A novel tricolor, dual-fusion fluorescence in situ hybridization method to detect BCR/ABL fusion in cells with t(9;22)(q34;q11.2) associated with deletion of DNA on the derivative chromosome 9 in chronic myelocytic leukemia

Fluorescence in situ hybridization (FISH): an increasingly demanded tool for biomarker research and personalized medicine

Extensive studies of the genetic aberrations related to human diseases conducted over the last two decades have identified recurrent genomic abnormalities as potential driving factors underlying a variety of cancers. Over the time, a series of cutting-edge high-throughput genetic tests, such as microarrays and next-generation sequencing, have been developed and incorporated into routine clinical practice. Although it is a classical low-throughput cytogenetic test, fluorescence in situ hybridization (FISH) does not show signs of fading; on the contrary, it plays an increasingly important role in detecting specific biomarkers in solid and hematologic neoplasms and has therefore become an indispensable part of the rapidly developing field of personalized medicine. In this article, we have summarized the recent advances in FISH application for both de novo discovery and routine detection of chromosomal rearrangements, amplifications, and deletions that are associated with the pathogenesis of various hematopoietic and non-hematopoietic malignancies. In addition, we have reviewed the recent developments in FISH methodology as well.

The role of FISH in hematologic cancer

SUMMARY Cytogenetic analysis is now considered a mandatory investigation in the diagnostic work-up of hematologic malignancies. Recurring structural aberrations serve as powerful markers not only for diagnosis and prognosis of these conditions, but also guide the selection of targeted drugs for personalized oncology. The FISH approach is established as an indispensable tool to complement conventional cytogenetics, in addition to basic and clinical research applications. FISH is used to identify specific chromosomal aberrations through the detection of target DNA sequences by fluorescently labeled DNA probes. Multicolor FISH analysis allows the accurate identification of recurring translocations in neoplastic cells by means of genomic probes that flank the breakpoints. This review summarizes the panel of FISH probes for selection and the current utilization of these FISH techniques in unraveling chromosomal aberrations. The niche of FISH analysis is also highlighted. Variant signal patterns of the clinically useful FISH probes for hematologic oncology illustrated here provide useful interpretative reference for molecular pathology laboratories. In addition, the recent application of FISH tests in contributing information on drug targets at the genomic level to support personalized oncology will also be discussed.

Arginine deprivation, autophagy, apoptosis (AAA) for the treatment of melanoma

The majority of melanoma cells do not express argininosuccinate synthetase (ASS), and hence cannot synthesize arginine from citrulline. Their growth and proliferation depend on exogenous supply of arginine. Arginine degradation using arginine deiminase (ADI) leads to growth inhibition and eventually cell death while normal cell which express ASS can survive. This notion has been translated into clinical trial. Pegylated ADI (ADI-PEG20) has shown antitumor activity in melanoma. However, the sensitivity to ADI is different among ASS(-) melanoma cells. We have investigated and reviewed the signaling pathways which are affected by arginine deprivation and their consequences which lead to cell death. We have found that arginine deprivation inhibits mTOR signaling but leads to activation of MEK and ERK with no changes in BRAF. These changes most likely lead to autophagy, a possible mechanism to survive by recycling intracellular arginine. However apoptosis does occur which can be both caspase dependent or independent In order to increase the therapeutic efficacy of this form of treatment, one should consider adding other agent(s) which can drive the cells toward apoptosis or inhibit the autophagic process.

Application of tri-colour, dual fusion fluorescence in situ hybridization (FISH) system for the characterization of BCR-ABL1 fusion in chronic myelogenous leukaemia (CML) and residual disease monitoring

Background

We studied the application of the BCR-ABL1 + 9q34 tri-colour dual fusion fluorescence in situ hybridization (FISH) system in the characterization of fusion signal pattern and the monitoring of residual disease in chronic myelogenous leukaemia (CML). The signal constellation on metaphases with the tri-colour dual fusion system was defined. The knowledge of various signal patterns obtained from the different genetic rearrangements was further applied to the analysis of hybridization signals on interphase nuclei.

Methods

BCR-ABL1 dual colour, dual fusion FISH (D-FISH) was performed on diagnostic samples of 22 CML patients. The tri-colour FISH system was performed on cases that showed aberrant signal patterns other than the classical 1 green (G) 1 orange (O) 2 fusions (F). Using the aqua band-pass filter, random signal overlap in interphase nuclei would be indicated by the presence of an aqua signal (ASS1), while genuine fusion was represented by the absence of the ASS1 signal.

Results

Using the D-FISH system, the signal patterns could be categorized into 4 groups: group 1 (n = 17) showed the classical 1G1O2F; group 2 (n = 2) showed 2G1O1F indicating ABL1 deletion; group 3 (n = 1) showed 1G2O1F indicating BCR deletion; group 4 (n = 2) with 1G1O1F indicating reciprocal ABL1-BCR deletion. The tri-colour dual fusion system correlated with the D-FISH system for cases with der(9) deletion. The added aqua-labelled ASS1 probe was useful in differentiating random signal overlap from genuine BCR-ABL1 fusion in the interphase cells (group 4).

Conclusion

Although the D-FISH probe was valuable in establishing the different patterns of aberrant signals and monitoring patients with the classic 2-fusion signals in CML, the tri-colour dual fusion probe should be used for patients with der(9) deletion to monitor response to treatment.

Automated Duet spot counting system and manual technologist scoring using dual-fusion fluorescence in situ hybridization (D-FISH) strategy: comparison and application to FISH minimal residual disease testing in patients with chronic myeloid leukemia

The automated BioView Duet system was compared with manual technologist scoring (MTS) using a BCR/ABL dual-fusion FISH (D-FISH) probe strategy for chronic myeloid leukemia (CML) specimens. In the first study, 500 nuclei were evaluated for 10 distinct signal patterns in various abnormal cell percentages from each of 89 specimens. The Duet system correctly identified all 27 normal specimens and the abnormal signal pattern of all 63 abnormal specimens. The percentage of abnormal nuclei detected was also concordant, with an average difference between MTS and the Duet system of only 2.7%. However, achievement of accurate quantitative results required reclassification by a technologist for nearly 50% of nuclei per specimen. Next, the Duet system was used to evaluate BCR/ABL D-FISH for FISH minimal residual disease (MRD) detection in CML patients. Up to 6,000 nuclei were evaluated for four signal pattern categories for each of 60 CML MRD samples. Excluding four abnormal specimens with insufficient samples, the Duet system correctly identified all of the abnormal specimens and identified four additional abnormal specimens previously diagnosed as normal by MTS. The technologist time required for evaluation and reclassification of the Duet system data for the FISH MRD samples averaged only 1 minute per case, saving significant technologist effort. We conclude that the Duet system appears to be more sensitive and cost-effective than MTS for CML FISH MRD testing.

Development of a D-FISH method to detect DEK/CAN fusion resulting from t(6;9)(p23;q34) in patients with acute myelogenous leukemia

The t(6;9)(p23;q34)-DEK/CAN fusion occurs with an incidence of 1-5% in adult patients with acute myelogenous leukemia (AML) and tends to have an unfavorable prognosis at diagnosis. Due to the subtle appearance of this chromosome rearrangement, both initial detection and minimal residual disease (MRD) tracking by conventional karyotyping can be difficult. Unfortunately, no commercial or previously published fluorescence in situ hybridization (FISH) strategies exist for this recurrent anomaly. We have developed a highly sensitive assay using dual-color, double-fusion FISH (D-FISH), which can be used both for initial detection and MRD monitoring. We analyzed archived bone marrow samples from 15 patients with a previously identified t(6;9)(p23;q34) and 10 corresponding post-treatment samples. The results demonstrate that our D-FISH method effectively identified all abnormal samples, including a low-level MRD sample that was considered to be normal by conventional cytogenetic analysis. Normal value ranges were established from 30 negative controls to be < 0.6% when 500 interphase nuclei were analyzed. The development of this sensitive D-FISH strategy for the detection of the t(6;9)(p23;q34) adds to the AML FISH testing repertoire, and is effective in the detection of low-level disease in post-treatment samples in these patients.

Interphase FISH to detect PBX1/E2A fusion resulting from the der(19)t(1;19)(q23;p13.3) or t(1;19)(q23;p13.3) in paediatric patients with acute lymphoblastic leukaemia

Approximately 6% of paediatric patients with precursor B-cell acute lymphoblastic leukaemia (B-ALL) harbour a rearrangement involving the gene regions of PBX1 (1q23) and E2A (19p13.3) which is visualized cytogenetically either as a der(19)t(1;19)(q23;p13.3) or the less common balanced t(1;19)(q23;p13.3). Unfortunately, no commercial dual-colour, double fusion fluorescence in situ hybridization (D-FISH) strategies are available to detect this recurrent anomaly. Therefore, we have created a D-FISH assay to detect these translocations and monitor minimal residual disease. This probe set was created using four bacterial artificial chromosomes (BACs) corresponding to the PBX1 gene region at 1q23 and four BACs corresponding to the E2A gene region at 19p13.3. We analysed 30 negative bone marrow controls and 20 diagnostic and post-treatment specimens from 13 paediatric B-ALL patients with a cytogenetically defined 1;19 translocation. Once unblinded, the results demonstrated that our D-FISH method effectively identified all diagnostic samples as abnormal and identified disease in four post-treatment samples that were previously considered to be normal by conventional cytogenetic analysis. The development of this FISH strategy for the detection of der(19)t(1;19)(q23;p13.3) and t(1;19)(q23;p13.3) proved to be an effective technique, allowing both the detection of disease in diagnostic samples and in post-treatment samples.

Fluorescent-labeled DNA probes applied to novel biological aspects of B-cell chronic lymphocytic leukemia

Fluorescent-labeled DNA probes were used to study 52 chronic lymphocytic leukemia (B-CLL) patients for (1) disease progression, (2) angiogenesis genes, (3) T-cell leukemia 1 gene (TCL1), (4) immunoglobulin heavy chain variable region (IGHv) and (5) chromosome 6q. Compared to stable disease, more patients with progressive disease had > or =2 anomalies and a high percentage of neoplastic nuclei. Anomalies of genes for basic fibroblast growth factor, interleukin 4, vascular endothelial growth factor or TCL1 were not detected. Deletions in IGHv occurred in 25% of patients and correlated with IGHv gene expression. Probes for 6q23 detected more deletions in 6q than probes for 6q21.

Monitoring minimal residual disease in BCR-ABL-positive chronic myeloid leukemia in the imatinib era

PURPOSE OF REVIEW

The total number of leukemia cells in the body is reduced very substantially in patients with BCR-ABL-positive chronic myeloid leukemia (CML) responding to imatinib. This reduction is seen first as restoration of Ph negativity in blood and marrow and thereafter as decreasing BCR-ABL transcript levels assayed by quantitative polymerase chain reaction (PCR). Most patients with newly diagnosed chronic-phase CML who receive imatinib achieve complete cytogenetic remission (CCYR) and low levels of BCR-ABL transcripts, a status that seems to predict for relatively long survival compared with previous treatments.

RECENT FINDINGS

Patients treated with 400 mg daily who achieved a reduction in BCR-ABL transcript numbers equal or greater than 3 logs compared with a baseline value have a significantly better progression-free survival than those who achieved lesser degrees of response. The presence of Ph-positive subclones with point mutations in the ABL kinase domain correlates with "acquired" resistance to imatinib and some mutations are associated with greater resistance than others. Preliminary evidence suggests that P-loop mutations are especially likely to be associated with progression to advanced-phase disease.

SUMMARY

Patients with CML should be monitored routinely by serial cytogenetic analysis of bone marrow until Ph negativity is achieved. Thereafter serial quantitative-PCR studies should be undertaken at approximately 3-month intervals and probably also bone marrow cytogenetic studies at longer intervals. Routine studies for ABL kinase domain mutations may also be advisable. The observation of increasing quantities of residual leukemia or expansion of a mutated clone suggests the need to modify therapy.