Direct visualization of the transposed ABL gene in a duplicated masked Ph chromosome

Chronic myeloid leukemia with insertion-derived BCR-ABL1 fusion: redefining complex chromosomal abnormalities by correlation of FISH and karyotype predicts prognosis

Chromosomal insertion-derived BCR-ABL1 fusion is rare and mostly cryptic in chronic myeloid leukemia (CML). Most of these cases present a normal karyotype, and their risk and/or prognostic category are uncertain. We searched our database and identified 41 CML patients (20 M/21 F, median age: 47 years, range 12-78 years) with insertion-derived BCR-ABL1 confirmed by various FISH techniques: 31 in chronic phase, 1 in accelerated phase, and 9 in blast phase at time of diagnosis. Conventional cytogenetics analysis showed a normal karyotype (n = 19); abnormal karyotype with morphologically normal chromosomes 9 and 22 (n = 5); apparent ins(9;22) (n = 2) and abnormal karyotype with apparent abnormal chromosomes 9, der(9) and/or 22, der(22) (n = 15). The locations of insertion-derived BCR-ABL1 were identified on chromosome 22 (68.3%), 9 (29.3%), and 19 (2.4%). Complex chromosomal abnormalities were often overlooked by conventional cytogenetics but identified by FISH tests in many cases. After a median follow-up of 58 months (range 1-242 months), 11 patients died, and 3 lost contact, while the others achieved different cytogenetic/molecular responses. The locations of BCR-ABL1 (der(22) vs. non-der(22)) and the karyotype results (complex karyotype vs. noncomplex karyotype) by conventional cytogenetics were not associated with overall survival in this cohort. However, redefining the complexity of chromosomal abnormality by correlating karyotype and FISH findings, CML cases with simple chromosomal abnormalities had a more favorable overall survival than that with complex chromosomal abnormalities. We conclude that insertion-derived BCR-ABL1 fusions often involve complex chromosomal abnormalities which are overlooked by conventional cytogenetics, but can be identified by one or more FISH tests. We also suggest that the traditional cytogenetic response criteria may not apply in these patients, and the complexity of chromosomal abnormalities redefined by correlating karyotype and FISH findings can plays a role in stratifying patients into more suitable risk groups for predicting prognosis. (Word count: 292).

Detection of a t(1;22)(q23;q12) translocation leading to an EWSR1-PBX1 fusion gene in a myoepithelioma

Chromosome banding as well as molecular cytogenetic methods are of great help in the diagnosis of mesenchymal tumors. Myoepithelial neoplasms of soft tissue including myoepitheliomas, mixed tumors, and parachordomas are diagnoses that have been increasingly recognized the last few years. It is still debated which neoplasms should be included in these morphologically heterogeneous entities, and the boundaries between them are not clear-cut. The pathogenetic mechanisms behind myoepithelial tumors are unknown. Only five parachordomas and one mixed tumor have previously been karyotyped, and nothing is known about their molecular genetic characteristics. We present a mesenchymal tumor classified as a myoepithelioma that had a balanced translocation t(1;22)(q23;q12) as the sole karyotypic change. A novel EWSR1-PBX1 fusion gene consisting of exons 1-8 of the 5'-end of EWSR1 and exons 5-9 of the 3'-end of PBX1 was shown to result from the translocation. Both genes are known to be targeted also by other neoplasia-specific translocations, PBX1 in acute lymphoblastic leukemia and EWSR1 in several solid tumors, most of which are malignant. Based on the structure of the novel fusion gene detected, its transforming mechanism is thought to be the same as for other fusion genes involving EWSR1 or PBX1.

Clinical implications of fluorescence in situ hybridization analysis in 13 chronic myeloid leukemia cases: Ph-negative and variant Ph-positive

Thirteen chronic myeloid leukemia (CML) patients, 10 with variant Philadelphia (Ph) translocations and 3 Ph negative cases, were analyzed by fluorescence in situ hybridization (FISH) with the use of BCR and ABL cosmid probes and a chromosome 22 painting probe. In the variant Ph translocations, the BCR-ABL fusion gene was located on the Ph chromosome; in 1 CML Ph-negative patient, the BCR-ABL fusion gene was located on the Ph chromosome; and, in 2 patients, it was located on chromosome 9. The chromosome 22 painting probe was detected on the third-party chromosome of the variant translocation, and in none of the variant translocations was there any detectable signal on chromosome 9. In CML patients with clonal evolution of a simple Ph, a signal of the chromosome 22 painting probe was detected on the der(9) of the Ph translocation. It was concluded that the variant Ph translocations evolved simultaneously in a three-way rearrangement. The clinical parameters of the 13 patients were similar to those of a large group of CML patients with a simple Ph translocation. It is suggested that, to determine the prognosis of CML patients with a complex karyotype, FISH analysis with a chromosome 22 painting probe be performed.

Amplification of BCR-ABL rearrangement in atypical Philadelphia chromosome: a new variant detected by fluorescence in situ hybridization in one case of acute lymphoblastic leukemia

We report on a 67-year-old woman with acute lymphoblastic leukemia (ALL) who was supposed to have a variant Philadelphia (Ph) translocation identified by conventional cytogenetic techniques. Fluorescence in situ hybridization (FISH) analysis demonstrated the presence of an amplification of BCR-ABL rearrangement at locus 22q11. This is the first observation, to our knowledge, of a duplicated BCR-ABL chimeric gene within the derived chromosome 22 in ALL. Our observation supports the possibility of detecting a variant Ph chromosome at the single-cell level by FISH analysis.

Chromosomal aberrations during progression of chronic myeloid leukemia identified by cytogenetic and molecular cytogenetic tools: implication of 1q12-21

To study the genomic abnormality underlying the acute transformation of chronic myeloid leukemia (CML), 15 CML patients in blast crisis (BC), 3 in accelerated phase (AP), and 20 in chronic phase (CP) were analyzed by conventional cytogenetics, comparative genomic hybridization (CGH), and dual-color chromosomal painting. Philadelphia (Ph) chromosome was identified in every case studied. Only 5 among 20 CP patients had additional abnormalities while 13 of 18 patients with disease progression (BC + AP) showed extra numerical and/or structural chromosomal aberrations. Cytogenetically, the most common chromosome gains during BC and AP were double or triple Ph chromosomes (5 of 14 cases) and trisomy 8 (5 of 14 cases). Trisomies 7 and 17 (1 of 14 cases each) were also observed. CGH analysis detected genetic imbalances in eight cases. Gains of chromosome 20 (3 cases) and 17q (2 cases) were observed, respectively. The recurrent chromosome loss was the deletion of the short arm of chromosome 17, seen in one case with i(17)(q10) and one case with an unbalanced translocation (1;17). In one case, a very complex chromosomal rearrangement, del(3),del(6),der(6)t(17;3;6),der(17)t(6;17), was seen. A novel finding of this work is the involvement of chromosome 1(q12-21qter) in CML disease progression. Overrepresentation of 1(q12-21qter) region was detected by CGH in one case which had a derivative chromosome 17. This abnormal chromosome was later confirmed by fluorescence in situ hybridization (FISH) painting to be a fusion between chromosome 1 and 17 to form the der(17)t(1;17) (q12-21;p11). Two other cases showed the same region being involved in translocations, t(1;10)(q12-21;q26) and t(1;11)(q12-21;p15). It is possible that one or more genes residing on chromosome 1q12-21 may be important in the acute transformation of CML. In conclusion, we find that the combined use of CGH, chromosome painting, and classic cytogenetic analysis allows a better evaluation of the genomic aberration involved in CML blastic transformation, and offers new directions for its further molecular investigations.

Identification of BCR-ABL fusion on chromosome 9 by fluorescence in situ hybridization in two chronic myeloid leukemia cases

We present two cases with hidden Philadelphia translocations that resulted from an insertion and a complex translocation. These cases were unusual in having the BCR/ABL fusion localized to chromosome 9q34. A review of cases with these uncommon presentations of BCR/ABL and prognostic presentation is presented.

Two different Philadelphia chromosomes in a cell line from an AML-M0 patient

A second Philadelphia (Ph) chromosome is one of the most common nonrandom secondary chromosome changes in leukemias with 9;22 translocations. It has been suggested, and observed in two studies of masked t(9;22), that the second Ph chromosome is an exact duplication of the entire derivative chromosome 22. In a cytogenetic study of bone marrow cells from an acute myelogenous leukemia patient, a cell line carrying two different Ph chromosomes evidenced by a chromosome 22 centromeric heteromorphism was found. From this observation arose the question whether the second der(22) was a true Ph chromosome or whether it was a deleted chromosome derived from the normal chromosome 22 that did not contain the bcr-abl rearrangement. A fluorescent in situ hybridization (FISH) study with the t(9;22) probe revealed two bcr-abl positive signals on 60 of 100 interphase nuclei. The second Ph could have resulted from a mitotic crossing over; or, analogously to late-appearing Philadelphia chromosomes, it may be derived from a new chromatid translocation between the chromosomes 9 and 22 not involved in the initial t(9;22).

Identification of variant translocations in chronic myeloid leukemia by fluorescence in situ hybridization

We studied two cases of chronic myeloid leukemia (CML) having variant complex translocations detected by trypsin G-banding and fluorescence in situ hybridization (FISH). Application of dual color- (DC-) FISH using abl and bor cosmid probes permitted us to detect the bor-abl fusion event on both interphase nuclei and metaphase spread. Furthermore, FISH using combinatorial hybridization (centromeric-library and library-library probes) demonstrated the content and the position of the translocations in CML patients with variant (complex type) Ph-positive rearrangements. FISH analysis appears to be superior than conventional cytogenetic analysis.

Detection of the breakpoint cluster region-ABL fusion in chronic myeloid leukemia with variant Philadelphia chromosome translocations by in situ hybridization

Fluorescence in situ hybridization (FISH) technique has been successfully used to detect the BCR-ABL gene fusion in chronic myeloid leukemia (CML) with the classic form of the Philadelphia chromosome (Ph). We applied FISH to study three CML patients showing variant Ph chromosome (either complex or simple type). The results demonstrate that the use of a yeast artificial chromosome (YAC)-derived probe (D107F9) and a cosmid probe (cos-abl 8), specific for BCR and ABL genes respectively, allows also the detection of the BCR-ABL fusion in CML patients with variant Ph.

Fluorescence in situ hybridization (FISH) is a reliable diagnostic tool for detection of the 9;22 translocation

The fluorescence in situ hybridization (FISH) technique for detection of the 9;22 translocation was compared with the "gold standard" of conventional cytogenetics. For this purpose, both methods were applied to 81 bone marrow aspirates and/or peripheral blood specimens comprising 50 CML cases and controls from 31 patients without CML. Independently, core biopsies of these 81 patients were investigated by three histopathologists. Conventional karyotype analysis from unstimulated bone marrow cells was successful in 71/81 cases and demonstrated the Ph-chromosome in 42/46 CML patients. With FISH, results were obtained in all 81 cases investigated, confirming fusion of the ber and abl genes in all cytogenetically Ph-positive patients. Among the five Ph-chromosome-negative specimens bcr/abl fusions were detected in only one patient. The percentage of cells found to be Ph-positive by both methods was correlated, but in individual cases considerable differences in the numbers of Ph-positive cells were observed. Different results may be due to selection of cells after in vitro cultivation predominantly. FISH proved to be a very reliable technique for specimens that do not contain dividing cells. With FISH, large numbers of cells can easily be scored which is an advantage compared to conventional cytogenetics. Therefore, this method is particularly suitable for those whose therapy is being monitored or a relapse is suspected. However, the FISH results should be evaluated critically with respect to the practical limit of sensitivity since non-specific fusion signals can also be observed in a small percentage of cells in non-CML cases. It is suggested that each laboratory define its own threshold of bcr/abl fusion signals for diagnosing Ph-positive CML by FISH.

Fluorescence in situ hybridization provides evidence for two-step rearrangement in a masked Ph chromosome formation

A chronic myelogenous leukemia (CML) patient with a masked Ph chromosome due to the translocation (9;10;22)(q34;q24;q11) is reported. Banding analysis showed a 9q+ chromosome typical of standard t(9;22)(q34;q11), and fluorescence in situ hybridization studies confirmed the involvement of a chromosome 10 in the masked Ph formation and also the presence of 3' ABL-DNA sequences in the der(22). This complex rearrangement could be explained by two consecutive translocations: the first, a standard t(9;22) (q34;q11), the second, a translocation between a chromosome 10 and the der(22) with a breakpoint in sequences derived from chromosome 9 telomeric to the ABL gene. By reverse transcription polymerase chain reaction (RT-PCR), we studied the BCR/ABL transcript junction: a chimeric m-RNA b3-a2, indicating a breakpoint within the major breakpoint cluster region, was found.