Assessment of the response to imatinib in chronic myeloid leukemia patients - comparison between the FISH, multiplex and RT-PCR methods

Detection of 22 common leukemic fusion genes using a single-step multiplex qRT-PCR-based assay

Background

Fusion genes generated from chromosomal translocation play an important role in hematological malignancies. Detection of fusion genes currently employ use of either conventional RT-PCR methods or fluorescent in situ hybridization (FISH), where both methods involve tedious methodologies and require prior characterization of chromosomal translocation events as determined by cytogenetic analysis. In this study, we describe a real-time quantitative reverse transcription PCR (qRT-PCR)-based multi-fusion gene screening method with the capacity to detect 22 fusion genes commonly found in leukemia. This method does not require pre-characterization of gene translocation events, thereby facilitating immediate diagnosis and therapeutic management.

Methods

We performed fluorescent qRT-PCR (F-qRT-PCR) using a commercially-available multi-fusion gene detection kit on a patient cohort of 345 individuals comprising 108 cases diagnosed with acute myeloid leukemia (AML) for initial evaluation; remaining patients within the cohort were assayed for confirmatory diagnosis. Results obtained by F-qRT-PCR were compared alongside patient analysis by cytogenetic characterization.

Results

Gene translocations detected by F-qRT-PCR in AML cases were diagnosed in 69.4% of the patient cohort, which was comparatively similar to 68.5% as diagnosed by cytogenetic analysis, thereby demonstrating 99.1% concordance. Overall gene fusion was detected in 53.7% of the overall patient population by F-qRT-PCR, 52.9% by cytogenetic prediction in leukemia, and 9.1% in non-leukemia patients by both methods. The overall concordance rate was calculated to be 99.0%. Fusion genes were detected by F-qRT-PCR in 97.3% of patients with CML, followed by 69.4% with AML, 33.3% with acute lymphoblastic leukemia (ALL), 9.1% with myelodysplastic syndromes (MDS), and 0% with chronic lymphocytic leukemia (CLL).

Conclusions

We describe the use of a F-qRT-PCR-based multi-fusion gene screening method as an efficient one-step diagnostic procedure as an effective alternative to lengthy conventional diagnostic procedures requiring both cytogenetic analysis followed by targeted quantitative reverse transcription (qRT-PCR) methods, thus allowing timely patient management.

Adherence to Monitoring Tests in Patients With Chronic Myeloid Leukemia in Lebanon

The present study was performed to determine whether the adherence to regular follow-up assessments using standardized real-time quantitative polymerase chain reaction (qPCR) and/or cytogenetic tests in Lebanese patients with chronic myeloid leukemia (CML) meet the European LeukemiaNet recommendations. The present study was a retrospective analysis of 34 patients diagnosed with chronic phase CML who had been treated with tyrosine kinase inhibitors and monitored with regular cytogenetic tests and/or measurement of the BCR-ABL transcript level at 3, 6, and 12 months from 2006 until 2015 in 3 university hospitals in Lebanon. All patients were included and monitored in an adherence program (SAWA program). The male/female ratio was 3:1. The median age was 50 years, and the mean age was 50 years. As frontline treatment, 29 patients started imatinib and 5 patients received second-generation tyrosine kinase inhibitors. We defined compliance to the monitoring tests as regulary realizing the qPCR at 3, 6, and 12 months. Of the 36 patients, 15 underwent the recommended tests at 3, 6, and 12 months, representing a compliance rate of 41.6%; 28 of the 34 patients underwent the recommended tests only twice in the first follow-up year. Only 14 patients underwent qPCR at 3 months. We believe that despite the inclusion of our patients in an adherence program, the compliance rate is still low. We also believe that greater effort is required to improve the adherence to regular follow-up examinations.

Multiplex RT-PCR Assay for Detection of Common Fusion Transcripts in Acute Lymphoblastic Leukemia and Chronic Myeloid Leukemia Cases

BACKGROUND

Acute lymphoblastic leukemia (ALL) is a heterogeneous disease which requires a risk-stratified approach for appropriate treatment. Specific chromosomal translocations within leukemic blasts are important prognostic factors that allow identification of relevant subgroups. In this study, we developed a multiplex RT-PCR assay for detection of the 4 most frequent translocations in ALL (BCR-ABL, TEL-AML1, MLL-AF4, and E2A- PBX1).

MATERIALS AND METHODS

A total of 214 diagnosed ALL samples from both adult and pediatric ALL and 14 cases of CML patients (154 bone marrow and 74 peripheral blood samples) were assessed for specific chromosomal translocations by cytogenetic and multiplex RT-PCR assays.

RESULTS

The results showed that 46 cases of ALL and CML (20.2%) contained the fusion transcripts. Within the positive ALL patients, the most prevalent cryptic translocation observed was mBCR-ABL (p190) at 8.41%. In addition, other genetic rearrangements detected by the multiplex PCR were 4.21% TEL-AML1 and 2.34% E2A-PBX1, whereas MLL-AF4 exhibited negative results in all tested samples. Moreover, MBCR-ABL was detected in all 14 CML samples. In 16 samples of normal karyotype ALL (n=9), ALL with no cytogentic result (n=4) and CML with no Philadelphia chromosome (n=3), fusion transcripts were detected.

CONCLUSIONS

Multiplex RT-PCR provides a rapid, simple and highly sensitive method to detect fusion transcripts for prognostic and risk stratification of ALL and CML patients.

Qualitative and quantitative evaluation of the BCR-ABL fusion gene in chronic myelogenous leukemia by flourescence in situ hybridization and molecular genetic methods

AIMS

Fluorescence in situ hybridization (FISH) and quantitative real-time polymerase chain reaction (QRT-PCR) were used to diagnose or screen for minimal residual disease (MRD) in Philadelphia (Ph) chromosome-positive leukemia. We compared the diagnostic utility of FISH and QRT-PCR at various time points in the course of chronic myelogenous leukemia (CML) and to determine the mean initial values for patients whose QRT-PCR results were not known at the time of diagnosis.

RESULTS

We analyzed 135 results for 78 CML patients tested by FISH and QRT-PCR for the Ph chromosomal translocation. All newly diagnosed cases were positive by both methods. On follow-up following treatment, 1 case was FISH positive and QRT-PCR negative; 61 cases were FISH negative and QRT-PCR positive. Overall concordance was 54.1%. There was good concordance between QRT-PCR results and cytogenetic response categories.

CONCLUSIONS

We confirmed that QRT-PCR allows precise measurement of low levels of BCR-ABL transcripts and can serve as a sensitive indicator of MRD. We also demonstrated 100% correlation between QRT-PCR and FISH in newly diagnosed CML.

Molecular monitoring of response to imatinib (Glivec) in chronic myeloid leukemia patients: experience at a tertiary care hospital in Saudi Arabia

AIM

The aim of this study was to evaluate the response and resistance of cases to chronic myeloid leukemia (CML) therapy with tyrosine kinase (TK) inhibitors (imatinib mesylate) and to search for mutations in the breakpoint cluster region (BCR)-Abelson murine leukemia (ABL) kinase domain prior to and during therapy.

METHODS

Molecular response was assessed with real-time quantitative reverse transcription-polymerase chain reaction and was expressed as the ratio between BCR-ABL and ABL (k562 cell line) x 100. In addition, we searched for mutations in BCR-ABL kinase domain by amplification and direct sequencing of cDNA products of archived RNA samples.

RESULTS

There were 85 cases of CML Philadelphia-chromosome-positive patients. Major molecular response [corrected] (MMR) of 0.05% was achieved in 40 (47%) of 85 patients and 3-log reduction was achieved in 37 (44%) after 6 months of imatinib therapy. When molecular monitoring was extended to 12 months in a subset of delayed responsive cases (17 cases) who did not achieve an MMR at 6 months, significant changes in BCR-ABL/ABL ratio were noticed. Fifteen de novo CML patients were started directly on treatment and were monitored for BCR-ABL/ABL ratio for a further period of up to 24 months. Their median of BCR-ABL/ABL ratio was 18% at diagnosis, 0.3% after 6 months, 0.2% after 12 months, and 0.01% after 18 and 24 months. Four (27%) of 15 patients achieved MMR as 3-log reduction after 6 months, 6 (40%) after 12 months, 9 (60%) after 18 months, and 7 (46%) after 24 months. No mutation(s) or polymorphism(s) were detected in all tested patients at diagnosis, at 6 months following imatinib and following 12 months for patients showing delayed response.

CONCLUSION

BCR-ABL mutations are rare in early chronic phase and increases with CML disease progression. Therefore, search for other causes in resistant cases at this phase should be sought.

Early intervention during imatinib therapy in patients with newly diagnosed chronic-phase chronic myeloid leukemia: a study of the Spanish PETHEMA group

BACKGROUND

Despite the favorable results of imatinib front line in chronic-phase chronic myeloid leukemia there is room for improvement.

DESIGN AND METHODS

Early intervention during imatinib therapy was undertaken in 210 adults with chronic-phase chronic myeloid leukemia less than three months from diagnosis (Sokal high risk: 16%). Patients received imatinib 400 mg/day. At three months, dose was increased if complete hematologic response was not achieved. At six months, patients in complete cytogenetic response were kept on 400 mg and the remainder randomized to higher imatinib dose or 400 mg plus interferon-alfa. At 18 months, randomized patients were switched to a 2(nd) generation tyrosine kinase inhibitor if not in complete cytogenetic response and imatinib dose increased in non-randomized patients not in major molecular response.

RESULTS

Seventy-two percent of patients started imatinib within one month from diagnosis. Median follow-up is 50.5 (range: 1.2-78) months. At three months 4 patients did not have complete hematologic response; at six months 73.8% were in complete cytogenetic response; among the remainder, 9 could not be randomized (toxicity or consent withdrawal), 17 were assigned to high imatinib dose, and 15 to 400 mg + interferon-alpha. The low number of randomized patients precluded comparison between the two arms. Cumulative response at three years was: complete hematologic response 98.6%, complete cytogenetic response 90% and major molecular response 82%. On an intention-to-treat basis, complete cytogenetic response was 78.8% at 18 months. At five years, survival was 97.5%, survival free from accelerated/blastic phase 94.3%, failure free survival 82.5%, and event free survival (including permanent imatinib discontinuation) 71.5%.

CONCLUSIONS

These results indicate the benefit of early intervention during imatinib therapy (ClinicalTrials.gov Identifier: NCT00390897).

Chronic myeloid leukemia: an update of concepts and management recommendations of European LeukemiaNet

PURPOSE

To review and update the European LeukemiaNet (ELN) recommendations for the management of chronic myeloid leukemia with imatinib and second-generation tyrosine kinase inhibitors (TKIs), including monitoring, response definition, and first- and second-line therapy.

METHODS

These recommendations are based on a critical and comprehensive review of the relevant papers up to February 2009 and the results of four consensus conferences held by the panel of experts appointed by ELN in 2008.

RESULTS

Cytogenetic monitoring was required at 3, 6, 12, and 18 months. Molecular monitoring was required every 3 months. On the basis of the degree and the timing of hematologic, cytogenetic, and molecular results, the response to first-line imatinib was defined as optimal, suboptimal, or failure, and the response to second-generation TKIs was defined as suboptimal or failure.

CONCLUSION

Initial treatment was confirmed as imatinib 400 mg daily. Imatinib should be continued indefinitely in optimal responders. Suboptimal responders may continue on imatinb, at the same or higher dose, or may be eligible for investigational therapy with second-generation TKIs. In instances of imatinib failure, second-generation TKIs are recommended, followed by allogeneic hematopoietic stem-cell transplantation only in instances of failure and, sometimes, suboptimal response, depending on transplantation risk.

Chronic myeloid leukemia: a prospective comparison of interphase fluorescence in situ hybridization and chromosome banding analysis for the definition of complete cytogenetic response: a study of the GIMEMA CML WP

In chronic myeloid leukemia, different methods are available to monitor the response to therapy: chromosome banding analysis (CBA), interphase fluorescence in situ hybridization (I-FISH), and real-time quantitative polymerase chain reaction (RT-Q-PCR). The GIMEMA CML WP (Gruppo Italiano Malattie Ematologiche Adulto Chronic Myeloid Leukemia Working Party) has performed a prospective study to compare CBA and I-FISH for the definition of complete cytogenetic response (CCgR). Samples (n = 664) were evaluated simultaneously by CBA and I-FISH. Of 537 cases in CCgR, the number of positive nuclei by I-FISH was less than 1% in 444 cases (82.7%). Of 451 cases with less than 1% positive nuclei by I-FISH, 444 (98.4%) were classified as CCgR by CBA. The major molecular response rate was significantly greater in cases with I-FISH less than 1% than in those with I-FISH 1% to 5% (66.8% vs 51.6%, P < .001) and in cases with CCgR and I-FISH less than 1% than in cases with CCgR and I-FISH 1% to 5% (66.1% vs 49.4%, P = .004). I-FISH is more sensitive than CBA and can be used to monitor CCgR. With appropriate probes, the cutoff value of I-FISH may be established at 1%. These trials are registered at http://www.clinicaltrials.gov as NCT00514488 and NCT00510926.

Comparison of imatinib 400 mg and 800 mg daily in the front-line treatment of high-risk, Philadelphia-positive chronic myeloid leukemia: a European LeukemiaNet Study

Imatinib mesylate (IM), 400 mg daily, is the standard treatment of Philadelphia-positive (Ph(+)) chronic myeloid leukemia (CML). Preclinical data and results of single-arm studies raised the suggestion that better results could be achieved with a higher dose. To investigate whether the systematic use of a higher dose of IM could lead to better results, 216 patients with Ph(+) CML at high risk (HR) according to the Sokal index were randomly assigned to receive IM 800 mg or 400 mg daily, as front-line therapy, for at least 1 year. The CCgR rate at 1 year was 64% and 58% for the high-dose arm and for the standard-dose arm, respectively (P = .435). No differences were detectable in the CgR at 3 and 6 months, in the molecular response rate at any time, as well as in the rate of other events. Twenty-four (94%) of 25 patients who could tolerate the full 800-mg dose achieved a CCgR, and only 4 (23%) of 17 patients who could tolerate less than 350 mg achieved a CCgR. This study does not support the extensive use of high-dose IM (800 mg daily) front-line in all CML HR patients. This trial was registered at www.clinicaltrials.gov as #NCT00514488.

Phenotypic and gene expression diversity of malignant cells in human blast crisis chronic myeloid leukemia

Chronic myeloid leukemia (CML) is considered as a paradigm of neoplasias developing through multistep track. It is believed that in the blast crisis (BC) terminal phase of the disease, blood-circulating blasts represent an expansion of a single CML clone. However, although these blasts grow mostly in suspension under standard culture conditions, a relatively small cell-fraction adheres to the plastic dish. Yet, it is unknown whether these two cell-fractions are distinct sub-populations that originated from a common CML clone and whether they have different biological and malignant properties. To address these questions, we have characterized the plastic-adherent and non-adherent sub-populations of various cell lines and primary cells derived from patients with CML in BC. This study indicated that the adherent-subsets retain repopulating ability with indications of increased malignant properties as greater anchorage-independent clonogenicity, impairment of cell-cell contact inhibition, loss of serum-dependent attenuation of plastic-adhesion, and a significant up-regulation of the oncogenes BCR-ABL, c-JUN, and c-FOS along with the adhesion-related genes KiSS-1, THBS3, and ITGB5. The adherent blasts stably retain their unique properties even after elimination of the adherence selection pressure. Sub-cloning analyses indicated that the adherent cells could be continuously evolved from any parental non-adherent clone in a unidirectional manner. This study provides new insights into the biology and the malignant evolution of CML, indicating that at the BC phase, circulating blasts are heterogeneous and consisting of at least two distinct populations of a common clonal origin. The existence of a minor "pool" of blasts of greater clonogenic capacity along with significantly higher expression level of BCR-ABL, individually or in conjunction with other cancer and adhesion-related genes, might also signify clonal evolution toward subsequent increased malignancy and lower therapeutic sensitivity.

Comparison of FISH and quantitative RT-PCR for the diagnosis and follow-up of BCR-ABL-positive leukemias

BACKGROUND

For Philadelphia chromosome positive (Ph+) leukemias (chronic myelogenous leukemia [CML], acute lymphoblastic leukemia [ALL], and rare other leukemias), both allogeneic transplantation and treatment with tyrosine kinase inhibitors offer chances of molecular remission (the molecular marker being consistently undetectable). Molecular remission is defined as a reduction in the quantification of BCR-ABL transcripts to an undetectable level by molecular diagnostic methods, and is considered as a surrogate marker for cure or long-term disease control. The molecular diagnostic methods including fluorescence in situ hybridization (FISH) and quantitative reverse transcription-polymerase chain reaction (QRT-PCR) are more sensitive than classical cytogenetic analysis for the detection of BCR-ABL positive cells. QRT-PCR, due to its superior sensitivity, is considered the gold standard for the follow-up of Ph+ leukemias treated with imatinib.

AIM

The objective of our study was to compare the diagnostic and clinical usefulness of FISH and QRT-PCR at different timepoints for Ph+ leukemias.

PATIENTS AND METHODS

We investigated 23 unselected patients with Ph+ CML (n = 21) or Ph+ ALL (n = 2) at 77 different timepoints in a comparative study with both FISH and QRT-PCR using commercially available reagents in a routine laboratory.

RESULTS

Our study demonstrated a good correlation of QRT-PCR with FISH in detecting the BCR-ABL fusion gene among patients with CML or ALL (coefficient of correlation = 0.77493, p < 0.0001, using Spearman's correlation procedure). All newly diagnosed or untreated cases were positive with both methods. Lower coefficients of correlation were found when FISH and QRT-PCR were correlated with the white blood cell count (WBC). An overall concordance of FISH and QRT-PCR (being either negative or positive in both tests) was found in 65 cases (84.4%) and a discrepancy identified in 12 cases (15.6%).

CONCLUSIONS

We confirm that QRT-PCR allows precise measurement of low levels of BCR-ABL transcripts and can serve as a sensitive indicator for minimal residual disease. In addition, we demonstrate in most cases a good correlation of QRT-PCR with FISH in detecting the BCR-ABL fusion gene among patients with CML or Ph+ ALL. FISH is not suitable for monitoring minimal residual disease.

Fluorescent in situ hybridization in the diagnosis, prognosis, and treatment monitoring of chronic myeloid leukemia

The unique molecular characteristic of chronic myeloid leukemia (CML), the disease-causing ABL (9q34) to BCR (22q11) translocation, has provided an invaluable tool for disease diagnosis and monitoring of treatment response. The traditional standard in this regard is bone marrow karyotype, also known as conventional cytogenetics (CC), which reveals a shortened chromosome 22, the Philadelphia chromosome, t(9;22)(q34;q11). CC in CML has also been effectively used for monitoring the response to drug therapy. However, this particular laboratory test misses submicroscopic BCR/ABL translocations and is suboptimal for minimal residual disease (MRD) assessment. Both fluorescence in situ hybridization (FISH) and reverse-transcriptase polymerase chain reaction (RT-PCR) feature higher sensitivity in terms of both diagnosis and MRD assessment in CML, compared to CC. Another advantage of these alternative tests is their effective applicability to peripheral blood specimens. The current review highlights the practical literature with respect to the use of FISH for CML whereas the use of RT-PCR has been extensively covered in recent communications.

Real-time reverse transcription PCR (qRT-PCR) and its potential use in clinical diagnosis

qRT-PCR (real-time reverse transcription-PCR) has become the benchmark for the detection and quantification of RNA targets and is being utilized increasingly in novel clinical diagnostic assays. Quantitative results obtained by this technology are not only more informative than qualitative data, but simplify assay standardization and quality management. qRT-PCR assays are most established for the detection of viral load and therapy monitoring, and the development of SARS (severe acute respiratory syndrome)-associated coronavirus qRT-PCR assays provide a textbook example of the value of this technology for clinical diagnostics. The widespread use of qRT-PCR assays for diagnosis and the detection of disease-specific prognostic markers in leukaemia patients provide further examples of their usefulness. Their value for the detection of disease-associated mRNA expressed by circulating tumour cells in patients with solid malignancies is far less apparent, and the clinical significance of results obtained from such tests remains unclear. This is because of conceptual reservations as well as technical limitations that can interfere with the diagnostic specificity of qRT-PCR assays. Therefore, although it is evident that qRT-PCR assay has become a useful and important technology in the clinical diagnostic laboratory, it must be used appropriately and it is essential to be aware of its limitations if it is to fulfil its potential.

Philadelphia-chromosome-positive T-lymphoblastic leukemia: acute leukemia or chronic myelogenous leukemia blastic crisis

The Ph1 chromosome has rarely been reported in T-lineage acute lymphoblastic leukemia (T-ALL), and the clinical relevance of this translocation in T-ALL is currently unknown. In chronic myelogenous leukemia (CML) some data indicate derivation of T-cells from the leukemic clone and only a few cases of T-derived blastic crisis have been reported and quite often disputed. Particularly in cases identified initially in blastic crisis it may be difficult to distinguish those from Ph1-positive T-ALL. We herein report 2 patients who presented with a clinical picture of Ph1-positive T-ALL and who raised a differential diagnosis from T-cell blastic crisis of CML. We review the literature and suggest clinical and laboratory features that can help in the diagnosis. According to our literature review, 23 cases of Ph1-positive T-ALL and 44 cases of T-cell blastic crisis of CML, including ours, were reported. Some major differences between the two entities could help in establishing a diagnosis of Ph1-positive T-cell blastic crisis of CML vs. Ph1-positive T-ALL: Male sex and younger age was more predominant in T-ALL. While in most cases of CML blastic crisis there was a history of CML there was no such history in the T-ALL cases. Medullary involvement with lymphoblastic leukemia was present in all cases of T-ALL but only in about half of the cases of CML blastic crisis. None of the CML-blastic crisis cases tested by RT-PCR showed the minor breakpoint transcript, while 2 cases with T-ALL had the minor breakpoint transcript and 1 had both transcripts. Combined morphologic and FISH analysis can help to distinguish between the two entities and was applied in one of our cases. Although both entities carry a severe prognosis, differentiating between them might have clinical relevance, especially in the imatinib era.

Chronic myeloid leukemia: current application of cytogenetics and molecular testing for diagnosis and treatment

Chronic myeloid leukemia provides an illustrative disease model for both molecular pathogenesis of cancer and rational drug therapy. Chronic myeloid leukemia is a clonal stem cell disease caused by an acquired somatic mutation that fuses, through chromosomal translocation, the abl and bcr genes on chromosomes 9 and 22, respectively. The bcr/abl gene product is an oncogenic protein that localizes to the cytoskeleton and displays an up-regulated tyrosine kinase activity that leads to the recruitment of downstream effectors of cell proliferation and cell survival and consequently cell transformation. Such molecular information on pathogenesis has facilitated accurate diagnosis, the development of pathogenesis-targeted drug therapy, and most recently the application of molecular techniques for monitoring minimal residual disease after successful therapy. These issues are discussed within the context of clinical practice.