutic target in HGSC, but that resistance to CDK2 inhibitors may emerge due to upregulation of CDK2 target protein and through preexisting cellular polyploidy.

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Deletion of the long arm of one chromosome 20 (del(20q)) is a well-recognized abnormality in acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) and is presumed to cause loss of a tumor suppressor gene at 20q12. In a previously published series of MDS and AML cases, which had lost this region via unbalanced translocation, around 40% of cases were shown to have additional copies of the chromosome 20 abnormalities, with resulting gain or amplification of the retained parts of chromosome 20, most often 20q11.2. We have used FISH and array comparative genomic hybridization, to define further the retained and amplified regions. We now report targeted amplification of 20q11.21 in four of the 22 cases selected for further study and in one new case. The shortest amplified region of 250 kb in a series of five patients with three to ten copies of the 20q11.21 region contained the complete HCK, TM9SF4, PLAGL2, and POFUT1 genes. By RT-PCR we have shown that there is correlation between amplification and increased expression of these four genes in most cases. Localized and high level amplification of the common 250 kb region is evidence for activation of an oncogene in this region in these MDS and AML cases. Cases with 20q11.21 amplification tended to have a high proportion of erythroblasts in the marrow, with two cases diagnosed as erythroleukemia (AML-M6). Chromosome sub-band 20q11.21 amplification may therefore prove to be a marker of a specific subset of AML/MDS with a significant erythroid component.