Acute leukemia with structural rearrangements of chromosome 3

Promoter-centred chromatin interactions associated with EVI1 expression in EVI1+3q- myeloid leukaemia cells

EVI1 expression is associated with poor prognosis in myeloid leukaemia, which can result from Chr.3q alterations that juxtapose enhancers to induce EVI1 expression via long-range chromatin interactions. More often, however, EVI1 expression occurs unrelated to 3q alterations, and it remained unclear if, in these cases, EVI1 expression is similarly caused by aberrant enhancer activation. Here, we report that, in EVI1+3q- myeloid leukaemia cells, the EVI1 promoter interacts via long-range chromatin interactions with promoters of distally located, active genes, rather than with enhancer elements. Unlike in 3q+ cells, EVI1 expression and long-range interactions appear to not depend on CTCF/cohesin, though EVI1+3q- cells utilise an EVI1 promoter-proximal site to enhance its expression that is also involved in CTCF-mediated looping in 3q+ cells. Long-range interactions in 3q- cells connect EVI1 to promoters of multiple genes, whose transcription correlates with EVI1 in EVI1+3q- cell lines, suggesting a shared mechanism of transcriptional regulation. In line with this, CRISPR interference-induced silencing of two of these sites minimally, but consistently reduced EVI1 expression. Together, we provide novel evidence of features associated with EVI1 expression in 3q- leukaemia and consolidate the view that EVI1 in 3q- leukaemia is largely promoter-driven, potentially involving long-distance promoter clustering.

3q26/EVI1 rearrangements in myeloid hemopathies: a cytogenetic review

ABSTRACT 

The EVI1 gene, located in chromosomal band 3q26, is a transcription factor that has stem cell-specific expression pattern and is essential for the regulation of self-renewal of hematopoietic stem cells. It is now recognized as one of the dominant oncogenes associated with myeloid leukemia. EVI1 overexpression is associated with minimal to no response to chemotherapy and poor clinical outcome. Several chromosomal rearrangements involving band 3q26 are known to induce EVI1 overexpression. They are mainly found in acute myeloid leukemia and blastic phase of Philadelphia chromosome-positive chronic myeloid leukemia, more rarely in myelodysplastic syndromes. They include inv(3)(q21q26), t(3;3)(q21;q26), t(3;21)(q26;q22), t(3;12)(q26;p13) and t(2;3)(p15–23;q26). However, many other chromosomal rearrangements involving 3q26/EVI1 have been identified. The precise molecular event has not been elucidated in the majority of these chromosomal abnormalities and most gene partners remain unknown.

A novel t(3;12)(q21;p13) translocation in a patient with accelerated chronic myeloid leukemia after imatinib and nilotinib therapy

The acquisition of secondary chromosomal aberrations in chronic myeloid leukemia (CML) patients with Philadelphia chromosome-positive (Ph+) karyotype signifies clonal evolution associated with the progression of the disease to its accelerated or blastic phase. Therefore, these aberrations have clinical and biological significance. T(3;12)(q26;p13), which is a recurrent chromosomal aberration observed in myeloid malignancies, is typically associated with dysplasia of megakaryocytes, multilineage involvement, short duration of any blastic phase, and extremely poor prognosis. We have identified a recurrent reciprocal translocation between chromosomes 3 and 12 with different breakpoint at bands 3q21 in the malignant cells from a 28-year-old man. The patient was initially diagnosed as having Ph+ CML in the chronic phase. The t(3;12)(q21;p13) translocation occurred 4 years after the patient was first diagnosed with CML while undergoing tyrosine kinase inhibitor therapy. We confirmed the t(3;12)(q21;p13) translocation via fluorescence in situ hybridization assay by using whole-chromosome paint probes for chromosomes 3 and 12. Our findings demonstrate that, similar to other recurrent translocations involving 3q26 such as t(3;3) and t(3;21), the t(3;12)(q21;p13) translocation is implicated not only in myelodysplastic syndrome and acute myeloid leukemia but also in the progression of CML. These findings extend the disease spectrum of this cytogenetic aberration.

Overexpression of EVI1 interferes with cytokinesis and leads to accumulation of cells with supernumerary centrosomes in G0/1 phase

Ectopic viral integration site 1 (EVI1), a transcription factor frequently overexpressed in myeloid neoplasias, has been implicated in the generation of malignancy-associated centrosomal aberrations and chromosomal instability. Here, we sought to investigate the underlying cause of centrosome amplification in EVI1-overexpressing cells. We found that overexpression of EVI1-HA in U2OS cells induced supernumerary centrosomes, which were consistently associated with enlarged nuclei or binuclear cells. Live cell imaging experiments identified cytokinesis failure as the underlying cause of this phenotype. In accordance with previous reports, EVI1 overexpression induced a partial cell cycle arrest in G0/1 phase, accompanied by elevated cyclin D1 and p21 levels, reduced Cdk2 activity and activation of the p53 pathway. Supernumerary centrosomes predominantly occurred in resting cells, as identified by low levels of the proliferation marker Ki-67, leading to the conclusion that they result from tetraploidization after cytokinesis failure and are confined to G0/1-arrested tetraploid cells. Depletion of p53 using siRNA revealed that further polyploidization of these cells was inhibited by the p53-dependent tetraploidy checkpoint.

Acute lymphoblastic leukaemia with unusual chromosomal abnormality: t(3;9) (p21;p13), del(10p12) [13]

We report a case of pre-B acute lymphoblastic leukaemia with an unusual translocation between chromosome 3 and 9, with del(10p12) [13]. The diagnosis at presentation was made by the morphology, cytochemistry and immunophenotyping. Cytogenetic analysis was also done at presentation. To the best of our knowledge and after literature search this appears to be a rare cytogenetic abnormality in ALL.

Expression and prognostic significance of different mRNA 5'-end variants of the oncogene EVI1 in 266 patients with de novo AML: EVI1 and MDS1/EVI1 overexpression both predict short remission duration

Rearrangements of chromosome band 3q26.2 lead to overexpression of the EVI1 gene and are associated with a poor prognosis in myeloid malignancies. EVI1 is also overexpressed in some cases without 3q26 rearrangements. To uncover its prognostic significance in this patient group, however, it may be necessary to distinguish among several known 5'-end variants of its mRNA. According to a recent report, overexpression of the transcript variant EVI1_1d was associated with shortened survival in acute myeloid leukemia (AML), but overexpression of MDS1/EVI1, whose protein product differs structurally and functionally from that of all other known EVI1 5'-end variants, was not. The aim of the present study was to determine, for the first time, the expression and prognostic significance of all known EVI1 5'-end variants in AML. Quantitative RT-PCR was used to measure the expression of EVI1_1a, EVI1_1b, EVI1_1d, EVI1_3L, and MDS1/EVI1 in 266 samples from patients with de novo AML. To correlate expression of the EVI1 5'-end variants with survival parameters, regression analyses were performed. 41/266 patients (15.4%) overexpressed at least one, but more often several or all, EVI1 transcript type(s). High expression of each of the EVI1 mRNA variants, including MDS1/EVI1, was significantly associated with shortened continuous complete remission in the total patient population as well as in the subgroups of patients with intermediate risk or normal cytogenetics. The present study therefore shows that high levels of each of the known EVI1 mRNA 5'-end variants represents an adverse prognostic factor in de novo AML without 3q26 rearrangements. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat.

The oncogene and developmental regulator EVI1: expression, biochemical properties, and biological functions

The EVI1 gene codes for a zinc finger transcription factor with important roles both in normal development and in leukemogenesis. Transcriptional activation of this gene through chromosome rearrangements or other, yet to be identified mechanisms leads to particularly aggressive forms of human myeloid leukemia. In vitro as well as in animal model systems, EVI1 affected cellular proliferation, differentiation, and apoptosis in cell type specific ways. Retroviral integrations into the EVI1 locus provided cells with increased abilities to engraft, survive, and proliferate in bone marrow transplantation experiments. Experimental overexpression of EVI1 by itself was insufficient to cause leukemia in animal model systems, but it cooperated with other genes in this process. This review summarizes the currently available experimental evidence for the proposed biochemical and biological functions of this important oncogene.

Targeted therapies in myelodysplastic syndromes: ASH 2003 review

The myelodysplastic syndromes (MDS) continue to pose conceptual and practical conundrums because of their heterogeneity and therapeutic challenges. They are not restricted to the presence of clonal cells that are prone to excessive proliferation and premature apoptosis. In MDS the bone marrow microenvironment also is abnormal and exhibits an excess of proinflammatory cytokines, especially tumor necrosis factor (TNF), neoangiogenesis, and poorly defined immune defects. Thalidomide, a drug with anti-TNF, antiangiogenic, and immunomodulatory activities, and other agents with anti-TNF effects, such as pentoxifylline, etanercept, and infliximab, have produced hematologic improvement in 20% to 40% of patients. These agents may provide effective therapy for a subset of lower-risk MDS patients, even if the drugs target the bone marrow microenvironment predominantly. However, in higher-risk MDS patients, especially those with more than 10% blasts, it is important to eliminate abnormal cell clones; drugs used for this purpose have included arsenic trioxide, topotecan, the farnesyl transferase inhibitor tipifarnib, and demethylating agents, such as 5-azacytidine and decitabine. To increase the therapeutic index, a combination strategy may be preferable for higher-risk MDS patients, in whom the seed (clone) and the soil (bone marrow microenvironment) must be targeted simultaneously. The challenge is to recognize the subset that is likely to respond to a given drug so that patients can be preselected for therapy.

Arsenic trioxide and thalidomide combination produces multi-lineage hematological responses in myelodysplastic syndromes patients, particularly in those with high pre-therapy EVI1 expression

Twenty-eight myelodysplastic syndromes (MDS) patients were treated with arsenic trioxide (ATO) and thalidomide. Seven patients responded including one complete hematologic and cytogenetic response and one with regression in spleen size. Two trilineage responses were seen in patients with inv(3)(q21q26.2). Three of five patients who had high pre-therapy EVI1 levels showed unexpectedly good responses while two died early in the first cycle. In vitro studies using 32Dcl3 cells forced to express EVI1 confirmed increased sensitivity of these cells to ATO. Both low/high risk MDS may benefit significantly from therapy with ATO/thalidomide, and those with high pre-therapy EVI1 expression may be uniquely sensitive.

Acute myelogenous leukemia associated with extreme symptomatic thrombocytosis and chromosome 3q translocation: case report and review of literature

Acute leukemias with thrombocytosis have been recently linked with structural abnormalities of the short arm of chromosome 3. A 46-year-old man with a 2-month history of recurrent transient ischemic attacks and abdominal pain developed an ischemic left foot and a gangrenous toe as his initial symptoms. Platelet count was 3.5 x 10(6)/microL, and despite plateletpheresis, the patient required left-leg amputation. Pathologic examination was remarkable for arterial thrombosis in the absence of atherosclerotic lesions. A diagnosis of acute myeloid leukemia with a novel translocation between chromosomes 3q21, 16, and 7 was made. Induction therapy was unsuccessful, and the patient died of overwhelming sepsis within 5 weeks of diagnosis. The striking features of this case were extreme symptomatic thrombocytosis, peripheral gangrene without atherosclerosis, and a novel three-way chromosomal translocation involving chromosome 3q21.

Rearrangements of chromosome band 3q21 in myeloid leukemia

Chromosome rearrangements affecting band 3q21, namely, the inv(3)(q21q26), the t(3;3)(q21;q26), and the t(1;3)(p36;q21), are associated with a particularly poor prognosis in myeloid leukemia or myelodysplasia. Originally, inv(3) and t(3;3) breakpoints have been reported to cluster in a region (breakpoint cluster region, BCR) of approximately 30 kb, which is located centromeric and downstream of the ribophorin I (RPN-I) gene. More recently, we established a PAC contig that includes the 3q21 BCR, and used these PAC clones to map breakpoints in patient samples by both metaphase and interphase fluorescence in situ hybridization (FISH) analysis. A significant proportion of inv(3) and t(3;3) breakpoints was located at sometimes considerable distances centromeric of the originally described BCR, in a region recently also implicated in t(1;3) rearrangements. These breakpoints may thus define a second, centromeric BCR (BCR-C), or extend the original 3q21 BCR to a size of approximately 100 kb. Activation of the EVI-1 gene in 3q26 by regulatory sequences of the housekeeping gene RPN-I has been suggested as a leukemogenic mechanism in patients with inv(3) and t(3;3). However, despite a number of characteristics that make EVI-1 an attractive candidate oncogene, its biological properties fail to fully explain the phenotype of leukemias carrying 3q rearrangements. Several additional candidate genes have been identified in or near the 3q21 breakpoint region, but their possible contribution to the characteristics of leukemias with 3q21 rearrangements remains to be explored.

Interphase fluorescence in situ hybridization assay for the detection of 3q21 rearrangements in myeloid malignancies

In myeloid malignancies, chromosome rearrangements involving band 3q21 are associated with a particularly poor prognosis of the disease. Their sensitive and unequivocal detection is therefore of great clinical importance. In this report, we describe the establishment of an interphase fluorescence in situ hybridization (FISH) assay that complements classical cytogenetic analysis in the diagnosis of such aberrations. PACs that map centromeric and telomeric of known 3q21 breakpoints were labeled with different fluorescent dyes, and the separation of the normally colocalizing signals was used as an indicator of the presence of a 3q21 rearrangement. Two cell lines and 10 primary samples from myeloid leukemia and myelodysplastic syndrome (MDS) patients with 3q21 rearrangements were investigated using the newly established method. The rate of false positivity was determined in 27 control samples from patients with various types of myeloid malignancies. In addition to providing a sensitive and rapid test for the detection of 3q21 aberrations, the interphase FISH assay yields preliminary information about the localization of individual breakpoints. Six of the 10 breakpoints in the patient samples map to an only recently described breakpoint cluster region (BCR) 60 kb centromeric of the originally reported 3q21 BCR. These findings may contribute to the understanding of the molecular basis of the clinical features associated with 3q21 rearrangements.

Mapping of leukaemia-associated breakpoints in chromosome band 3q21 using a newly established PAC contig

Chromosome aberrations affecting band 3q21 are associated with a particularly poor prognosis in patients with acute myeloid leukaemia. To facilitate the molecular characterization of such rearrangements, we established a PAC contig covering the relevant genomic region. Using these PACs as probes in fluorescence in situ hybridization (FISH) experiments, we showed that a number of 3q21 breakpoints in patient samples map to a previously defined 'breakpoint cluster region'. Others, however, are located at varying distances centromeric of it. These results have important implications in the search for genes affected by 3q21 rearrangements.

Transcription factor GATA-2 gene is located near 3q21 breakpoints in myeloid leukemia

Rearrangements affecting chromosome band 3q21 are observed in a subgroup of patients with acute myeloid leukemia (AML) or myelodysplastic syndrome (MDS). However, little is known about the molecular consequences of such aberrations. We therefore established a PAC contig in the 3q21 breakpoint region and identified potential protein coding sequences by exon trapping. One of the exons isolated was from the human GATA-2 gene, which we showed to be transcribed from telomere to centromere. The majority of 3q21 breakpoints are located telomeric to the transcribed portion of this gene in a region that in mice appears to be necessary for proper promoter function. Results of GATA-2 expression analyses in leukemic cell lines as well as primary patient samples are compatible with the hypothesis that 3q21 aberrations contribute to leukemogenesis through deregulation of the hematopoietic transcription factor GATA-2.

A novel translocation t(3;22)(q21;q11) involving 3q21 in myelodysplastic syndrome-derived overt leukemia with thrombocytosis

We report here a novel translocation t(3;22)(q21;q11) in myelodysplastic syndrome (MDS)-derived overt leukemia with thrombocytosis. A 44-year-old female was initially diagnosed as MDS with a low platelet count and normal karyotype. After 4 months, blood leukemic cells and platelets rapidly increased concomitantly and a diagnosis of acute myeloblastic leukemia (AML M1) was made. Chromosome analysis showed 46, XX, t(3;22)(q21;q11) in 14 of 20 metaphases. Fluorescence in situ hybridization analysis confirmed both the der(3)t(3;22) and the der(22)t(3;22). Our results suggest that unidentified gene(s) at 3q21 breakpoint may be implicated in the pathogenesis of abnormal thrombopoiesis as observed in the 3q21q26 syndrome.

Chronic myelomonocytic leukemia with t(1;3)(p36;q21) and a synchronous gastric cancer

The translocation t(1;3)(p36;q21) has been reported previously in patients with the myelodysplastic syndrome and with acute nonlymphocytic leukemia. It has been reported in only 5 cases of chronic myelomonocytic leukemia and t(1;3)(p36;q21). We observed a case of chronic myelomonocytic leukemia with t(1;3)(p36;q21) complicated by a gastric cancer at the time of diagnosis.

Mutagen exposures and chromosome 3 aberrations in acute myelocytic leukemia

Thirteen patients with acute myelocytic leukemia (AML) and with clonal aberrations involving chromosome 3 were studied. Three patients had monosomy 3, four had trisomy 3, and six had structural aberrations of chromosome 3. In the majority of cases chromosome 3 aberrations were parts of complex karyotypes, but in two patients, the abnormalities appeared as single aberrations, one as an interstitial deletion del(3)(p13p21) and the other as monosomy 3. All breakpoints of chromosome 3 were found in the fragile site regions 3p14.2, 3q21 and 3q26-27. All patients with monosomy 3 or structural aberrations of chromosome 3 and one of the four patients with trisomy 3 had been exposed to mutagens, such as occupational exposures to organic solvents and/or petroleum products or treatments with irradiation or antineoplastic agents. The association among mutagen exposure, structural chromosome 3 aberrations and fragile sites in AML may indicate that targeting of the mutagens to these sites is of importance for the etiology of the disease. Leukemia (2000) 14, 112-118.

Translocation (2;3)(p21;q26) as the sole anomaly in a case of primary myelofibrosis

Translocation t(2p;3q) is a rare but recurrent finding in myeloid disorders. We present the first case of primary myelofibrosis with t(2;3)(p21;q26) as the sole chromosomal anomaly. The comparison with the 11 other previously published myeloid-associated t(2p;3q) cases confirms that this nonrandom translocation involves a pluripotent stem cell and is associated with a poor prognosis.

Fluorescence in situ hybridization characterization of the chromosomal breakpoints in a case with ins(17;3)(q11.2;q21q26.3) and acute monocytic leukemia

A 63-year-old patient with acute myeloid leukemia of FAB M5 subtype revealing chromosomal breakpoints in 3q21 and 3q26 is presented. Although rearrangements of 3q21 and 3q26 are relatively common in patients with myelocytic malignancies, this is the first report of ins(17;3)(q11.2;q21q26.3). We defined the chromosomal breakpoints and the extent of the insertion by fluorescence in situ hybridization (FISH) with yeast artificial chromosomes (YACs).

A patient with meningioma showing multiple cytogenetic abnormalities and a constitutional translocation (3;9)(q13.3;q22)

Several different clonal abnormalities in both hypo- and hyperdiploid cell lines were observed in tumor cells of a 35-year-old man with a syncytial meningioma. A translocation involving chromosomes 3 and 9, t(3;9)(q13.3;q22), was present in all analyzable tumor cells and proved to be constitutional. The breakpoints 3q13.3 and 9q22 are involved in acquired karyotypic abnormalities in a number of tumors and might be situated near a tumor suppressor gene. The development of malignancies has been observed in patients with constitutional translocations involving 3q13.3 but not 9q22. We conclude that translocations involving 3q13.3 and maybe 9q22 could present constitutional chromosomal abnormalities predisposing for the development of a malignancy. Patients in whose tumor cells a translocation involving 3q13.3 or 9q22 is observed should be checked for a similar constitutional abnormality.

Leukemia breakpoint region in 3q21 is gene rich

Rearrangements of the long arm of human chromosome 3, including reciprocal translocations, inversions and deletion/duplication of bands 3q21-3q26, as well as deletions of 3q21 and reciprocal translocations between 3q21 and other chromosomes, are well documented in leukemia. Previous studies showed that the breakpoints within 3q21 cluster within a 10-40 kb region but no candidate genes were described. In this work, we have identified partial cDNAs corresponding to five to nine new transcripts from an 80 kb P1 clone that spans ten breakpoints. These transcripts, with one exception, appear to be expressed only at low levels in the set of cancer cell lines examined. Four transcripts are located between the previously mapped Ribophorin I gene and the most centromeric breakpoint; three map directly within the 20 kb spanning nine independent breakpoints. These data (i) show that among characterized leukemia breakpoint regions 3q21 is unusually gene rich, (ii) provide new candidates for relevance to leukemia in 3q21, and (iii) suggest possibilities for chromatin configuration effects.

Diagnostic and prognostic significance of cytogenetics in adult primary myelodysplastic syndromes

Cytogenetic analysis has proven to be a mandatory part of the diagnosis of myelodysplastic syndromes (MDS) as well as a major indicator for predicting clinical course and outcome. This review concentrates on the cytogenetic classifications, the incidence and types of chromosome defects and the prognostic significance of the karyotype in adult primary MDS. Two cytogenetic classifications are currently used: one is based on the karyotype complexity (normal, single, double or complex defects), the other on clonal status (all metaphases normal, abnormal or admixture of normal and abnormal clones). Chromosome abnormalities are of both numerical and structural types. Aside from the 5q-syndrome, no specific clinico-cytogenetic entity has been reported. However, several distinct clinical and cellular features have been identified that correlate with the presence of specific chromosome defects such as inv(3)/t(3;3), +6, t(5;12), del(17p) and del(20q). The presence of complex defects is associated with reduced survival and a high risk of leukemic transformation. Among single defects, specific abnormalities may define distinct prognostic groups. Patients with del(5q) as a sole chromosome defect and a refractory anemia without excess of blasts have a favourable prognosis. For patients with trisomy 8 or monosomy 7 there may be distinct types of clinical evolution. Most patients with the 3q21q26 syndrome have a short survival. The presence of two chromosome defects may constitute an independent cytogenetic entity probably associated with relative poor prognosis. Karyotypic evolution generally represents a poor risk factor. The combination of cytogenetics with clinical and hematological features has proven to provide for a better prediction of patients' survival, leukemic transformation and response to treatment. Several scoring systems have been developed. They have to be improved by the study of new patients according to strict clinical and cytogenetic criteria and by the addition of newly recognized prognostic indicators such as histopathological features and molecular genetic mutations.

Structural characterization and fine chromosomal mapping of the human P2Y1 purinergic receptor gene (P2RY1)

Using P2Y1 specific oligonucleotide primers in a Polymerase Chain Reaction on human genomic DNA, we have amplified a region encoding the P2Y1 receptor Restriction analysis and Southern hybridization of the PCR product revealed that the entire open reading frame of the human P2Y1 receptor is coded by an intronless gene. We have previously localized the P2Y1 receptor gene to human chromosome 3. The gene was further localized to a region of chromosome 3 using a subchromosomal hybrid panel containing different segments of chromosome 3. Based on the specific PCR product obtained and its Southern hybridization to the human P2Y1 receptor cRNA, the P2Y1 receptor gene was mapped to human chromosome 3q25.

Abnormalities of 3q21 and 3q26 in myeloid malignancy: a United Kingdom Cancer Cytogenetic Group study

Cytogenetic and clinical details are presented for 66 patients with myeloid malignancy and chromosome abnormalities of 3q21 and/or 3q26 (3qabns). Bone marrow and/or peripheral blood morphology was assessed for 52 cases. 3qabns in Philadelphia negative (Ph-ve) and positive (Ph+ve) cases were inv(3)(q21q26), (21 Ph-ve, 6 Ph+ve); t(3;3)(q21;q26) (nine Ph-ve, four Ph+ve); and t(3;21)(q26;q22) (four Ph-ve, six Ph+ve). Ph-ve cases also had t(1;3)(p36;q21) (three cases), and t(3;5)(q21;q31)/(q21;q35)/(q26;q21) (five cases aged < 40 years). Three cases, aged < 30 years, had t(3;12)(q26;p13) which defines a new 3qabn subgroup. Monosomy 7 and/or 5q- accompanied inv(3) or t(3;3) in 17/30 cases. All cases had a myeloid malignancy (predominantly AML M1, M4 or M7), frequent trilineage myelodysplasia, and markedly abnormal megakaryopoiesis with micromegakaryocytes (< 30 microns). Thrombocytosis occurred in two cases only. Most Ph+ve cases were in myeloid blast crisis and in Ph+ve cases alone, micro-megakaryocytes were uniquely small (10 microns) in 7/11 cases. There were equal numbers of males and females. Seven secondary leukaemias were found in Ph-ve cases with inv(3), t(3;3), t(3;21), t(1;3) or del(3)(q21). Three cases with t(3;21) (one Ph+ve) were de novo AML or had de novo aplastic anaemia. Survival was rarely greater than 12 months from detection of the 3qabn.