BCR-ABL Fusion Gene Transcripts Research Articles

Outcome of pediatric chronic myeloid leukemia with management focusing on the monitoring of BCR-ABL fusion gene transcript levels.

Background and objectiveClinical, laboratory and outcome data were reviewed for pediatric patients who were diagnosed with chronic myeloid leukemia (CML) and managed at two tertiary care hospitals in Saudi Arabia, between January 2011 and December 2017 to assess the response to tyrosine kinase inhibitors (TKI) focusing on the monitoring of BCR-ABL fusion gene transcript levels and to look at the overall outcome.MethodsCML patients were identified based on the cytogenetic and molecular results.ResultsTwelve pediatric patients diagnosed with CML at a median age of 8.4 year; treated with TKI as first-line therapy, 11 (91.7%) patients were started with imatinib (first-generation TKI), while one received dasatinib (second-generation TKI) due to his three-way Philadelphia chromosome sensitivity. Eight patients (72.7%) starting on imatinib were switched to dasatinib (six patients due to drug resistance, and two patients due to intolerance of Imatinib) and two patients (25%) of whom had already achieved major molecular response (MMR) on Imatinib. Response rate to imatinib in terms of achieving MMR as first-line therapy was achieved in five out of 11 patients (45.5%) and only three of them continued to maintain their MMR. Six out of eight patients who were switched to dasatinib achieved MMR. Two patients underwent hematopoietic stem cell transplant (SCT): one due to blast crisis and one due to the side effects of TKI. With a median follow-up time of 78 months (range, 40.5–108), all of our patients were alive at last update.ConclusionWe report an excellent outcome with an overall survival (OS) of 100% at 5-year and disease-free survival (DFS) of 91.7% (8.0%). All our patients achieved MMR and only one patient had loss of MMR on follow-up. Eight patients (66.7%) achieved complete molecular response (CMR).

Phytohemagglutinin-Induced Peripheral Blood Cytogenetics: A Valid Means for Diagnosis and Imatinib Therapy Monitoring of Chronic Phase Chronic Myeloid Leukemia Patients

Background: Conventional cytogenetic studies have been viewed as the standard follow-up method for Chronic Myeloid Leukemia patients on Imatinib. However, this approach is beset with high probability of poor metaphase index. In this study, we evaluated the application of Phytohemagglutinin (PHA)-induced peripheral blood culture based cytogenetic analysis (Karyotyping) in diagnosis and Imatinib treatment monitoring of the Chronic Phase CML patients. Methods: The patient samples were subjected to the PHA-induced peripheral blood culture based cytogenetic technique (Karyotyping) to establish their baseline cytogenetic status followed by their follow up Karyotyping twice at the end of 3 and 6 months of treatment. The simultaneous quantitative PCR (q-PCR) assay for BCR-ABL fusion gene transcript on the samples corresponding to their baseline as well as the follow up cytogenetic status was also carried out to authenticate the cytogenetic findings. Results: Complete Cytogenetic Response (CCR) and Partial Cytogenetic Response (PCR) was initially observed in 09 (30%) and 16 (53.3%) respectively of 30 CML patients with 05 (16.6%) patients showing no such response at the end of 3 months. At 6 months, 25 (83.3%) and 02 (6.6%) showed CCR and PCR respectively with 03 (10%) of patients without any response. The findings completely correlated with the hematological response, the q-PCR assay as well as the overall disease condition observed in the patients. Conclusion: As acquiring bone-marrow sample involves morbid consequences for patients and metaphases yielded thereby are difficult to analyze, PHA-induced peripheral blood Karyotyping was explored as an alternative. It was found to have significant potential in serving as a valid tool in the diagnosis and assessment of follow up response to Imatinib mesylate treatment of patients with chronic phase CML.

The Impact Of Novel Splicing Abnormalities Of BCR-ABL On The Pathogenesis Of CML

BackgroundChronic myeloid leukemia (CML) is effectively treated with tyrosine kinase inhibitors (TKIs), but reactivation of BCR-ABL frequently occurs through acquisition of kinase domain point mutations. The mechanism of resistance in patients without BCR-ABL kinase domain point mutation is still elusive. Previous studies have revealed the abnormal splicing of BCR-ABL kinase domain, including Exon8/9 junction 35bp insertion and exon-skipping of Exon 7 (T O'Hare et al, Blood 2011. Gaillard JB, et al. Mol Cancer Ther 2010). The insertion of 35 intronic nucleotides at the exon 8/9 splice junction introduces a stop codon after 10 intron-encoded residues and inactive tyrosine kinase activity. The effect of these splicing abnormalities on susceptibility of cells against TKIs is still controversial. Furthermore, the conventional direct sequence techniques could not evaluate splicing abnormalities in major molecular response (MMR)- complete molecular response (CMR) CML patients, who achieved clinically leukemia-free state with a small number residual CML stem cells. AimsThe aim of this study is to evaluate the frequency and the patterns of splicing abnormalities of BCR-ABL in CML patients, especially who achieved MMR-CMR by TKI treatment. MethodsWe analyzed peripheral blood samples from healthy individuals and CML chronic phase patients. We extracted total RNA from these samples and synthesized cDNA, and then performed PCR-amplification of BCR-ABL kinase domain in CML patients and ABL kinase domain in healthy individuals, respectively. PCR products were subjected to the amplicon sequence: We deeply sequenced BCR-ABL fusion gene transcripts, and evaluated splicing forms of BCR-ABL by using HiSeq 2000 (illumina). ResultsWe successfully established a novel analysis method, which can detect the pattern of splicing abnormalities even in MMR-CMR patients. Using the amplicon sequence technique, we detected abnormal splicing patterns of BCR-ABL in 5 out of 15 CML patients. We also found that the splicing abnormalities were not restricted to 35bp insertion at the exon8/9 junction, thus intronic retention of intron 8 and intron 9 could be frequently detected with or without the 35bp insertion in CML patients (Table 1). Of note, these abnormal splicing patterns always co-existed with wild type BCR-ABL transcripts in all 5 cases analyzed. In addition to the novel splicing abnormalities in CML, we unexpectedly found in healthy individuals that splicing abnormalities such as 35bp insertion at the exon8/9 junction and intronic retention could be detected in ABL1 transcripts (Table 1). This result suggests that this sort of splicing abnormalities could occur at a certain frequency in steady state human hematpoiesis, and is not specific to BCR-ABL. Summary / ConclusionWe have newly established an analysis system to efficiently detect splicing abnormalities of BCR-ABL even in MMR-CMR CML patients. Using this highly efficient amplicon sequence technique, we identified novel splicing abnormalities both in healthy individuals and CML patients, and found that the wild type BCR-ABL transcripts always co-exist with abnormally spliced BCR-ABL transcripts. These results collectively suggest that splicing abnormalities within the ABL1 kinase domain are not specific to CML patients treated with TKIs, and that the detection of such kinase domain splicing abnormalities do not reflect insusceptibility of the remaining cells during TKI treatment. Disclosures:No relevant conflicts of interest to declare.

Clinical and laboratorial analysis for 15 adult cases of mixed phenotypic acute leukemia with Ph chromosome and/or positive BCR-ABL

The purpose of this study was to summary the clinical and laboratorial features in 15 adult cases of mixed phenotypic acute leukemia with Ph chromosome and/or BCR-ABL fusion gene positive (Ph(+)MPAL), 15 adult patients with Ph(+)MPAL were defined by WHO-2008 classification. The clinical characteristics, results of morphology, immunology, cytogenetics and molecular genetic detections and results of follow-up in 15 adult patients with Ph(+)MPAL were analyzed retrospectively. The results showed that 15 patients among 87 cases of MPAL demonstrated Ph(+)MPAL (17.2%; 15/87) (7 males and 8 females), their median age was 51 (range 16-81) year old and median WBC count at diagnosis was 69 (12.7-921)×10(9)/L. Based on FAB criteria, these patients showed different morphologic types, including AML (13.3%; 2/15), ALL (40.0%; 6/15), HAL (46.7%; 7/15). Immunologic analysis indicated that 15 cases of Ph(-)MPAL were all classified as B-lymphoid +myeloid mixed immunophenotype. Except one patient, all expressed CD34 antigen on the surface of leukemia cells with 64.3% strong positive, only Ph (53.3%; 8/15), Ph with additional chromosomal abnormalities (33.3%; 5/15) and normal karyotype (13.3%; 2/15) were cytogenetically identified. BCR-ABL fusion gene transcript positive were detected by multiplex reverse transcription PCR in all cases, with e1a2 subtype (p190) (40.0%; 6/15) and b2a2 or b3a2 (p210) subtype (60.0%; 9/15). Four out of 7 (57.1%) patients were found to have IKZF1 gene deletion, without other common gene mutations. Seven out of 10 cases (70.0%) achieved complete remission (CR) after one cycle of induction chemotherapy. In the induction stage, CR rate seemed higher when tyrosine kinase inhibitors (TKI) were added to chemotherapy (83.3%:50.0%; P = 0.206). Overall survival (OS) in 4 patients received allogeneic hematopoietic stem cell transplantation (allo-HSCT) was longer than that in 4 patients received chemotherapy alone (P = 0.004). It is concluded that Ph(+)MPAL mainly is expressed as B+My phenotype. The majority of patients is older and has CD34 overexpression. In the aspect of molecular genetics, the Ph(+)MPAL is similar to other acute leukemia with Ph chromosome. Ph(+)MPAL is a subtype of acute leukemia with poor prognosis. WBC count at diagnosis is an independent prognostic factor. The combination of TKI and allo-HSCT can improve their long-term survival, which needs to be confirmed through carrying out a prospective and multicenter clinical trial for newly diagnosed Ph(+)MPAL.

Very Late Relapse of a Philadelphia Positive Acute Megakaryocytic Leukemia Post Allogenic Bone Marrow Transplant

Abstract 4518A 33 year old male initially diagnosed with myelodysplastic syndrome presented with acute leukemia, his bone marrow demonstrating sheets of abnormal megakaryocytes. Cytogenetics revealed two cell lines, 44X –Y, –C and 46XY, both positive for the Philadelphia chromosome mutation. He underwent busulphan and cyclophosphamide conditioning and allogeneic bone marrow transplant in the absence of a course of induction chemotherapy. One year later he was free of leukemia. Ten years after the transplant he was discharged from hematology follow-up, declared cured.Twenty-two years later, the patient re-presented with significant anemia and circulating blasts. One year previous he had normal blood counts. Bone marrow biopsy revealed acute megakaroblastic leukemia (M7), with cytogenetics demonstrating Philadelphia chromosome positivity and two identified cell lines, one with deletion of the Y chromosome. The patient underwent induction chemotherapy with idarubicin and cytarabine in addition to imatinib. His recovery marrow revealed no residual leukemia, including normal cytogenetics. He remained BCR-ABL fusion gene transcript positive, and was maintained on single agent imatinib. Four hundred and forty one days after induction chemotherapy he received a second sibling matched allogeneic stem cell bone marrow transplant. One year later he remains free of leukemia with no detectable BCR-ABL fusion gene transcript.Acute megakaryoblastic leukemia is a rare entity representing <1% of AML seen in adults. Prognosis is poor due to a high rate of relapse with disease free survival of 17% at 5 years. Even with allogeneic stem cell transplant, overall survival at 3 years is 43% with a relapse rate of 64%. With definitive diagnostic criteria for megakaryoblastic leukemia only being first described in 1985, at the time of our patient's first transplant he was one of the first M7-AML to receive a transplant.How did this patient, with such an aggressive subtype of leukemia, manage to stay in remission for over 20 years? Looking at all types of AML relapse, very late relapse, defined as occurring >5 years from the day that complete remission, occurs in 1–3% of cases. To our knowledge, this is the first reported case of very late relapse in an M7 leukemia. Fortunately, the rate of achieving a second complete remission state is higher in those patients who have a very late relapse with a second remission attained in up to 87% of cases. This may be influenced by the aggressiveness of the initial consolidation regime; those having more intense initial chemotherapy may have subsequently developed more resistant disease rendering them less sensitive to the second chemotherapy regimen. The fact that our patient never received induction chemotherapy when he initially presented may have contributed to the success of attaining remission when he was exposed to the standard 3+7 model used today.The pathogenesis for very late relapses remains a topic of debate. One hypothesis suggests that cells with malignant potential retain viability after chemotherapy treatments awaiting re-activation into a malignant state via either intrinsic errors in genetic division or an external stressor such as a viral infection or acquired immunodeficiency state. In this circumstance, the immune system is able to keep the tumor burden below the limits of minimal residual disease detection. It is also possible that residual very slow growing malignant cells remain after chemotherapy that are resistant to anti-tumor treatments. A third possibility is the presumed relapse is actually a de novo tumor with characteristics similar to its predecessor. Other late recurrences of AML have demonstrated both identical and different cytogenetic and molecular profiles to the original disease, which substantiates the premise for multiple mechanisms.In this case, one could also question whether the second transplant was necessary. He was maintained with a 2–3 log reduction in BCR/ABL fusion transcript level, but no morphologic evidence of leukemia, on only imatinib for over one year. The rationale for pursuing transplantation was the presumed aggressiveness of an M7 leukemia; it is unknown how long he could have been maintained on only a tyrosine kinase inhibitor. A second generation tyrosine kinase inhibitor would have been an option if the major molecular response was not maintained, and remains an option if our patient is unfortunate enough to have a second relapse. Disclosures:No relevant conflicts of interest to declare.

Abstract 2232: Effectiveness evaluation of an in vitro nucleic acid amplification test for quantification of BCR-ABL fusion transcript variants in human whole blood

Abstract Quantitative measurement of BCR-ABL fusion gene transcripts in whole blood by quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) is a clinically validated method to monitor tyrosine kinase inhibitor drug response in patients diagnosed with chronic myelogenous leukemia (CML). Monitoring of BCR-ABL expression in blood of cML patients under treatment with a tyrosine kinase inhibitor of BCR-ABL is considered standard of care. A three log or greater reduction in BCR-ABL expression from baseline is considered a Maximum Molecular Response (MMR). A subsequent 0.5 log increase in BCR-ABL from MMR is considered a sign of treatment failure sufficient to trigger change in treatment. The challenge is to develop a test with sufficient analytical performance characteristics and quality control to reliably measure BCRABL in MMR samples in which there may be less than 10 molecules in 300 of RNA extracted from whole blood. A method validation protocol was developed using the International Committee on Harmonization (ICH) Q2(R1) international validation guidelines. BCRABL variants b2a2 and b3a2 as well as the housekeeping gene GUSB were measured in KCL22 cell line RNA and Stratagene Universal Human Reference RNA test articles in extreme linear dilution assay, robustness testing conditions, and in multiple laboratories. Quality controls were developed to enable loading as much whole blood RNA into the assay as possible without assay interference. These included a reverse transcription (RT) standardization mixture comprising External RNA Control Consortium (ERCC) reagents to control for RT interference, and controls for genomic DNA contamination, RNA integrity, and PCR interference. Results: This test for b2a2 and b3a2 variants of BCR-ABL meets ICHQ2(R1) guidelines for specificity, linearity, accuracy, LOD and LOQ, imprecision, robustness, and reproducibility. Each analyte comprised by the test was linear (R2 &amp;gt; 0.97) over more than 3 logs10, and demonstrated inter-experimental and inter-laboratory imprecision low enough to enable measurement of a 3-fold difference as significant (P &amp;lt;0.05) from a value as low as five molecules/assay. Experiments are underway to quantify the amount of whole blood RNA that can be loaded into RT reaction without interference. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2232. doi:10.1158/1538-7445.AM2011-2232

The Recent Thymic Output Function Might Relate with BCR-ABL mRNA Level in Patients with CML.

Objective In order to analyze the relationship between the content of T-cell receptor excision DNA circles (TRECs) and BCR-ABL mRNA levels, evaluating the prognostic significance of thymic recent output function monitoring in patients with chronic myelogenous leukemia (CML).Methods Quantitative detection of TRECs and BCR-ABL fusion gene transcripts in peripheral blood from 15 CML patients were preformed using real-time PCR technique. And the TREC-number was related to the number of T-cells by determination of the number of CD3-positive cells. The change of BCR-ABL level in 6 CML patients was followed-up for two years.Results There was no significant correlation between TRECs and BCR-ABL mRNA in peripheral blood from CML patients at the first diagnose. Patients who had higher TRECs at diagnosis had a larger reduction of BCR-ABL level after 2 years of follow-up. While in 2 patients who underwent haemopoietic stem cell transplantation(HSCT), BCR-ABL in one patient with higher pre-transplantation TRECs value became undetectable with three consecutive detections during the first year post transplantation, but low level of BCR-ABL could be identified in the other patient.Conclusion High thymic output function in CML patients could be helpful for anti-residual CML cells.

The Presence of Typical and Atypical BCR-ABL Fusion Genes in Leukocytes of Normal Individuals: Biologic Significance and Implications for the Assessment of Minimal Residual Disease

The number of genetic lesions necessary to generate leukemia in humans is unknown, but it is possible that certain specific abnormalities, eg, fusion genes, known to be associated with acute and chronic leukemia are produced relatively frequently in human cells but require other events to occur before the leukemia becomes manifest. We investigated this possibility by studying peripheral blood leukocytes from normal individuals and various hematopoietic cell lines for the presence and expression of the p210 and the p190 types of the BCR-ABL gene associated with chronic myeloid leukemia (CML) and acute lymphoblastic leukemia. We used two-step reverse transcriptase-polymerase chain reaction (RT-PCR) assays in which batches of 108 cells per sample were tested in 40 replicate reactions. We estimate that this assay is 1.5 logs more sensitive than the two-step RT-PCR assays that we use routinely to assess minimal residual disease. BCR-ABL fusion gene transcripts of various configurations were found in circulating leukocytes from 12 of the 16 healthy adults analyzed. Transcripts with an e1a2 junction (p190 BCR-ABL) were present in 11 and p210-type transcripts with b2a2 and/or b3a2 junctions were detected in 4 individuals. The same RT-PCR assays in non-CML cell lines showed the presence of classical or aberrant p210-type mRNA in 3 of 7 lines and of p190-type transcripts in all 7 lines of hematopoietic origin (HL60, KG1, U937, Kasumi, Jurkat, JVM13, and JVM25), whereas the NIH3T3 murine fibroblast line was reproducibly negative for these fusion genes. These findings confirm and extend previous reports on the detection of leukemia-associated genes in normal leukocytes and suggest that certain fusion genes are generated relatively frequently in hematopoietic cells, but only infrequently do the cells acquire the additional changes necessary to produce leukemia in humans. Although there is only a small probability that such innocent BCR-ABL–carrying leukocytes are detected by conventional RT-PCR assays, they may be the source of some sporadically positive tests in leukemia patients in long-term remission. © 1998 by The American Society of Hematology.

The Presence of Typical and Atypical BCR-ABL Fusion Genes in Leukocytes of Normal Individuals: Biologic Significance and Implications for the Assessment of Minimal Residual Disease

AbstractThe number of genetic lesions necessary to generate leukemia in humans is unknown, but it is possible that certain specific abnormalities, eg, fusion genes, known to be associated with acute and chronic leukemia are produced relatively frequently in human cells but require other events to occur before the leukemia becomes manifest. We investigated this possibility by studying peripheral blood leukocytes from normal individuals and various hematopoietic cell lines for the presence and expression of the p210 and the p190 types of the BCR-ABL gene associated with chronic myeloid leukemia (CML) and acute lymphoblastic leukemia. We used two-step reverse transcriptase-polymerase chain reaction (RT-PCR) assays in which batches of 108 cells per sample were tested in 40 replicate reactions. We estimate that this assay is 1.5 logs more sensitive than the two-step RT-PCR assays that we use routinely to assess minimal residual disease. BCR-ABL fusion gene transcripts of various configurations were found in circulating leukocytes from 12 of the 16 healthy adults analyzed. Transcripts with an e1a2 junction (p190 BCR-ABL) were present in 11 and p210-type transcripts with b2a2 and/or b3a2 junctions were detected in 4 individuals. The same RT-PCR assays in non-CML cell lines showed the presence of classical or aberrant p210-type mRNA in 3 of 7 lines and of p190-type transcripts in all 7 lines of hematopoietic origin (HL60, KG1, U937, Kasumi, Jurkat, JVM13, and JVM25), whereas the NIH3T3 murine fibroblast line was reproducibly negative for these fusion genes. These findings confirm and extend previous reports on the detection of leukemia-associated genes in normal leukocytes and suggest that certain fusion genes are generated relatively frequently in hematopoietic cells, but only infrequently do the cells acquire the additional changes necessary to produce leukemia in humans. Although there is only a small probability that such innocent BCR-ABL–carrying leukocytes are detected by conventional RT-PCR assays, they may be the source of some sporadically positive tests in leukemia patients in long-term remission.© 1998 by The American Society of Hematology.