Use of denaturing HPLC for detection of mutations in the BCR-ABL kinase domain in patients resistant to Imatinib

Chronic Myeloid Leukemia--Prognostic Value of Mutations

Chronic myeloid leukemia (CML) is a stem cell disorder characterized by unrestricted proliferation of the myeloid series that occurs due to the BCR-ABL fusion oncogene as a result of reciprocal translocation t(9;22) (q34;q11). This discovery has made this particular domain a target for future efforts to cure CML. Imatinib revolutionized the treatment options for CML and gave encouraging results both in case of safety as well as tolerability profile as compared to agents such as hydroxyurea or busulfan given before Imatinib. However, about 2-4% of patients show resistance and mutations have been found to be one of the reasons for its development. European Leukemianet gives recommendations for BCR-ABL mutational analysis along with other tyrosine kinase inhibitors (TKIs) that should be administered according to the mutations harbored in a patient. The following overview gives recommendations for monitoring patients on the basis of their mutational status.

Advances in treatment of chronic myeloid leukemia with tyrosine kinase inhibitors: the evolving role of Bcr–Abl mutations and mutational analysis

Over the last decade, the treatment of chronic myeloid leukemia has progressed tremendously. The first-generation tyrosine kinase inhibitor imatinib is now flanked by two second-generation molecules, dasatinib and nilotinib – and others are in advanced clinical development. One of the reasons for such intensive research on novel compounds is the problem of resistance, that is thought to be caused, in a proportion of cases, by point mutations in Bcr–Abl. In this article, the authors review how the biological and clinical relevance of Bcr–Abl mutations has evolved in parallel with the availability of more and more therapeutic options. The authors also discuss the practical relevance of Bcr–Abl mutation analysis and how this tool should best be integrated in the optimal clinical management of chronic myeloid leukemia patients.

BCR-ABL1 kinase domain mutations: methodology and clinical evaluation

The introduction of tyrosine kinase inhibitors (TKIs), starting with imatinib and followed by second and third generation TKIs, has significantly changed the clinical management of patients with chronic myeloid leukemia (CML). Despite their unprecedented clinical success, a proportion of patients fail to achieve complete cytogenetic remission by 12 months of treatment (primary resistance) while others experience progressive resistance after an initial response (secondary resistance). BCR-ABL1 kinase domain (KD) mutations have been detected in a proportion of patients at the time of treatment failure, and therefore their identification and monitoring plays an important role in therapeutic decisions particularly when switching TKIs. When monitoring KD mutations in a clinical laboratory, the choice of method should take into account turnaround time, cost, sensitivity, specificity, and ability to accurately quantify the size of the mutant clone. In this article, we describe in a "manual" style the methods most widely used in our laboratory to monitor KD mutations in patients with CML including direct sequencing, D-HPLC, and pyrosequencing. Advantages, disadvantages, interpretation of results, and their clinical applications are reviewed for each method.

The myeloproliferative neoplasms including the eosinophilia-related myeloproliferations associated with tyrosine kinase mutations: changes and issues in classification and diagnosis criteria

The classification and diagnostic criteria of the myeloproliferative neoplasms have changed significantly in the 2008 World Health Organization monograph on the classification of hematologic malignancies. Many of the changes arose from the findings that the different malignancies are associated with abnormal cell signaling because of translocations or mutations in genes for protein tryosine kinases involved in the normal growth and regulation of hematopoietic cells. These include ABL1, PDGFRA, PDGFRB, FGFR1, JAK2, MPL, and KIT. The new classification attempts to reflect the related molecular pathogenesis of the different entities and incorporates the identification of the molecular defects into the diagnostic criteria for some of the individual diseases. Issues concerning the new classification are discussed, and the new diagnostic criteria are reviewed and commented upon.

The role of molecular genetic analysis within the diagnostic haemato-oncology laboratory

The identification of the molecular genetic basis to many haematological malignancies along with the increased use of molecularly targeted therapy has heralded an increasing role for molecular genetic-based techniques. Demonstration of acquired changes such as the JAK2 V617F mutation within myeloproliferative neoplasms has quickly moved from a research setting to the diagnostic laboratory. Disease-specific genetic markers, such as the BCR-ABL1 fusion gene in chronic myeloid leukaemia, enable sensitive molecular genetic methods to be applied for the detection and quantification of low-level residual disease, allowing early identification of relapse. Consequently, molecular genetics now plays a crucial role in diagnosis, the identification of prognostic markers and monitoring of haematological malignancies. The development of high-throughput whole-genome approaches offers the potential to rapidly screen newly diagnosed patients for all disease-associated molecular genetic changes.

BCR-ABL kinase domain mutation analysis in chronic myeloid leukemia patients treated with tyrosine kinase inhibitors: recommendations from an expert panel on behalf of European LeukemiaNet

Mutations in the Bcr-Abl kinase domain may cause, or contribute to, resistance to tyrosine kinase inhibitors (TKIs) in chronic myeloid leukemia patients. Recommendations aimed to rationalize the use of BCR-ABL mutation testing in chronic myeloid leukemia have been compiled by a panel of experts appointed by the European LeukemiaNet (ELN) and European Treatment and Outcome Study and are here reported. Based on a critical review of the literature and, whenever necessary, on panelists' experience, key issues were identified and discussed concerning: (1) when to perform mutation analysis, (2) how to perform it, and (3) how to translate results into clinical practice. In chronic phase patients receiving imatinib first-line, mutation analysis is recommended only in case of failure or suboptimal response according to the ELN criteria. In imatinib-resistant patients receiving an alternative TKI, mutation analysis is recommended in case of hematologic or cytogenetic failure as provisionally defined by the ELN. The recommended methodology is direct sequencing, although it may be preceded by screening with other techniques, such as denaturing-high performance liquid chromatography. In all the cases outlined within this abstract, a positive result is an indication for therapeutic change. Some specific mutations weigh on TKI selection.

Prognostic Significance of Treatment Response in CML in View of Current Recommendations for Treatment and Monitoring

The use of small-molecule kinase inhibitors has redefined the management of cancer. Chronic myelogenous leukaemia (CML) has become the paradigm for targeted cancer treatment. Imatinib has become the gold standard in the treatment of CML with excellent and durable responses and minimal side effects. Molecular diagnostics constitute an integral part of the routine monitoring. Results of cytogenetic analysis and quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) indicate suboptimal response or treatment failure and guide treatment. New Abl kinase inhibitors such as nilotinib or dasatinib are options after the failure of or intolerance to imatinib, and both are available for first-line treatment of newly diagnosed CML. This review focuses on the prognostic significance of achieving a response at specific time points in patients with CML treated with imatinib, nilotinib or dasatinib in view of available data and current treatment recommendations.

Cause and management of therapy resistance

A minority of patients treated with imatinib are either refractory to imatinib or eventually relapse. Relapse frequently depends on re-emergence of BCR-ABL kinase activity but may also indicate BCR-ABL-independent disease progression. Over 90 point mutations coding for single amino acid substitutions in the BCR-ABL kinase domain have been isolated from CML patients resistant to imatinib treatment. These mutations affect amino acids involved in imatinib binding or in regulatory regions of the BCR-ABL kinase domain, resulting in decreased sensitivity to imatinib while retaining aberrant kinase activity. The early detection of BCR-ABL mutants during therapy may aid in risk stratification as well as molecular-based treatment decisions. Therapeutic strategies of imatinib resistant disease include novel tyrosine kinase inhibitors with activity against imatinib-resistant mutations and/or with inhibition of alternative pathways, dose escalation to optimise imatinib levels, treatment interruption to stop selection of resistant cells and allogeneic stem cell transplantation in eligible patients.

Detection of drug-resistant clones in chronic myelogenous leukemia patients during dasatinib and nilotinib treatment

BACKGROUND

Imatinib effectively inhibits the tyrosine kinase activity conferred by the BCR-ABL gene [fusion gene of BCR (breakpoint cluster region) and ABL1 (c-abl oncogene 1, receptor tyrosine kinase)] and thereby appreciably improves outcomes for chronic myelogenous leukemia (CML). A small percentage of patients relapse because of the proliferation of escape clones; such relapses can be treated with second-generation drugs. Early detection and monitoring of resistant clones may provide clinical benefit. We describe the development and testing of a new approach for quantitative monitoring of CML resistance.

METHODS

We designed mutation-specific assays that use hydrolysis probes and an array of allele-specific primers containing nucleotides mismatched at various positions. All assays were tested with plasmids containing corresponding mutant or wild-type sequences, allowing identification of optimal assays for specific and effective amplification of the target template. Clinical samples were then used to compare the results of selected assays with those of standard genotyping.

RESULTS

We used a modified amplification refractory mutational system approach and testing with plasmid constructs to design assays that allowed highly selective detection of resistance for all target mutations. By taking advantage of single-step performance and high PCR efficiency, we were able to quantitatively track the absolute amount of resistance conferred by a specific mutation over 4 orders of magnitude. Moreover, we designed an integrated test for dasatinib resistance that uses multiple primers simultaneously.

CONCLUSIONS

These single-step, closed-tube assays specifically target mutations associated with resistance to dasatinib or nilotinib. Compared with standard genotyping, such biased genotyping improves the detection of resistance or alternative features via quantitative analysis of the absolute amount of resistance.

The myeloproliferative neoplasms: insights into molecular pathogenesis and changes in WHO classification and criteria for diagnosis

In the 2008 World Health Organization-sponsored classification of hematopoietic and lymphoid malignancies, changes were made in the classification and criteria for the diagnosis of some of the myeloproliferative disorders. These changes were initiated by recent insights into the molecular pathogenesis of these disorders. In this article, the changes made to the myeloproliferative neoplasm and the basis of the new classification and altered diagnostic criteria are summarized and discussed.

A co-operative evaluation of different methods of detecting BCR-ABL kinase domain mutations in patients with chronic myeloid leukemia on second-line dasatinib or nilotinib therapy after failure of imatinib

BACKGROUND

Various techniques have been employed to detect BCR-ABL kinase domain mutations in patients with chronic myeloid leukemia who are resistant to imatinib. This has led to different reported frequencies of mutations and the finding of a heterogeneous pattern of individual mutations.

DESIGN AND METHODS

We compared direct sequencing alone and in combination with denaturing high-performance liquid chromatography and two high-sensitivity allele-specific oligonucleotide polymerase chain reaction approaches for analysis of BCR-ABL mutations in 200 blinded cDNA samples prior to and during second-line dasatinib or nilotinib therapy in patients with chronic myeloid leukemia in whom imatinib treatment had failed.

RESULTS

One hundred and fourteen mutations were detected by both direct sequencing alone or in combination with high performance liquid chromatography and 13 mutations were additionally detected by the combined technique. Eighty of 83 mutations (96%) within a selected panel of 11 key mutations were confirmed by both allele-specific oligonucleotide polymerase chain reaction techniques and 62 mutations were identified in addition to those detected by combined liquid chromatography and direct sequencing, indicating the presence and a high prevalence of low-level mutations in this cohort of patients. Furthermore, 125 mutations were detected by only one allele-specific oligonucleotide polymerase chain reaction technique. Pre-existing mutations were traceable 4.5 months longer and emerging clones were detectable 3.0 months earlier by allele-specific oligonucleotide polymerase chain reaction than by direct sequencing together with liquid chromatography.

CONCLUSIONS

Our results suggest that denaturing high performance liquid chromatography combined with direct sequencing is a reliable screening technique for the detection of BCR-ABL kinase domain mutations. Allele-specific oligonucleotide polymerase chain reaction further increases the number of detected mutations and indicates a high prevalence of mutations at a low level. The clinical impact of such low-level mutations remains uncertain and requires further investigation. Allele-specific oligonucleotide polymerase chain reaction allows detection of defined mutations at a lower level than does denaturing high performance liquid chromatography combined with direct sequencing and may, therefore, provide clinical benefit by permitting early reconsideration of therapeutic strategies.

Improved single nucleotide polymorphisms detection using conjugated polymer/surfactant system and peptide nucleic acid

An improved assay for the detection of single nucleotide polymorphisms (SNP) of mutant DNA using a combination of peptide nucleic acid (PNA) probes, a cationic conjugated polymer (CCP) and non-ionic surfactant is reported. A comparison between CCP/surfactant and CCP alone shows enhancement in the discrimination between mutant and wild type DNA by a factor of two. A discrimination factor of 70% and 92% was calculated for single and five bases mismatched mutants, respectively when using CCP/surfactant. Furthermore, CCP/surfactant provides a strong emissive donor which increases signal to noise ratio and prevents fluctuation in the output signal caused by the suspension nature of the CCP (due to polymer aggregation) in water. The fluorescence resonance energy transfer (FRET) ratio which defined as the ratio of PL emission of the acceptor to that of the donor, was found to be 20% better when the location of the mutation is five bases away from the duplex terminal compared to that in the centre of the duplex. The enhance discrimination referred to the difference in the FRET and reabsorption rates in different types of duplex. The FRET ratio can be very sensitive to the sample excitation strength, emission collection and spectrometer setting.

Part I: mechanisms of resistance to imatinib in chronic myeloid leukaemia

The introduction of selective tyrosine-kinase inhibitors (TKIs) for the treatment of chronic myeloid leukaemia has changed patient outcome and, consequently, management of this disease. Imatinib is now the treatment of choice for most newly diagnosed patients. Excellent responses, in terms of symptom control and haematological parameters, are usually obtained. However, failure to completely eradicate leukaemic cells and the escape of these cells from previous control has led to an intensive search for the mechanisms of resistance and subsequent treatments by which to overcome this resistance. Up to now, there has been considerable focus on the role of ABL-kinase-domain mutations as mediators of resistance to imatinib, thereby encouraging the development of a second generation of TKIs capable of inhibiting these mutant proteins. However, studies have increasingly shown that these mutations do not account for all cases of resistance and have a negligible role in the inability of TKIs to eradicate residual disease in patients who are good responders. More recently, attention has turned to the relative roles of drug bioavailability and drug efflux and drug influx proteins in the development of resistance to imatinib. This review is the first of two papers and discusses imatinib resistance and its potential causes. The second paper will focus on the assessment and subsequent management of patients with less than optimum responses to imatinib.

Advances in molecular diagnostics of myeloproliferative disorders

Incremental advances in the molecular pathogenesis of myeloproliferative disorders (MPDs) have had a substantial impact on clinical practice in terms of both diagnosis and treatment. An array of novel molecular methods are being developed and integrated into the current battery of tests for diagnosis and monitoring of treatment response. Primarily, subjective clinico-histologic approaches to diagnosis are being replaced by more objective semimolecular diagnostic algorithms. Furthermore, identification of disease-specific molecular markers has facilitated the development of small-molecule drugs for targeted therapy. This review provides an overview of MPDs with emphasis on molecular diagnostic tests and their incorporation into contemporary diagnostic and therapeutic algorithms.

Alkaline Phosphatase-Catalyzed Silver Deposition for Electrochemical Detection

Alkaline phosphatase (AP) is one of the most used enzymatic labels for the development of ELISAs, immunosensors, DNA hybridization assays, etc. This enzyme catalyzes the dephosphorylation of a substrate into a detectable product usually quantified by optical or electrochemical measurements. This work is based on a substrate (3-indoxyl phosphate) that produces a compound able to reduce silver ions in solution into a metallic deposit, which is localized where the enzymatic label AP is attached. The deposited silver is electrochemically stripped into solution and measured by anodic stripping voltammetry. Its application to an enzymatic genosensor on streptavidin-modified screen-printed carbon electrodes for the detection of virulence nucleic acid determinants of autolysin gene, exclusively present on the genome of the human pathogen Streptococcus pneumoniae, is described. Compared with the direct voltammetric detection of indigo carmine, the anodic stripping voltammetry of silver ions is 14-fold more sensitive.

Kinase domain mutations of BCR-ABL frequently precede imatinib-based therapy and give rise to relapse in patients with de novo Philadelphia-positive acute lymphoblastic leukemia (Ph+ ALL)

Acquired imatinib resistance in advanced Philadelphia-positive acute lymphoblastic leukemia (Ph(+) ALL) has been associated with mutations in the kinase domain (KD) of BCR-ABL. We examined the prevalence of KD mutations in newly diagnosed and imatinib-naive Ph(+) ALL patients and assessed their clinical relevance in the setting of uniform frontline therapy with imatinib in combination with chemotherapy. Patients enrolled in the German Multicenter Study Group for Adult Acute Lymphoblastic Leukemia (GMALL) trial ADE10 for newly diagnosed elderly Ph(+) ALL were retrospectively examined for the presence of BCR-ABL KD mutations by denaturing high-performance liquid chromatography (D-HPLC), cDNA sequencing, and allele-specific polymerase chain reaction (PCR). A KD mutation was detected in a minor subpopulation of leukemic cells in 40% of newly diagnosed and imatinib-naive patients. At relapse, the dominant cell clone harbored an identical mutation in 90% of cases, the overall prevalence of mutations at relapse was 80%. P-loop mutations predominated and were not associated with an inferior hematologic or molecular remission rate or shorter remission duration compared with unmutated BCR-ABL. BCR-ABL mutations conferring high-level imatinib resistance are present in a substantial proportion of patients with de novo Ph(+) ALL and eventually give rise to relapse. This provides a rationale for the frontline use of kinase inhibitors active against these BCR-ABL mutants.

Resistance to Targeted Therapy in Chronic Myelogenous Leukemia

The advent of the Bcr-Abl selective tyrosine kinase inhibitor imatinib mesylate (Glivec, Gleevec, Novartis, East Hanover, NJ) has substantially changed the treatment landscape for chronic myelogenous leukemia (CML). However, some patients, primarily those with advanced disease, are either initially refractory to imatinib or eventually develop imatinib resistance. Imatinib resistance or intolerance frequently depends on the re-emergence of Bcr-Abl kinase activity, but can also indicate Bcr-Abl-independent disease progression. Results from phase II/III trials suggest rates of resistance and relapse correlate with stage of disease and with the monitoring parameters: hematologic, cytogenetic, and molecular responses. To date, more than 40 different point mutations that code for distinct single amino acid substitutions in the Bcr-Abl kinase domain have been isolated from imatinib-resistant patients. These mutations affect amino acids involved in imatinib binding or in regulatory regions of the Bcr-Abl kinase domain, resulting in decreased sensitivity to imatinib while retaining aberrant kinase activity. Early mutation detection may aid in risk stratification and molecular-based treatment decisions. To overcome imatinib-resistant disease, novel tyrosine kinase inhibitors with activity against imatinib-resistant mutations and/or with inhibition of alternative pathways, such as Src activation, have recently been developed. Additional strategies include imatinib dose escalation, combination therapy, and treatment interruption to stop clonal selection of resistant cells.

Monitoring CML patients responding to treatment with tyrosine kinase inhibitors: review and recommendations for harmonizing current methodology for detecting BCR-ABL transcripts and kinase domain mutations and for expressing results

The introduction in 1998 of imatinib mesylate (IM) revolutionized management of patients with chronic myeloid leukemia (CML) and the second generation of tyrosine kinase inhibitors may prove superior to IM. Real-time quantitative polymerase chain reaction (RQ-PCR) provides an accurate measure of the total leukemiacell mass and the degree to which BCR-ABL transcripts are reduced by therapy correlates with progression-free survival. Because a rising level of BCR-ABL is an early indication of loss of response and thus the need to reassess therapeutic strategy, regular molecular monitoring of individual patients is clearly desirable. Here we summarize the results of a consensus meeting that took place at the National Institutes of Health (NIH) in Bethesda in October 2005. We make suggestions for (1) harmonizing the differing methodologies for measuring BCR-ABL transcripts in patients with CML undergoing treatment and using a conversion factor whereby individual laboratories can express BCR-ABL transcript levels on an internationally agreed scale; (2) using serial RQ-PCR results rather than bone marrow cytogenetics or fluorescence in situ hybridization (FISH) for the BCR-ABL gene to monitor individual patients responding to treatment; and (3) detecting and reporting Philadelphia (Ph) chromosome-positive subpopulations bearing BCR-ABL kinase domain mutations. We recognize that our recommendations are provisional and will require revision as new evidence emerges.

Detection and monitoring of minimal residual disease by quantitative real-time PCR

BACKGROUND

The detection of malignant cells by quantitative real-time PCR has become state of the art for diagnosis, monitoring response to treatment and detection of minimal residual disease (MRD) in patients with leukemia or lymphoma. In order to be used in high-throughput analyses technical details have to be standardized to improve reproducibility and comparability of quantitative results obtained in different laboratories.

METHODS

Molecular monitoring of disease activity during and after treatment based on the detection of malignant cells in circulation or bone marrow by quantitative real-time PCR will be helpful to develop individualized treatment strategies for every patient.

CONCLUSIONS

The effectiveness of any kind of innovative treatment with specific antibodies, cellular immunotherapy or molecules designed for specific targets of tumor cells can be controlled at a very high level of sensitivity and accuracy. Based on quantitative results indicative for success or treatment failure, therapeutic changes upon the detection of progressive disease at the molecular level can be made even before symptoms or signs of clinical relapse occur. Hopefully, this will lead to higher cure rates and improved long-term survival.

A single nucleotide polymorphism in the coding region of ABL and its effects on sensitivity to imatinib

We have identified a gene polymorphism (K247R) within or close to the P-loop of BCR-ABL, which leads to the substitution of arginine for lysine. We investigated the allelic frequency of K247R by screening 157 CML patients and 213 healthy blood donors with conventional sequencing, restriction enzyme digest and single strand conformational polymorphism analysis, and found the arginine allele to be rare. Three out of five CML patients with the arginine allele of K247R failed to achieve a major cytogenetic response to imatinib, suggesting that the arginine allele may have reduced sensitivity. However, despite K247R's position in or near to the P-loop, biochemical and cellular assays of imatinib and dasatinib sensitivity showed no alteration compared to wild type. Clinicians should be aware that possession of the arginine allele of K247R does not reflect a mutation that necessitates a change in the therapeutic strategy, unless there are other signs of inadequate response to drug.

Molecular genetic analysis of haematological malignancies: I. Acute leukaemias and myeloproliferative disorders

Molecular genetic techniques are now routinely applied to haematological malignancies within a clinical laboratory setting. The detection of genetic rearrangements not only assists with diagnosis and treatment decisions, but also adds important prognostic information. In addition, genetic rearrangements associated with leukaemia can be used as molecular markers allowing the detection of low levels of residual disease. This review will concentrate on the application of molecular genetic techniques to the acute leukaemias and myeloprolferative disorders.

Chronic Myelogenous Leukemia and Myeloproliferative Disease

In Section I, Dr. Stephen O’Brien reviews the latest data on the clinical use of imatinib (STI571, Gleevec, Glivec) in CML. His review focuses on the use of imatinib in newly diagnosed chronic phase patients and summarizes cytogenetic and molecular response data, as well as use of the agent at high doses and in combination with other drugs. A brief summary of the prospective international Phase III studies that are currently ongoing is also provided, and the issues of resistance and definition of suboptimal therapeutic response are also covered. Finally, therapeutic decision-making and treatment strategy are considered.

In Section II, Dr. Ayalew Tefferi considers the latest developments in the biology and therapy of myeloid metaplasia/myelofibrosis. Dr. Tefferi covers what is currently understood of the biology of the disease and reviews established therapies for the condition as well as novel agents that are being used in clinical trials. The development of optimal management strategies for the disease is considered.

In Section III, Dr. Peter Valent reviews the classification of mast cell proliferative disorders and covers the clinical and pathological presentation of this group of neoplasms. He reviews the state-of-the-art regarding the molecular biology of mastocytosis along with diagnostic criteria and novel treatment concepts.