Integration of molecular methods for detection of balanced translocations in the diagnosis and follow-up of patients with leukemia

Rapid detection of BCR-ABL fusion genes using a novel combined LUX primer, in-cell RT-PCR and flow cytometric method

Currently, quantitative and semiquantitative assays for minimal residual disease detection include fluorescence in situ hybridisation, multiparameter flow cytometric immunophenotyping and real-time quantitative polymerase chain reaction (RQ-PCR). We have developed a new approach to detect hybrid breakpoint cluster region and Abelson proto-oncogene (BCR-ABL) transcripts inside suspension cells using in situ RT-PCR and light upon extension (LUX) primer, followed by rapid quantitative analysis with flow cytometry. After cellular permeabilization and fixation of single cell suspension, the neoplastic mRNA was reverse transcribed and amplified by PCR with LUX primer. The results demonstrated that a strong positive yellow-green signal was observed in 99-100% cells of K562 cell line, only the red nucleus was detected in NB4 cell line and normal controls. The technique has been utilised to study 12 patients with chronic myeloid leukemia, and the results were compared with those of BCR-ABL fusion mRNA by RT-PCR and BCR-ABL fusion gene of the interphase cells by fluorescence in situ hybridization (FISH). In the five diagnosed patients, 90-98% cells were strongly positive. Four patients, including three patients treated with interferon-alpha and hydroxyurea and one patient treated with imatinib mesylate, had 26-82.5% positive cells. Three patients treated with imatinib mesylate were negative. The in situ RT-PCR results demonstrated complete concordance with the results of I-FISH and RT-PCR. A fluorescence signal was detectable at 1/10(4) cells and became negative below this threshold with flow cytometry. The results of the present study suggest that (1) LUX primers can be used to efficiently detect BCR-ABL fusion mRNA by in-cell RT-PCR; (2) the novel technique is a specific and sensitive way of detecting fusion gene with potential clinical usefulness.

Prevalence estimates of recurrent balanced cytogenetic aberrations and gene fusions in unselected patients with neoplastic disorders

Chromosome abnormalities have been reported in more than 46,000 benign and malignant neoplastic disorders, leading to the identification of numerous recurrent abnormalities. A substantial number of recurrent balanced aberrations (RBAs), in particular, reciprocal translocations, occur with remarkable specificity in association with clinical and tumor characteristics. This information has become increasingly important both in basic cancer research, as a means to identify pathogenetically important genes, and clinically, as a diagnostic and prognostic instrument. Knowledge of the frequencies of such aberrations thus is of theoretical as well as practical value. However, it is unknown to what extent the data available in the literature reflect reality. A large proportion of the published cases, at least 40%, are biased, in the sense that they were reported because of a specific or unusual karyotypic feature. We have systematically ascertained all RBAs and present data on the frequencies of these abnormalities and their molecular genetic consequences among unselected patients, that is, those studied as part of investigations of consecutive series of individuals with a particular neoplastic disorder. The salient features of the present study are: (1) published data clearly overestimate the prevalence of individual RBAs in most tumor types as well as the proportion of patients having such aberrations. In fact, several well-known published RBAs are not recurrent or have not even been seen among unselected patients, and in no tumor entity, except for chronic myeloid leukemia, does the frequency of unselected cytogenetically abnormal neoplasms with RBAs exceed 35%; (2) the proportions of unselected cases characterized by RBAs among those tumor entities in which at least one RBA has been identified vary considerably both within and among hematologic malignancies, malignant lymphomas, and solid tumors; and (3) the molecular consequences of a substantial proportion, ranging from 19% in hematologic malignancies to 65% in epithelial tumors, of the most common RBAs in unselected patients remain to be clarified.

A real-time quantitative RT-PCR assay for monitoring DEK-CAN fusion transcripts arising from translocation t(6;9) in acute myeloid leukemia

We have developed a real-time quantitative RT-PCR (RQ-PCR) assay for the DEK-CAN fusion transcript, which results from t(6;9)(p23;q34) and is found in about 1% of acute myeloid leukemia (AML) cases. In diagnostic samples from three acute myeloid leukemia patients an RQ-PCR assay sensitivity of 1:396-1:3446 was obtained. In a single patient followed closely for 57 weeks, an increasing DEK-CAN level was detected 40 days before an early hematological relapse. This assay should enable the widespread longitudinal minimal residual disease (MRD) follow-up in this rare subgroup of AML patients, thus adding to our knowledge of its course.

[Application of molecular biology techniques to malignant haematology]

Malignant hemopathies, although heterogeneous in their prognosis and oncogenesis, represent an interesting model for studying cancer genesis mechanisms in man through the recurrent presence of genetic abnormalities involved in oncogenesis and the availability of tumour material. Nowadays, molecular biology techniques are very much used for the diagnosis, the treatment and the follow-up of these diseases. Firstly used for research, the new techniques have completely changed our ability to characterise malignant hemopathies and to understand the cancer-inducing processes, permitting us to perform the biological assessment of patients with malignant hemopathies, the diagnosis, and to estimate and follow the outcome of patients after treatment. At a more fundamental level, the structural and functional analysis of the deregulated genes implied in leukaemia and lymphoma has improved our knowledge and understanding of oncogenic and physiologic mechanisms significantly.

Core binding factor (CBF) acute myeloid leukemia: is molecular monitoring by RT-PCR useful clinically?

Clonal chromosomal abnormalities are the most important prognostic indicators in acute myeloid leukemia (AML). Two of the most prevalent cytogenetic subtypes of adult primary AML, t(8;21)(q22;q22) and inv(16)(p13q22)/t(16;16)(p13;q22), are characterized by disruption of the AML1(CBFA2, RUNX1) and CBFbeta genes, respectively, which encode subunits of core binding factor (CBF), a regulator of normal hematopoiesis. At the molecular level, t(8;21) and inv(16)/t(16;16) result in the creation of novel fusion genes, AML1/ETO and CBFbeta/MYH11, respectively, which encode fusion transcripts readily detectable by the reverse transcription-polymerase chain reaction (RT-PCR). Although the detection of t(8;21) or inv(16)/t(16;16) in adult patients with primary AML represents a favorable independent prognostic indicator for achievement of cure following intensive chemotherapy or stem cell transplantation, a substantial number of these patients (i.e. 40-50%) relapse and eventually die of their disease. Therefore, timely identification and therapeutic stratification of those patients deemed at high risk for disease relapse could ultimately result in a further improvement of clinical outcome within these cytogenetic subgroups of AML. As relapse is likely to occur as the result of failure of treatment to completely eradicate leukemic blasts, the detection of the AML1/ETO and CBFbeta/MYH11 fusion transcripts using sensitive RT-PCR assays has been utilized as a surrogate marker for resistant disease and, in turn, to predict disease recurrence during remission. The purpose of this paper is to review the applicability of this strategy to the clinical management of t(8;21) and inv(16)/t(16;16) primary AML, here collectively referred to as CBF AML.

Molecular biology of leukemia

OBJECTIVE

To review the current tests for diagnosis and the implications of cytogenetic analysis in leukemia.

DATA SOURCES

Professional journals, books.

CONCLUSION

Leukemia is a genetic disorder with more than 500 recurring translocations. Recurrent chromosomal changes occur in more than one half of all cases of leukemia. Testing includes bone marrow biopsy and aspirate, histochemical staining, immunophenotyping, cytogenetics, and molecular markers. Characterization of specific chromosome changes provides information in determining initial therapy and post-remission therapy.

IMPLICATIONS FOR NURSING PRACTICE

Nurses must continually educate themselves to stay current with developing technology and the results of continuing research. This professional education must then be translated to the bedside throughout the continuum of care.

Validation and clinical implication of a quantitative real-time PCR determination of MDR1 gene expression: comparison with semi-quantitative PCR in 101 patients with acute myeloid leukemia

INTRODUCTION

The multidrug resistance protein 1 (MDR1) has the capacity to extrude chemotherapeutics and has been implicated in treatment failure in acute myeloid leukemia (AML). Previous methods for determination of MDR1 expression have included dye exclusion, demonstration of P-glycoprotein by flow cytometry and/or immunohistochemistry, and molecular polymerase chain reaction (PCR)-based assays for RNA expression. However, these assays have either proven difficult to standardize or tedious to perform. We have therefore designed a real-time quantitative (RQ)-PCR based assay measuring MDR1 gene expression and validated it in AML patients by direct comparison with a competitive reverse transcriptase polymerase chain reaction (RT-PCR) assay.

PATIENTS AND METHODS

Bone marrow or peripheral blood from 101 AML patients diagnosed (1987-96) at our department were assessed for quantitative expression of MDR1 employing TaqMan RQ-PCR. These data were compared with results obtained by a semi-quantitative competitive PCR assay employing an artificial internal RNA construct.

RESULTS

While the RQ-PCR method was able to determine MDR1 gene expression in a continuous fashion over five logs, the semi-quantitative PCR only yielded data in a discontinuous fashion and over four logs at best. Compared with the MDR1 positive and negative cell lines 8226 DOX40 and REH AML cells exhibited variation of 10 PCR cycles, equivalent to a 1000-fold difference. A significant correlation was observed between the two methods, Spearman's correlation coefficient = -0.502, P-value = 10-5.

CONCLUSION

We conclude that, RQ-PCR is a novel methodology, which enables sensitive and quantitative measurement of MDR1 gene expression. This assay is moreover suitable because of its high throughput for longitudinal follow-up and large number of patients.

Rapid detection of leukemia-associated translocation fusion genes using a novel combined RT-PCR and flow cytometric method

Efficient detection of recurrent translocation-associated fusion genes is of critical importance for the diagnosis, prognosis and post-therapeutic monitoring of many leukemias. Typically, the presence of such translocations is revealed by RT-PCR technique, followed by Southern blot hybridization to ensure specificity of the PCR product. Though widely employed, post-PCR analysis of this type is relatively laborious and time-intensive. As a departure from standard analytic approaches, we have developed a robust novel method combining both high specificity and sensitivity, based on polystyrene bead capture of fluorescently labeled PCR products, with subsequent analysis by flow cytometry. Results from cell line and patient sample evaluations indicate that this method may be easily incorporated into the diagnostic molecular laboratory as a rapid and cost-effective alternative to currently employed techniques.