1
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Elshazly AM, Xu J, Melhem N, Abdulnaby A, Elzahed AA, Saleh T, Gewirtz DA. Is Autophagy Targeting a Valid Adjuvant Strategy in Conjunction with Tyrosine Kinase Inhibitors? Cancers (Basel) 2024; 16:2989. [PMID: 39272847 PMCID: PMC11394573 DOI: 10.3390/cancers16172989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 08/21/2024] [Accepted: 08/23/2024] [Indexed: 09/15/2024] Open
Abstract
Tyrosine kinase inhibitors (TKIs) represent a relatively large class of small-molecule inhibitors that compete with ATP for the catalytic binding site of tyrosine kinase proteins. While TKIs have demonstrated effectiveness in the treatment of multiple malignancies, including chronic myelogenous leukemia, gastrointestinal tumors, non-small cell lung cancers, and HER2-overexpressing breast cancers, as is almost always the case with anti-neoplastic agents, the development of resistance often imposes a limit on drug efficacy. One common survival response utilized by tumor cells to ensure their survival in response to different stressors, including anti-neoplastic drugs, is that of autophagy. The autophagic machinery in response to TKIs in multiple tumor models has largely been shown to be cytoprotective in nature, although there are a number of cases where autophagy has demonstrated a cytotoxic function. In this review, we provide an overview of the literature examining the role that autophagy plays in response to TKIs in different preclinical tumor model systems in an effort to determine whether autophagy suppression or modulation could be an effective adjuvant strategy to increase efficiency and/or overcome resistance to TKIs.
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Affiliation(s)
- Ahmed M Elshazly
- Department of Pharmacology and Toxicology, School of Medicine, Virginia Commonwealth University, 401 College St., Richmond, VA 23298, USA
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
| | - Jingwen Xu
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Nebras Melhem
- Department of Anatomy, Physiology and Biochemistry, Faculty of Medicine, The Hashemite University, Zarqa 13133, Jordan
| | - Alsayed Abdulnaby
- Department of Pharmacognosy, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
| | - Aya A Elzahed
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
| | - Tareq Saleh
- Department of Pharmacology and Public Health, Faculty of Medicine, Hashemite University, Zarqa 13133, Jordan
| | - David A Gewirtz
- Department of Pharmacology and Toxicology, School of Medicine, Virginia Commonwealth University, 401 College St., Richmond, VA 23298, USA
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2
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Tungjitviboonkun S, Wachirapornpruet P, Unsuwan S. Concomitant L248V With E225V Mutation in the BCR-ABL Gene Associated With Rapid Chronic Myeloid Leukemia Lymphoid Blast Crisis. Cureus 2024; 16:e58972. [PMID: 38800235 PMCID: PMC11127122 DOI: 10.7759/cureus.58972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2024] [Indexed: 05/29/2024] Open
Abstract
Chronic myeloid leukemia (CML) is a myeloproliferative neoplasm characterized by the presence of the Philadelphia chromosome (Ph), resulting from the t(9;22)(q34;q11.2) translocation. Imatinib, a tyrosine kinase inhibitor (TKI), has revolutionized the treatment of CML. However, despite the initial response, some patients may progress to an advanced stage, such as a blast crisis. We report a 40-year-old female who presented with CML chronic phase (CP) taking imatinib 400 mg/day and achieved a complete hematological response (CHR) after one month of treatment. She achieved a suboptimal response in the third month (BCR-ABL positive 10.29% IS). However, five months into therapy, she developed a sudden lymphoid blast crisis with chromosomal aberrations involving chromosomes 10 and 12. Molecular analysis detected concomitant L248V with partial exon 4 deletion and E225V mutations within the BCR-ABL1 fusion gene. The patient received intensive chemotherapy and dasatinib. We report the first case of concomitant mutation of L248V with partial exon 4 deletion and E255V on BCR-ABL1 gene mutation, which contributes to a sudden precursor B-cell lymphoid blast crisis.
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3
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Kato K, Takagi S, Takano H, Tsunoda S, Watanabe O, Yamaguchi K, Kageyama K, Kaji D, Taya Y, Nishida A, Ishiwata K, Yamamoto H, Yamamoto G, Asano-Mori Y, Koike Y, Makino S, Wake A, Taniguchi S, Uchida N. A case report of a truncated ABL1 mutation in 2 cases with Philadelphia chromosome-positive B cell precursor acute lymphoblastic leukemia. Int J Hematol 2024; 119:205-209. [PMID: 38236369 DOI: 10.1007/s12185-023-03691-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 12/03/2023] [Accepted: 12/19/2023] [Indexed: 01/19/2024]
Abstract
Acquired point mutations in the ABL1 gene are widely recognized as a cause of Philadelphia chromosome-positive B cell precursor acute lymphoblastic leukemia (Ph+ B-ALL) that is resistant to tyrosine kinase inhibitors, whereas there are few reports about other types of the ABL1 mutation. Here, we report 2 cases of Ph+ B-ALL gaining a partial deletion type mutation of the ABL1 gene (Δ184-274 mutation), which resulted in truncation of the ABL1 molecule and loss of kinase activity. In both cases, the disease was refractory to multiple agents in the recurrent phase after allogeneic hematopoietic cell transplantation. This is a case report of a truncated ABL1 mutation in 2 patients with Ph+ B-ALL.
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Affiliation(s)
- Kana Kato
- Department of Hematology, Toranomon Hospital, 2-2-2 Toranomon, Minato-ku, Tokyo, 105-0001, Japan
| | - Shinsuke Takagi
- Department of Hematology, Toranomon Hospital, 2-2-2 Toranomon, Minato-ku, Tokyo, 105-0001, Japan.
- Center for Long-Term Follow-Up After Hematopoietic Cell Transplantation, Toranomon Hospital, Tokyo, Japan.
- Okinaka Memorial Institute for Medical Research, Tokyo, Japan.
| | - Hirofumi Takano
- Department of Hematology, Toranomon Hospital, 2-2-2 Toranomon, Minato-ku, Tokyo, 105-0001, Japan
| | - Shinichi Tsunoda
- Department of Hematology, Toranomon Hospital, 2-2-2 Toranomon, Minato-ku, Tokyo, 105-0001, Japan
| | - Otoya Watanabe
- Department of Hematology, Toranomon Hospital, 2-2-2 Toranomon, Minato-ku, Tokyo, 105-0001, Japan
| | - Kyosuke Yamaguchi
- Department of Hematology, Toranomon Hospital Kajigaya, Kanagawa, Japan
| | - Kosei Kageyama
- Department of Hematology, Toranomon Hospital Kajigaya, Kanagawa, Japan
| | - Daisuke Kaji
- Department of Hematology, Toranomon Hospital, 2-2-2 Toranomon, Minato-ku, Tokyo, 105-0001, Japan
- Department of Transfusion Medicine, Toranomon Hospital, Tokyo, Japan
| | - Yuki Taya
- Department of Hematology, Toranomon Hospital, 2-2-2 Toranomon, Minato-ku, Tokyo, 105-0001, Japan
- Department of Transfusion Medicine, Toranomon Hospital, Tokyo, Japan
| | - Aya Nishida
- Department of Hematology, Toranomon Hospital, 2-2-2 Toranomon, Minato-ku, Tokyo, 105-0001, Japan
| | - Kazuya Ishiwata
- Department of Hematology, Toranomon Hospital Kajigaya, Kanagawa, Japan
| | - Hisashi Yamamoto
- Department of Hematology, Toranomon Hospital, 2-2-2 Toranomon, Minato-ku, Tokyo, 105-0001, Japan
- Center for Long-Term Follow-Up After Hematopoietic Cell Transplantation, Toranomon Hospital, Tokyo, Japan
| | - Go Yamamoto
- Department of Hematology, Toranomon Hospital, 2-2-2 Toranomon, Minato-ku, Tokyo, 105-0001, Japan
| | - Yuki Asano-Mori
- Center for Long-Term Follow-Up After Hematopoietic Cell Transplantation, Toranomon Hospital, Tokyo, Japan
- Department of Transfusion Medicine, Toranomon Hospital, Tokyo, Japan
| | - Yukako Koike
- Department of Clinical Laboratory, Toranomon Hospital, Tokyo, Japan
| | | | - Atsushi Wake
- Department of Hematology, Toranomon Hospital Kajigaya, Kanagawa, Japan
| | - Shuichi Taniguchi
- Department of Hematology, Toranomon Hospital, 2-2-2 Toranomon, Minato-ku, Tokyo, 105-0001, Japan
| | - Naoyuki Uchida
- Department of Hematology, Toranomon Hospital, 2-2-2 Toranomon, Minato-ku, Tokyo, 105-0001, Japan
- Okinaka Memorial Institute for Medical Research, Tokyo, Japan
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4
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Ward RA, Fawell S, Floc'h N, Flemington V, McKerrecher D, Smith PD. Challenges and Opportunities in Cancer Drug Resistance. Chem Rev 2020; 121:3297-3351. [PMID: 32692162 DOI: 10.1021/acs.chemrev.0c00383] [Citation(s) in RCA: 189] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
There has been huge progress in the discovery of targeted cancer therapies in recent years. However, even for the most successful and impactful cancer drugs which have been approved, both innate and acquired mechanisms of resistance are commonplace. These emerging mechanisms of resistance have been studied intensively, which has enabled drug discovery scientists to learn how it may be possible to overcome such resistance in subsequent generations of treatments. In some cases, novel drug candidates have been able to supersede previously approved agents; in other cases they have been used sequentially or in combinations with existing treatments. This review summarizes the current field in terms of the challenges and opportunities that cancer resistance presents to drug discovery scientists, with a focus on small molecule therapeutics. As part of this review, common themes and approaches have been identified which have been utilized to successfully target emerging mechanisms of resistance. This includes the increase in target potency and selectivity, alternative chemical scaffolds, change of mechanism of action (covalents, PROTACs), increases in blood-brain barrier permeability (BBBP), and the targeting of allosteric pockets. Finally, wider approaches are covered such as monoclonal antibodies (mAbs), bispecific antibodies, antibody drug conjugates (ADCs), and combination therapies.
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Affiliation(s)
- Richard A Ward
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Stephen Fawell
- Oncology R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
| | - Nicolas Floc'h
- Bioscience, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | | | - Paul D Smith
- Bioscience, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
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Hauser K, Negron C, Albanese SK, Ray S, Steinbrecher T, Abel R, Chodera JD, Wang L. Predicting resistance of clinical Abl mutations to targeted kinase inhibitors using alchemical free-energy calculations. Commun Biol 2018; 1:70. [PMID: 30159405 PMCID: PMC6110136 DOI: 10.1038/s42003-018-0075-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 05/15/2018] [Indexed: 12/13/2022] Open
Abstract
The therapeutic effect of targeted kinase inhibitors can be significantly reduced by intrinsic or acquired resistance mutations that modulate the affinity of the drug for the kinase. In cancer, the majority of missense mutations are rare, making it difficult to predict their impact on inhibitor affinity. This complicates the practice of precision medicine, pairing of patients with clinical trials, and development of next-generation inhibitors. Here, we examine the potential for alchemical free-energy calculations to predict how kinase mutations modulate inhibitor affinities to Abl, a major target in chronic myelogenous leukemia (CML). We find these calculations can achieve useful accuracy in predicting resistance for a set of eight FDA-approved kinase inhibitors across 144 clinically-identified point mutations, achieving a root mean square error in binding free energy changes of 1.1 0.9 1.3 kcal/mol (95% confidence interval) and correctly classifying mutations as resistant or susceptible with 88 82 93 % accuracy. Since these calculations are fast on modern GPUs, this benchmark establishes the potential for physical modeling to collaboratively support the rapid assessment and anticipation of the potential for patient mutations to affect drug potency in clinical applications.
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Affiliation(s)
| | | | - Steven K Albanese
- Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | | | | | | | - John D Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
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6
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Woywod C, Gruber FX, Engh RA, Flå T. Dynamical models of mutated chronic myelogenous leukemia cells for a post-imatinib treatment scenario: Response to dasatinib or nilotinib therapy. PLoS One 2017; 12:e0179700. [PMID: 28678800 PMCID: PMC5497988 DOI: 10.1371/journal.pone.0179700] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 06/02/2017] [Indexed: 01/05/2023] Open
Abstract
Targeted inhibition of the oncogenic BCR-ABL1 fusion protein using the ABL1 tyrosine kinase inhibitor imatinib has become standard therapy for chronic myelogenous leukemia (CML), with most patients reaching total and durable remission. However, a significant fraction of patients develop resistance, commonly due to mutated ABL1 kinase domains. This motivated development of second-generation drugs with broadened or altered protein kinase selectivity profiles, including dasatinib and nilotinib. Imatinib-resistant patients undergoing treatment with second-line drugs typically develop resistance to them, but dynamic and clonal properties of this response differ. Shared, however, is the observation of clonal competition, reflected in patterns of successive dominance of individual clones. We present three deterministic mathematical models to study the origins of clinically observed dynamics. Each model is a system of coupled first-order differential equations, considering populations of three mutated active stem cell strains and three associated pools of differentiated cells; two models allow for activation of quiescent stem cells. Each approach is distinguished by the way proliferation rates of the primary stem cell reservoir are modulated. Previous studies have concentrated on simulating the response of wild-type leukemic cells to imatinib administration; our focus is on modelling the time dependence of imatinib-resistant clones upon subsequent exposure to dasatinib or nilotinib. Performance of the three computational schemes to reproduce selected CML patient profiles is assessed. While some simple cases can be approximated by a basic design that does not invoke quiescence, others are more complex and require involvement of non-cycling stem cells for reproduction. We implement a new feedback mechanism for regulation of coupling between cycling and non-cycling stem cell reservoirs that depends on total cell populations. A bifurcation landscape analysis is also performed for solutions to the basic ansatz. Computational models reproducing patient data illustrate potential dynamic mechanisms that may guide optimization of therapy of drug resistant CML.
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Affiliation(s)
- Clemens Woywod
- Centre for Theoretical and Computational Chemistry, Chemistry Department, University of Tromsø - The Arctic University of Norway, N-9037 Tromsø, Norway
- * E-mail:
| | - Franz X. Gruber
- NORSTRUCT, Chemistry Department, University of Tromsø - The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Richard A. Engh
- NORSTRUCT, Chemistry Department, University of Tromsø - The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Tor Flå
- Centre for Theoretical and Computational Chemistry, Chemistry Department, University of Tromsø - The Arctic University of Norway, N-9037 Tromsø, Norway
- Mathematics Department, University of Tromsø - The Arctic University of Norway, N-9037 Tromsø, Norway
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7
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Abstract
All chronic myeloid leukemia (CML) patients have the BCR-ABL fusion gene. The constitutively activated BCR-ABL tyrosine kinase is a critical pathogenetic event in CML. Tyrosine kinase inhibitors (TKIs), such as imatinib, are synthesized small molecules that primarily target BCR-ABL tyrosine kinases and have become a first-line treatment for CML. Detection of BCR-ABL transcript level by real-time quantitative polymerase chain reaction (RQ-PCR) is a clinical routine for evaluating TKI treatment efficacy and predicting long-term response. Furthermore, because they are a main TKI resistance mechanism, the BCR-ABL tyrosine kinase domain (TKD) point mutations that are detected by Sanger sequencing can help clinicians make decisions on subsequent treatment selections. Here, we present protocols for the two abovementioned molecular methods for CML analysis.
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Affiliation(s)
- Ya-Zhen Qin
- Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Peking University People's Hospital, Peking University Institute of Hematology, No. 11 Xizhimen South Street, Beijing, China
| | - Xiao-Jun Huang
- Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Peking University People's Hospital, Peking University Institute of Hematology, No. 11 Xizhimen South Street, Beijing, China.
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8
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Qin Y, Wang D, Qiao C, Shen H, Geng S, Cao Z, Huang X. [A multicenter comparison study on the detection of BCR-ABL tyrosine kinase domain point mutation]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2015; 36:902-5. [PMID: 26632460 PMCID: PMC7342421 DOI: 10.3760/cma.j.issn.0253-2727.2015.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Indexed: 11/23/2022]
Abstract
OBJECTIVE To investigate the accuracy and consistency of the detection of BCR-ABL tyrosine kinase domain point mutation among different laboratories. METHODS Every one of 6 laboratories prepared 10 cDNA samples from tyrosine kinase inhibitors resistant BCR-ABL (P210 or P190) positive patients'bone marrow or peripheral blood. Each cDNA sample was divided into 6 aliquots and delivered to the laboratories. All 6 laboratories tested BCR-ABL point mutations of 60 samples according to their own protocols. Peking University People's Hospital analyzed the comparison results based on both the reports and sequencing chromatogram from all laboratories. RESULTS All laboratories reported the same nucleotide and corresponding amino acid mutations in 37 samples (61.7%). Of 60 samples, 53 had confirmed mutation types, and a total of 23 types were included; 1 had no mutation; mutation types of 6 samples could not be determined because of the big differences among chromatograms from different laboratories. Low percentages of mutants were significantly related to results inconsistency (P=0.008). Inconsistent result of one sample was caused by the unique chromatogram of the mutant L248V, and one by the non-coverage amplification of PCR product from different laboratories. Amplification was failed in 3 samples. Testing or sequencing mistakes occurred in 7 samples. The differences in the mutant percentages among laboratories were less than 20% in the 80.6% of samples with confirmed results. Low internal control gene copies (ABL<10 000) were significantly related to both failed amplification and big differences among chromatograms from different laboratories (P=0.005 and <0.001, respectively). CONCLUSION Problems in the clinical routine detection of BCR-ABL point mutation could be exposed and improvement could be achieved by sample exchange and comparison. Low percentage of mutant is the main reason which causes the discrepancy of BCR-ABL point mutation results among different laboratories.
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Affiliation(s)
- Yazhen Qin
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China
| | | | | | | | | | | | - Xiaojun Huang
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China
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9
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Egan DN, Beppu L, Radich JP. Patients with Philadelphia-positive leukemia with BCR-ABL kinase mutations before allogeneic transplantation predominantly relapse with the same mutation. Biol Blood Marrow Transplant 2014; 21:184-9. [PMID: 25300870 DOI: 10.1016/j.bbmt.2014.09.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 09/10/2014] [Indexed: 10/24/2022]
Abstract
Despite the successes of tyrosine kinase inhibitors (TKIs) in improving outcomes in patients with chronic myeloid leukemia (CML) and Philadelphia-positive acute lymphoblastic leukemia (Ph + ALL), allogeneic hematopoietic stem cell transplantation (HSCT) continues to be an important and potentially curative option for selected patients with either disease. After HSCT, TKIs are increasingly being used to treat or prevent disease relapse, and practice patterns suggest that these TKIs are often chosen empirically without regard to pre-HSCT mutation status. We investigated whether ABL kinase domain mutations persist after transplantation and, thus, whether pre-HSCT mutation status should inform the selection of post-HSCT TKIs in these patients. We retrospectively analyzed adults who underwent allogeneic HSCT for CML and Ph + ALL at our institution between 2000 and 2010, and we identified subjects who had detectable BCR-ABL transcripts by polymerase chain reaction (PCR), as well as available RNA for Sanger sequencing of the ABL kinase domain, in both the pre- and post-HSCT settings. In total, 95 CML and 20 Ph + ALL patients with positive PCR transcripts were identified, of which 10 (10.5%) and 4 (20.0%), respectively, were found to have pre-HSCT ABL kinase mutations known to confer TKI resistance. In 9 (64.2%) of these 14 patients, the same kinase mutation was also detectable at an average time of 191 days after HSCT. Seven (50.0%) of the 14 harboring mutations had relapsed/refractory disease by last follow-up, of which, in retrospect, 6 had received a predictably ineffective TKI within the first 100 days after transplantation based on our mutation analysis. These data support the idea that pre-existing mutations in the ABL kinase domain, frequently associated with resistance to TKIs and prevalent in a transplantation population, are persistently detectable in the majority of patients after transplantation. We propose that such resistance patterns should be considered when selecting TKIs in the post-HSCT setting, including clinical trials of post-HSCT TKI prophylaxis.
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Affiliation(s)
- Daniel N Egan
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, Washington.
| | - Lan Beppu
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, Washington
| | - Jerald P Radich
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, Washington
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10
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Kastner R, Zopf A, Preuner S, Pröll J, Niklas N, Foskett P, Valent P, Lion T, Gabriel C. Rapid identification of compound mutations in patients with Philadelphia-positive leukaemias by long-range next generation sequencing. Eur J Cancer 2013; 50:793-800. [PMID: 24365090 DOI: 10.1016/j.ejca.2013.11.030] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 11/21/2013] [Accepted: 11/25/2013] [Indexed: 01/21/2023]
Abstract
An emerging problem in patients with Philadelphia (Ph)-positive leukaemias is the occurrence of cells with multiple mutations in the BCR-ABL1 tyrosine kinase domain (TKD) associated with high resistance to different tyrosine kinase inhibitors. Rapid and sensitive detection of leukaemic subclones carrying such changes, referred to as compound mutations, is therefore of increasing clinical relevance. However, current diagnostic methods including next generation sequencing (NGS) of short fragments do not optimally meet these requirements. We have therefore established a long-range (LR) NGS approach permitting massively parallel sequencing of the entire TKD length of 933bp in a single read using 454 sequencing with the GS FLX+ instrument (454 Life Sciences). By testing a series of individual and consecutive specimens derived from six patients with chronic myeloid leukaemia, we demonstrate that long-range NGS analysis permits sensitive identification of mutations and their assignment to the same or to separate subclones. This approach also facilitates readily interpretable documentation of insertions and deletions in the entire BCR-ABL1 TKD. The long-range NGS findings were reevaluated by an independent technical approach in select cases. Polymerase chain reaction (PCR) amplicons of the BCR-ABL1 TKD derived from individual specimens were subcloned into pGEM®-T plasmids, and >100 individual clones were subjected to analysis by Sanger sequencing. The NGS results were confirmed, thus documenting the reliability of the new technology. Long-range NGS analysis therefore provides an economic approach to the identification of compound mutations and other genetic alterations in the entire BCR-ABL1 TKD, and represents an important advancement of the diagnostic armamentarium for rapid assessment of impending resistant disease.
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Affiliation(s)
- R Kastner
- Children's Cancer Research Institute, Vienna, Austria; Labdia Labordiagnostik GmbH, Vienna, Austria
| | - A Zopf
- Red Cross Transfusion Service for Upper Austria, Linz, Austria
| | - S Preuner
- Children's Cancer Research Institute, Vienna, Austria; Labdia Labordiagnostik GmbH, Vienna, Austria
| | - J Pröll
- Red Cross Transfusion Service for Upper Austria, Linz, Austria
| | - N Niklas
- Red Cross Transfusion Service for Upper Austria, Linz, Austria
| | - P Foskett
- Imperial Molecular Pathology Laboratory, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - P Valent
- Department of Medicine I, Division of Hematology and Hemostaseology and Ludwig Boltzmann Cluster Oncology, Medical University of Vienna, Vienna, Austria
| | - T Lion
- Children's Cancer Research Institute, Vienna, Austria; Labdia Labordiagnostik GmbH, Vienna, Austria; Department of Pediatrics, Medical University of Vienna, Austria.
| | - C Gabriel
- Red Cross Transfusion Service for Upper Austria, Linz, Austria
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11
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Press RD, Kamel-Reid S, Ang D. BCR-ABL1 RT-qPCR for monitoring the molecular response to tyrosine kinase inhibitors in chronic myeloid leukemia. J Mol Diagn 2013; 15:565-76. [PMID: 23810242 DOI: 10.1016/j.jmoldx.2013.04.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 03/14/2013] [Accepted: 04/08/2013] [Indexed: 12/16/2022] Open
Abstract
The pathognomonic genetic alteration in chronic myeloid leukemia is the formation of the BCR-ABL1 fusion gene, which produces a constitutively active tyrosine kinase that drives leukemic transformation. Targeted tyrosine kinase inhibitor treatment with imatinib, nilotinib, dasatinib, bosutinib, and ponatinib is the cornerstone of modern therapy for this hematologic malignancy. Real-time quantitative RT-PCR (RT-qPCR, also RQ-PCR) of BCR-ABL1 RNA is a necessary laboratory technique for monitoring the efficacy of tyrosine kinase inhibitor therapy and quantitatively assessing minimal residual disease. The molecular response measured by BCR-ABL1 RT-qPCR assists in identifying suboptimal responses and can help inform the decision to switch to alternative therapies that may be more efficacious (or to pursue more stringent monitoring). Furthermore, the tyrosine kinase inhibitor-mediated molecular response provides valuable risk stratification and prognostic information on long-term outcomes. Despite these attributes, informed, universal, practical utilization of this well-established monitoring test will require heightened efforts by the molecular diagnostics laboratory community to adopt the standardized reporting units of the International Scale. Without widespread adoption of the International Scale, the consensus major molecular response and early molecular response treatment thresholds will not be definable, and optimal clinical outcomes for patients with chronic myeloid leukemia may not be achieved.
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Affiliation(s)
- Richard D Press
- Department of Pathology and Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97201, USA.
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12
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Abstract
Pre-messenger RNA splicing is significantly changed in cancer cells leading to the expression of cancer-specific transcripts. These transcripts have the potential to be used as cancer biomarkers and also as targets for new therapeutic approaches. In addition, the cancer-specific transcripts have the potential to alter the drug response of the cancer cells creating a chemo-resistant state. This later property of alternative splicing presents a challenge to clinicians in the design of effective therapeutic regimens. When a patient's cancer relapses it is frequently refractory to standard chemotherapies resulting in a poor clinical outcome. Therefore, understanding the mechanisms of how alternative splicing can lead to chemo-resistance is critical to the effective delivery of treatment. Here, we will discuss the impact of alternative splicing variants on drug metabolism and activation; on drug interactions with cell signaling pathways; and on cell death pathways in cancer therapeutics. In addition to the initial characterization of splicing variants, the mechanisms leading to alterations in splicing are being studied in the setting of chemo-resistance and will be discussed here. The promise of therapeutic intervention to obviate the impact of these splicing variants will significantly enhance treatment options for cancer patients.
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13
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Gniot M, Wasilewska EM, Lewandowski K. K356dup--an in-frame insertion in the BCR-ABL gene in an imatinib-resistant chronic myeloid leukemia. Int J Lab Hematol 2012; 34:e3-6. [PMID: 25998099 DOI: 10.1111/j.1751-553x.2012.01443.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M Gniot
- Department of Hematology, University of Medical Sciences, Poznan, Poland.
| | - E M Wasilewska
- Department of Hematology, University of Medical Sciences, Bialystok, Poland
| | - K Lewandowski
- Department of Hematology, University of Medical Sciences, Poznan, Poland
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Tan Y, Chen X, Qi X, Li G, Wang J, Bian S, Xu Z, Wang H. Acute lymphoblastic leukemia expressing b3a2 (p210), e1a2 (p190), and variant e1a2 BCR-ABL transcripts: a case report and review of the literature. Acta Haematol 2012; 128:119-23. [PMID: 22760091 DOI: 10.1159/000338261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Accepted: 03/16/2012] [Indexed: 11/19/2022]
Affiliation(s)
- Yanhong Tan
- Institute of Hematology, Second Hospital of Shanxi Medical University, Taiyuan, PR China
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Characterization of ABL exon 7 deletion by molecular genetic and bioinformatic methods reveals no association with imatinib resistance in chronic myeloid leukemia. Med Oncol 2011; 29:2136-42. [DOI: 10.1007/s12032-011-0092-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Accepted: 10/11/2011] [Indexed: 10/15/2022]
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16
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Alternative splicing in oncogenic kinases: from physiological functions to cancer. J Nucleic Acids 2011; 2012:639062. [PMID: 22007291 PMCID: PMC3189609 DOI: 10.1155/2012/639062] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Accepted: 07/14/2011] [Indexed: 01/13/2023] Open
Abstract
Among the 518 protein kinases encoded by the human kinome, several of them act as oncoproteins in human cancers. Like other eukaryotic genes, oncogenes encoding protein kinases are frequently subjected to alternative splicing in coding as well as noncoding sequences. In the present paper, we will illustrate how alternative splicing can significantly impact on the physiological functions of oncogenic protein kinases, as demonstrated by mouse genetic model studies. This includes examples of membrane-bound tyrosine kinases receptors (FGFR2, Ret, TrkB, ErbB4, and VEGFR) as well as cytosolic protein kinases (B-Raf). We will further discuss how regular alternative splicing events of these kinases are in some instances implicated in oncogenic processes during tumor progression (FGFR, TrkB, ErbB2, Abl, and AuroraA). Finally, we will present typical examples of aberrant splicing responsible for the deregulation of oncogenic kinases activity in cancers (AuroraB, Jak2, Kit, Met, and Ron).
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Ernst T, La Rosée P, Müller MC, Hochhaus A. BCR-ABL Mutations in Chronic Myeloid Leukemia. Hematol Oncol Clin North Am 2011; 25:997-1008, v-vi. [DOI: 10.1016/j.hoc.2011.09.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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18
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Abstract
Caspases, a family of aspartate-specific cysteine proteases, play a major role in apoptosis and a variety of physiological and pathological processes. Fourteen mammalian caspases have been identified and can be divided into two groups: inflammatory caspases and apoptotic caspases. Based on the structure and function, the apoptotic caspases are further grouped into initiator/apical caspases (caspase-2, -8, -9, and -10) and effector/executioner caspases (caspase-3, -6, and -7). In this paper, we discuss what we have learned about the role of individual effector caspase in mediating both apoptotic and nonapoptotic events, with special emphasis on leukemia-specific oncoproteins in relation to effector caspases.
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Nadarajan VS, Ang CH, Syed-Sultan MK, Bee PC. Imatinib resistance and blast transformation of chronic myeloid leukemia associated with a novel tri-nucleotide insertion mutation of BCR-ABL kinase domain at position K294. Ann Hematol 2011; 91:125-7. [DOI: 10.1007/s00277-011-1215-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Accepted: 03/09/2011] [Indexed: 12/13/2022]
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BCR-ABL isoforms associated with intrinsic or acquired resistance to imatinib: more heterogeneous than just ABL kinase domain point mutations? Med Oncol 2011; 29:219-26. [PMID: 21221851 DOI: 10.1007/s12032-010-9781-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Accepted: 12/09/2010] [Indexed: 10/18/2022]
Abstract
Imatinib, a small molecule inhibitor of ABL, PDGFR and C-KIT, has revolutionized treatment of chronic myeloid leukaemia (CML). However, resistance to treatment is of increasing importance and often is due to point mutations in the Abl kinase domain (Abl KD). Here, we analysed clinical outcome and mutation status in two independent Nordic populations (n = 77) of imatinib-resistant CML patients. We detected BCR-ABL transcripts containing point mutations of residues in the P-loop, A-loop and other kinase domain residues in 32 patients (42%). In contrast to previous data, mutations in BCR-ABL were as frequently found in patients with primary resistance (56%) as with secondary resistance (53%). No T315I mutations were found in the study cohort. BCR-ABL splice variants were identified in a significant number of our cases (19%): BCR-ABL transcripts of variable length; a variant fusion transcript joining BCR exon 14 sequences to ABL exon 4; partial, in-frame-deletion of exon 4 due to induction of a cryptic splice site by the L248V and finally, alternative splicing of ABL exon 7 sequences. Though the majority of splice variants observed in this study do not encode functional proteins, alternative splicing appears to represent a common phenomenon in the biology of CML. We conclude that Abl KD point mutations represent a major mechanism of imatinib resistance. Other sequence irregularities were also detected, but their significance in conferring resistance is unclear. Diagnostic strategies looking for imatinib-resistant clones should be designed to detect a broader profile of BCR-ABL variants than just point mutations.
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Gaillard JB, Arnould C, Bravo S, Donadio D, Exbrayat C, Jourdan E, Reboul D, Chiesa J, Lavabre-Bertrand T. Exon 7 deletion in the bcr-abl gene is frequent in chronic myeloid leukemia patients and is not correlated with resistance against imatinib. Mol Cancer Ther 2010; 9:3083-9. [PMID: 21045136 DOI: 10.1158/1535-7163.mct-10-0595] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Chronic myeloid leukemia (CML) patients treated with imatinib develop frequent resistance generally due to a point mutation. Recently, large rearrangements of abl sequence have also been described. In this study, we focused on the complete deletion of exon 7. We screened for bcr-abl(delexon7) in 63 resistant patients by high-resolution melting (HRM) analysis and direct sequencing. Moreover, we analyzed expression of abl(delexon7) and bcr-abl(delexon7) in 17 CML patients at diagnosis, 32 patients at resistance, and 20 negative controls by quantitative PCR or fragment length analysis. bcr-abl(delexon7) was detected on 34 (54%) among 63 resistant patients by HRM, showing an increase in the sensitivity of screening, because only 3.2% could be detected by direct sequencing. This deletion was not associated with a point mutation (P = 0.3362). In addition, abl(delexon7) was found in all tested samples with the same pattern of expression, suggesting an alternative splicing mechanism. In the bcr-abl component, there was no statistical difference between CML patients at diagnosis and resistant patients (P = 0.2815) as regarding bcr-abl(delexon7) proportion, thus arguing against involvement of deletion in resistance. Moreover, among two patients harboring bcr-abl(delexon7) at diagnosis, one experienced a complete disappearance of this transcript, and the other decreased >75% at resistance. In conclusion, bcr-abl(delexon7) is frequently observed in CML patients when using sensitive techniques. It seems to be the result of an alternative splicing mechanism and to be independent from the occurrence of resistance.
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Affiliation(s)
- Jean-Baptiste Gaillard
- Department of Clinical Cytology and Cytogenetics, Nîmes University Hospital, Nîmes, France
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22
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Branford S, Hughes TP. Practical Considerations for Monitoring Patients With Chronic Myeloid Leukemia. Semin Hematol 2010; 47:327-34. [DOI: 10.1053/j.seminhematol.2010.06.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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23
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Khorashad JS, Milojkovic D, Reid AG. Variant isoforms of BCR-ABL1 in chronic myelogenous leukemia reflect alternative splicing of ABL1 in normal tissue - letter. Mol Cancer Ther 2010; 9:2152. [PMID: 20571070 DOI: 10.1158/1535-7163.mct-10-0311] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Gruber FX, Ernst T, Kiselev Y, Hochhaus A, Mikkola I. Detection of drug-resistant clones in chronic myelogenous leukemia patients during dasatinib and nilotinib treatment. Clin Chem 2009; 56:469-73. [PMID: 20040619 DOI: 10.1373/clinchem.2009.133843] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
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.
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Affiliation(s)
- Franz X Gruber
- Department of Pharmacy, Section of Pharmacology, University of Tromsø, Tromsø, Norway
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25
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Hayette S, Chabane K, Tchirkov A, Berger MG, Nicolini FE, Tournilhac O. Detection of twelve nucleotides insertion in the BCR-ABL kinase domain in an imatinib-resistant but dasatinib-sensitive patient with bi-phenotypic acute leukemia. Haematologica 2009; 94:1324-6. [PMID: 19734429 DOI: 10.3324/haematol.2009.007864] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
MESH Headings
- Base Sequence/genetics
- Benzamides
- Dasatinib
- Drug Resistance, Neoplasm
- Female
- Fusion Proteins, bcr-abl/antagonists & inhibitors
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/metabolism
- Humans
- Imatinib Mesylate
- Leukemia, Biphenotypic, Acute/drug therapy
- Leukemia, Biphenotypic, Acute/enzymology
- Leukemia, Biphenotypic, Acute/genetics
- Middle Aged
- Piperazines/administration & dosage
- Protein Kinase Inhibitors/administration & dosage
- Protein Structure, Tertiary/genetics
- Protein-Tyrosine Kinases/antagonists & inhibitors
- Protein-Tyrosine Kinases/genetics
- Protein-Tyrosine Kinases/metabolism
- Pyrimidines/administration & dosage
- Sequence Deletion
- Thiazoles/administration & dosage
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26
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Ma W, Kantarjian H, Yeh CH, Zhang ZJ, Cortes J, Albitar M. BCR-ABL truncation due to premature translation termination as a mechanism of resistance to kinase inhibitors. Acta Haematol 2009; 121:27-31. [PMID: 19332983 DOI: 10.1159/000210060] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2009] [Accepted: 02/05/2009] [Indexed: 01/18/2023]
MESH Headings
- Animals
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Fusion Proteins, bcr-abl/antagonists & inhibitors
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/metabolism
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/enzymology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Mutation
- Peptide Chain Termination, Translational/drug effects
- Peptide Chain Termination, Translational/genetics
- Philadelphia Chromosome
- Protein Kinase Inhibitors/pharmacology
- Protein Kinase Inhibitors/therapeutic use
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Affiliation(s)
- Wanlong Ma
- Department of Hematology and Oncology, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA 92675, USA
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Passetti F, Ferreira CG, Costa FF. The impact of microRNAs and alternative splicing in pharmacogenomics. THE PHARMACOGENOMICS JOURNAL 2009; 9:1-13. [PMID: 19156160 DOI: 10.1038/tpj.2008.14] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- F Passetti
- Laboratory of Bioinformatics and Computational Biology, Division of Clinical and Translational Research, Research Coordination (CPQ), Instituto Nacional de Câncer, Rio de Janeiro, Brazil
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Abstract
AbstractThe remarkable progress made in the treatment of chronic myeloid leukemia (CML) over the past decade has been accompanied by steady improvements in our capacity to accurately and sensitively monitor response to therapy. After the initial target of therapy, complete cytogenetic response (CCR), is achieved, peripheral blood BCR-ABL transcript levels measured by real-time quantitative reverse transcriptase PCR (RQ-PCR) define the subsequent response targets, major and complete molecular response (MMR and CMR). The majority of patients on first-line imatinib therapy achieve a “safe haven” defined as a confirmed MMR, but 20% to 30% stop imatinib due to intolerance and/or resistance. Many imatinib-resistant patients can be effectively treated with second generation tyrosine kinase inhibitors (TKIs), but the actual drug selected should be based on the resistance profile of each inhibitor, in addition to issues of tolerance and disease phase. The main purpose of monitoring response with cytogenetics and RQ-PCR is to identify patients likely to achieve better long-term outcome if they are switched early to second-line therapy, either another TKI or an allograft. Mutation screening is most valuable in cases of loss of response to imatinib or a second-line TKI, but there are other settings where a high yield of mutations may justify regular mutation screening.
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Numata K, Yoshida R, Nagasaki M, Saito A, Imoto S, Miyano S. ExonMiner: Web service for analysis of GeneChip Exon array data. BMC Bioinformatics 2008; 9:494. [PMID: 19036125 PMCID: PMC2621370 DOI: 10.1186/1471-2105-9-494] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2008] [Accepted: 11/26/2008] [Indexed: 12/22/2022] Open
Abstract
Background Some splicing isoform-specific transcriptional regulations are related to disease. Therefore, detection of disease specific splice variations is the first step for finding disease specific transcriptional regulations. Affymetrix Human Exon 1.0 ST Array can measure exon-level expression profiles that are suitable to find differentially expressed exons in genome-wide scale. However, exon array produces massive datasets that are more than we can handle and analyze on personal computer. Results We have developed ExonMiner that is the first all-in-one web service for analysis of exon array data to detect transcripts that have significantly different splicing patterns in two cells, e.g. normal and cancer cells. ExonMiner can perform the following analyses: (1) data normalization, (2) statistical analysis based on two-way ANOVA, (3) finding transcripts with significantly different splice patterns, (4) efficient visualization based on heatmaps and barplots, and (5) meta-analysis to detect exon level biomarkers. We implemented ExonMiner on a supercomputer system in order to perform genome-wide analysis for more than 300,000 transcripts in exon array data, which has the potential to reveal the aberrant splice variations in cancer cells as exon level biomarkers. Conclusion ExonMiner is well suited for analysis of exon array data and does not require any installation of software except for internet browsers. What all users need to do is to access the ExonMiner URL . Users can analyze full dataset of exon array data within hours by high-level statistical analysis with sound theoretical basis that finds aberrant splice variants as biomarkers.
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Affiliation(s)
- Kazuyuki Numata
- Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan.
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30
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Characterization of BCR-ABL deletion mutants from patients with chronic myeloid leukemia. Leukemia 2008; 22:1184-90. [DOI: 10.1038/leu.2008.65] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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31
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Engh R. Protein Kinase Inhibitors Highlight the Complexities of Drug-Target Non-Covalent Interactions. BIOTECHNOL BIOTEC EQ 2008. [DOI: 10.1080/13102818.2008.10817551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Kaur P, Feldhahn N, Zhang B, Trageser D, Müschen M, Pertz V, Groffen J, Heisterkamp N. Nilotinib treatment in mouse models of P190 Bcr/Abl lymphoblastic leukemia. Mol Cancer 2007; 6:67. [PMID: 17958915 PMCID: PMC2169263 DOI: 10.1186/1476-4598-6-67] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2007] [Accepted: 10/25/2007] [Indexed: 11/10/2022] Open
Abstract
Background Ph-positive leukemias are caused by the aberrant fusion of the BCR and ABL genes. Nilotinib is a selective Bcr/Abl tyrosine kinase inhibitor related to imatinib, which is widely used to treat chronic myelogenous leukemia. Because Ph-positive acute lymphoblastic leukemia only responds transiently to imatinib therapy, we have used mouse models to test the efficacy of nilotinib against lymphoblastic leukemia caused by the P190 form of Bcr/Abl. Results After transplant of 10,000 highly malignant leukemic cells into compatible recipients, untreated mice succumbed to leukemia within 21 days, whereas mice treated with 75 mg/kg nilotinib survived significantly longer. We examined cells from mice that developed leukemia while under treatment for Bcr/Abl kinase domain point mutations but these were not detected. In addition, culture of such cells ex vivo showed that they were as sensitive as the parental cell line to nilotinib but that the presence of stromal support allowed resistant cells to grow out. Nilotinib also exhibited impressive anti-leukemia activity in P190 Bcr/Abl transgenic mice that had developed overt leukemia/lymphoma masses and that otherwise would have been expected to die within 7 days. Visible lymphoma masses disappeared within six days of treatment and leukemic cell numbers in peripheral blood were significantly reduced. Treated mice survived more than 30 days. Conclusion These results show that nilotinib has very impressive anti-leukemia activity but that lymphoblastic leukemia cells can become unresponsive to it both in vitro and in vivo through mechanisms that appear to be Bcr/Abl independent.
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Affiliation(s)
- Pavinder Kaur
- Section of Molecular Carcinogenesis, Division of Hematology/Oncology, Saban Research Institute, Childrens Hospital Los Angeles and the Keck School of Medicine, University of Southern California, Los Angeles, California, USA.
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Curvo RPM, Zalcberg IR, Scholl V, Pires V, Moellmann-Coelho A, Moreira MAM. A recurrent splicing variant without c-ABL Exon 7 in Imatinib-resistant patients. Leuk Res 2007; 32:508-10. [PMID: 17570524 DOI: 10.1016/j.leukres.2007.04.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2007] [Revised: 04/19/2007] [Accepted: 04/25/2007] [Indexed: 10/23/2022]
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