Fluorescence in situ hybridization characterization of different cryptic BCR-ABL rearrangements in chronic myeloid leukemia

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).

Prognostic significance of a normal karyotype in adult patients with BCR-ABL1-positive acute lymphoblastic leukemia in the tyrosine kinase inhibitor era

OBJECTIVE

The occurrence of cryptic Philadelphia (Ph) chromosome translocation is rare in BCR-ABL1-positive acute lymphoblastic leukemia (BCR-ABL1+ ALL) and is of unknown significance in the tyrosine kinase inhibitor (TKI) era.

METHODS

We retrospectively studied a series of adult patients receiving TKI-based therapy to evaluate the prognostic impact of the normal karyotype (NK) (n=22) in BCR-ABL1+ ALL by comparison with the isolated Ph+ karyotype (n=54).

RESULTS

There were no statistically significant differences in clinical characteristics and complete remission rate between the two groups. Compared with the isolated Ph+ group, the NK/BCR-ABL1+ group had a higher relapse rate (55.0% versus 29.4%, p=0.044). Overall survival (OS) and disease-free survival (DFS) were significantly shorter in the NK/BCR-ABL1+ group than in the isolated Ph+ group [median OS: 24.5 versus 48.6 (months), p=0.013; median DFS: 11.0 (months) versus undefined, p=0.008]. The five-year OS and DFS for patients with NK/BCR-ABL1+ were 19.2% and 14.5%, respectively; those for patients with isolated Ph+ were 49.5% and 55.7%, respectively. Thirty-four (44.7%) patients underwent allogeneic hematopoietic stem cell transplantation (allo-HSCT) in this study. Among the patients who received allo-HSCT, the median OS and DFS in the NK/BCR-ABL+ group (n=9) were 35.5 and 27.5 months, respectively, while those in the isolated Ph+ group (n=25) were undefined. There was a trend of significant statistical difference in the OS between the two subgroups (p=0.066), but no significant difference in the DFS. Multivariate analysis revealed that NK was independently associated with worse OS and DFS in BCR-ABL1+ ALL patients [Hazard ratio (HR) 2.256 (95% confidence interval (CI), 1.005-5.066), p=0.049; HR 2.711 (95% CI, 1.319-5.573), p=0.007].

CONCLUSION

Our results suggest that the sub-classification of an NK could be applied in the prognostic assessments of BCR-ABL1+ ALL. In addition, allo-HSCT should be actively performed to improve prognosis in these patients.

Cryptic BCR-ABL fusion gene as variant rearrangement in chronic myeloid leukemia: molecular cytogenetic characterization and influence on TKIs therapy

At diagnosis, about 5% of Chronic Myeloid Leukemia (CML) patients lacks Philadelphia chromosome (Ph), despite the presence of the BCR/ABL rearrangement. Two mechanisms have been proposed about the occurrence of this rearrangement: the first one is a cryptic insertion between chromosomes 9 and 22; the second one involves two sequential translocations: a classic t(9;22) followed by a reverse translocation, which reconstitutes the normal morphology of the partner chromosomes. Out of 398 newly diagnosed CML patients, we selected 12 Ph-negative cases. Six Ph-negative patients treated with tyrosine kinase inhibitors (TKIs) were characterized, in order to study the mechanisms leading to the rearrangement and the eventual correlation with prognosis in treatment with TKIs. FISH analysis revealed cryptic insertion in 5 patients and classic translocation in the last one. In more detail, we observed 4 different patterns of rearrangement, suggesting high genetic heterogeneity of these patients. In our cases, the BCR/ABL rearrangement mapped more frequently on 9q34 region than on 22q11 region, in contrast to previous reports. Four patients, with low Sokal risk, achieved Complete Cytogenetic Response and/or Major Molecular Response after TKIs therapy. Therapy resistance was observed in one patient with duplication of BCR/ABL rearrangement and in another one with high risk. Even if the number patient is inevitably low, we can confirm that the rare Ph-negative CML patients do not constitute a “warning” category, meanwhile the presence of further cytogenetic abnormalities remains an adverse prognostic factor even in TKI era.

Diagnostic and prognostic cytogenetics of chronic myeloid leukaemia: an update

INTRODUCTION

Despite the advent of molecular assessment, banding cytogenetics and fluorescence in situ hybridization (FISH) still have a significant role in diagnostic and prognostic approaches to chronic myeloid leukaemia (CML). Area covered: At diagnosis and during treatment with tyrosine kinase inhibitors (TKIs), cytogenetics is used to detect the Philadelphia chromosome, with its typical translocation t(9;22)(q34;q11.2), and any additional or other chromosomal aberrations (ACAs and OCAs) that may arise in 5-10% of cases, the latter associated to transformation of the disease in blast phases. In this review, the potential role of banding cytogenetics and FISH is discussed through a review of published papers on the prognostic impact of these tools in CML treatment and monitoring. Expert commentary: Cytogenetic techniques, including banding cytogenetics and FISH, continue to maintain a crucial role in CML monitoring. At diagnosis and after 3 months of therapy, banding cytogenetics will continue to be an essential test to perform, but it will become redundant after the achievement of a major molecular response (MMR) assessed with molecular techniques. FISH analysis maintains its usefulness in monitoring the response to TKIs only in special situations.

Comprehensive Molecular Analyses in a Case of Masked Philadelphia Chronic Myeloid Leukemia

Here, we report the case of an 80-year-old woman with masked Philadelphia chronic myeloid leukemia (Ph CML). At diagnosis, qualitative PCR demonstrated the presence of a typical e14a2 configuration, and chromosome analysis showed an apparently normal female karyotype. However, FISH with BCR-ABL1 dual fusion probes gave a positive signal in 152/200 analyzed nuclei, with the fusion signal detected on the long arm of a cytogenetically normal chromosome 9. Using locus-specific probes for chromosome 9 and 22 telomeres, a third chromosome involvement was excluded. Furthermore, microarray analysis from the same specimens showed a normal result. Due to a high Charlson Comorbidity Index, the patient was treated with a reduced dose of imatinib, achieving a rapid hematological response after 1 month. However, after 6 months of imatinib therapy, she had to be considered as warning (Ph+ 26.5%, BCR-ABL1 >1%) according to the European LeukemiaNet 2013 recommendations. In conclusion, we confirmed the importance of a combination of cytogenetic and molecular techniques for the diagnosis and therapy monitoring of masked Ph CML, but, different from what has been reported in the literature so far, we cannot completely exclude the fact that the unusual cytogenetic pattern of this patient may have negatively influenced her response to tyrosine kinase inhibitor therapy.

Location of the BCR/ABL Fusion Genes on Both Chromosomes 9 in Ph Negative Young CML Patients: An Indian Experience

The BCR/ABL gene rearrangement is cytogenetically visualized in most chronic myeloid leukemia (CML) cases. About 5-10 % of CML patients lack its cytogenetic evidence, however, shows BCR/ABL fusion by molecular methods. We describe two CML patients with Philadelphia (Ph) negative (-ve) and BCR/ABL positive by fluorescence in situ hybridization (FISH). Both the cases were in chronic phase at diagnosis. Conventional cytogenetics and different FISH assays were adopted using BCR/ABL probes. Home-brew FISH assay using bacterial artificial clone (BAC) for BAC-CTA/bk 299D3 for chromosomal region 22q13.31-q13.32 was performed in case 1. Both the patients were Ph-ve. In first case, dual color dual fusion (DCDF)-FISH studies revealed 1 Red (R) 2 Green (G) 1 Fusion (F) signal pattern in 80 % of cells indicating BCR/ABL fusion signals on chromosomes 9 instead of Ph and 2G2F signal pattern in 20 % of cells indicating two BCR/ABL fusions on both chromosomes 9q34 on presentation. In second case, FISH studies revealed the 1R1G1F signal pattern indicating BCR/ABL fusion signals on chromosomes 9 instead of Ph in 100 % of cells at presentation. During follow-up, both the patients exhibited 2G2F signal pattern indicating two BCR/ABL fusions on both chromosomes 9q34, which indicated a clonal evolution in 100 % cells. Both the patients did not achieve therapeutic response. Relocation of BCR/ABL fusion sequence on sites other than 22q11 represents a rare type of variant Ph, the present study highlights the hot spots involved in CML pathogenesis and signifies their implications in Ph-ve BCR/ABL positive CML. This study demonstrated the genetic heterogeneity of this subgroup of CML and strongly emphasized the role of metaphase FISH, especially in Ph-ve CML cases, as it detects variations of the classical t(9;22).

Early landmark analysis of imatinib treatment in CML chronic phase: less than 10% BCR-ABL by FISH at 3 months associated with improved long-term clinical outcome

Imatinib has dramatically improved the clinical outcome in chronic myeloid leukemia, chronic phase (CMLcp), but a risk of resistance and serious disease progression still prevails. We have studied 45 newly diagnosed CMLcp patients initiated on imatinib, assessing treatment responses by interphase extral signal (ES)-fluorescence in situ hybridization (FISH), quantitative real-time (q-RT) polymerase chain reaction (PCR), and chromosome banding analysis. In a landmark analysis, an early favorable response, defined as less than 10% BCR-ABL-positive cells by FISH after 3 months of treatment, was identified as a predictive marker of an improved long-term clinical outcome. Of evaluable patients, 51% achieved this response. A large majority, 95% of such responders reached complete cytogenetic responses (CCyR) within 12 months and 100% event-free survival (EFS) at 48 months, when compared with 67 and 65%, respectively, of patients with higher breakpoint cluster region - Abelson (BCR-ABL) positivity at 3 months (P = 0.04; P = 0.006). No similar, significant correlations were noted between early disease assessments with PCR of BCR-ABL mRNA transcripts or of cytogenetics versus a 12-month CCyR or long-term EFS. Our data, based on a limited patient cohort, indicate that (i) FISH can effectively be used in the early assessment of remaining Ph-positive cells to identify patients at risk for a long-term nonoptimal response to imatinib and that (ii) FISH may be more useful than PCR for this purpose.

Molecular cytogenetic characterization of Philadelphia-negative rearrangements in chronic myeloid leukemia patients

BACKGROUND

The BCR/ABL gene rearrangement is generated by a reciprocal translocation t(9;22)(q34;q11) in chronic myeloid leukemia (CML) patients. In most cases, it is cytogenetically visualized by the Philadelphia (Ph) chromosome. About 5-10% of CML patients lack cytogenetic evidence of the Ph translocation but show BCR/ABL fusion by fluorescence in situ hybridization (FISH) or reverse transcriptase-polymerase chain reaction (RT-PCR). Deletions around the breakpoints on derivative chromosome 9 including 5'ABL and 3'BCR sequences occur in 10-15% of Ph-positive CML patients and are thought to have prognostic significance.

METHODS

We explored cryptic rearrangements involving chromosomes 9 and 22 in 3 CML patients with an apparently normal bone marrow karyotypes using multiplex RT-PCR and FISH with commercial and home-brew probes.

RESULTS

The BCR/ABL fusion transcripts were detected by RT-PCR. Using commercial FISH probes, the BCR/ABL fusion gene was found on chromosome 22 in two patients and on chromosome 9 in one patient. Consecutive FISH assays clarified the mechanism of the masked Ph chromosome: in the 3 patients, Ph rearrangement resulted from double mechanism consisting in standard translocation t(9;22)(q34;q11) followed by a second reversed translocation t(9;22)(q34;q11). One patient achieved major cytogenetic response after 6 months of imatinib therapy, and one patient had successful bone marrow transplant.

CONCLUSIONS

In this study, we have characterized three Ph-negative CML patients with cryptic BCR/ABL rearrangement generated after an uncommon mechanism involving two sequential translocations and confirm that the BCR/ABL hybrid gene may be located on other sites than 22q11. Ph-negative CML patients with BCR/ABL fusion gene have the same prognosis as patients with classical t(9;22).

Non random distribution of genomic features in breakpoint regions involved in chronic myeloid leukemia cases with variant t(9;22) or additional chromosomal rearrangements

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.

Evolutionarily conserved cytogenetic changes in hematological malignancies of dogs and humans--man and his best friend share more than companionship

The pathophysiological similarities shared by many forms of human and canine disease, combined with the sophisticated genomic resources now available for the dog, have placed 'man's best friend' in a position of high visibility as a model system for a variety of biomedical concerns, including cancer. The importance of nonrandom cytogenetic abnormalities in human leukemia and lymphoma was recognized over 40 years ago, but the mechanisms of genome reorganization remain incompletely understood. The development of molecular cytogenetics, using fluorescence in situ hybridization (FISH) technology, has played a significant role in our understanding of cancer biology by providing a means for 'interrogating' tumor cells for a variety of gross genetic changes in the form of either numerical or structural chromosome aberrations. Here, we have identified cytogenetic abnormalities in naturally occurring canine hematopoietic tumors that are evolutionarily conserved compared with those that are considered characteristic of the corresponding human condition. These data suggest that humans and dogs share an ancestrally retained pathogenetic basis for cancer and that cytogenetic evaluation of canine tumors may provide greater insight into the biology of tumorigenesis.

Molecular cytogenetic characterization of deletions on der(9) in chronic myelocytic leukemia

The t(9;22)(q34;q11), generating the Philadelphia chromosome, is found in more than 90% of patients with chronic myelocytic leukemia (CML). Deletions adjacent to the translocation breakpoint on the derivative chromosome 9 have been described by several groups. These studies revealed two primary points: (1) genomic microdeletions were concomitant with the t(9;22) rearrangement; and (2) the location of the deleted sequence was centromeric to ABL and telomeric to BCR genes. We report on a detailed molecular cytogenetic characterization of chromosomal rearrangements in two CML patients bearing a complex variant t(9;22) and insertions of chromosome 22 sequences in 9q34. Our study shows that the location of the deleted sequences was downstream of the ABL gene and that genomic microdeletions were concomitant with the ins(9;22)(q34;q11q11) rearrangement.