1
|
Tadesse F, Asres G, Abubeker A, Gebremedhin A, Radich J. Spectrum of BCR-ABL Mutations and Treatment Outcomes in Ethiopian Imatinib-Resistant Patients With Chronic Myeloid Leukemia. JCO Glob Oncol 2021; 7:1187-1193. [PMID: 34292760 PMCID: PMC8457809 DOI: 10.1200/go.21.00058] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Despite the successes achieved in chronic myeloid leukemia (CML) with tyrosine kinase inhibitor (TKI) therapy, resistance remains an obstacle. The most common mechanism of resistance is the acquisition of a point mutation in the BCR-ABL kinase domain. Few studies have reported African patients with CML in regard to such mutations. We here report the types of BCR-ABL mutations in Ethiopian imatinib-resistant patients with CML and their outcome.
Collapse
Affiliation(s)
| | - Getahun Asres
- University of Gondar, College of Medicine and Health Sciences, Gondar, Ethiopia
| | - Abdulaziz Abubeker
- Addis Ababa University College of Health Sciences, Addis Ababa, Ethiopia
| | - Amha Gebremedhin
- Addis Ababa University College of Health Sciences, Addis Ababa, Ethiopia
| | | |
Collapse
|
2
|
Fergany AAM, Tatarskiy VV. RNA Splicing: Basic Aspects Underlie Antitumor Targeting. Recent Pat Anticancer Drug Discov 2020; 15:293-305. [PMID: 32900350 DOI: 10.2174/1574892815666200908122402] [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: 03/31/2020] [Revised: 07/15/2020] [Accepted: 07/29/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND RNA splicing, a fundamental step in gene expression, is aimed at intron removal and ordering of exons to form the protein's reading frame. OBJECTIVE This review is focused on the role of RNA splicing in cancer biology; the splicing abnormalities that lead to tumor progression emerge as targets for therapeutic intervention. METHODS We discuss the role of aberrant mRNA splicing in carcinogenesis and drug response. RESULTS AND CONCLUSION Pharmacological modulation of RNA splicing sets the stage for treatment approaches in situations where mRNA splicing is a clinically meaningful mechanism of the disease.
Collapse
Affiliation(s)
- Alzahraa A M Fergany
- Department of Occupational and Environmental Health, Graduate School of Pharmaceutical Science, Tokyo University of Science, Chiba, Japan
| | - Victor V Tatarskiy
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russian Federation
| |
Collapse
|
3
|
Sakurai M, Okamoto S, Matsumura I, Murakami S, Takizawa M, Waki M, Hirano D, Watanabe-Nakaseko R, Kobayashi N, Iino M, Mitsui H, Ishikawa Y, Takahashi N, Kawaguchi T, Suzuki R, Yamamoto K, Kizaki M, Ohnishi K, Naoe T, Akashi K. Treatment outcomes of chronic-phase chronic myeloid leukemia with resistance and/or intolerance to a 1st-line tyrosine kinase inhibitor in Japan: the results of the New TARGET study 2nd-line. Int J Hematol 2020; 111:812-825. [DOI: 10.1007/s12185-020-02843-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 11/27/2022]
|
4
|
Chien SH, Liu HM, Chen PM, Ko PS, Lin JS, Chen YJ, Lee LH, Hsiao LT, Chiou TJ, Gau JP, Yang MH, Liu CY. The landscape of BCR-ABL mutations in patients with Philadelphia chromosome-positive leukaemias in the era of second-generation tyrosine kinase inhibitors. Hematol Oncol 2020; 38:390-398. [PMID: 32011024 DOI: 10.1002/hon.2721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 08/24/2019] [Accepted: 01/12/2020] [Indexed: 11/09/2022]
Abstract
BCR-ABL mutations are associated with resistance to tyrosine kinase inhibitors (TKIs) in Philadelphia chromosome-positive leukaemia. The emergence of these mutations in the era of second-generation TKIs, such as dasatinib and nilotinib, remains an evolving field. We conducted a retrospective study to quantitatively characterize the BCR-ABL transcript and mutation status during treatment with first-generation and second-generation TKI therapies. BCR-ABL mutations were detected by direct sequencing for patients with Philadelphia chromosome-positive leukaemia receiving TKI therapies. The efficacy of TKI therapy was quantitatively assessed by calculating the log reduction of BCR-ABL transcripts, which was measured using real-time quantitative polymerase chain reaction. Fisher's exact test was performed to analyse the associations of log reduction <3 and mutation status. We found 35 patients harbouring 55 mutations of 43 different types, of which 30% occurred in patients receiving imatinib, 27% in nilotinib, and 43% in dasatinib. We found a novel germline mutation, N336 N (AAC➔AAT), and two novel frameshift mutations, Asn358Thr fs*14 and Gly251Ala fs*16. T315I was the most common missense mutation, followed by V299L and F317L. Intron 8 35-bp insertion was the most frequent frameshift mutation. Both missense and multiple BCR-ABL mutations were significantly associated with worse molecular response compared with the molecular response of patients without mutation. Missense mutations, rather than frameshift, were associated with less log reduction, while the T315I, F317L, and T315A mutations were significantly correlated with poor log reduction. Collectively, amino acid substitutions at T315I, F317L, and T315A accounted for the majority of missense mutations and the loss of major molecular response. Mutation analysis is essential for patients receiving TKI therapy who exhibit an unfavourable response. The present study provided a landscape of BCR-ABL mutations in the era of second-generation TKIs.
Collapse
Affiliation(s)
- Sheng-Hsuan Chien
- Division of Transfusion Medicine, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan.,Faculty of Medicine, National Yang-Ming University, Taipei, Taiwan.,Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan.,Division of Hematology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Hsueng-Mei Liu
- Division of Transfusion Medicine, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Po-Ming Chen
- Department of Food and Science and biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Po-Shen Ko
- Faculty of Medicine, National Yang-Ming University, Taipei, Taiwan.,Division of Hematology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Jeong-Shi Lin
- Division of Transfusion Medicine, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan.,Faculty of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Ying-Ju Chen
- Division of Transfusion Medicine, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Li-Hsuan Lee
- Division of Transfusion Medicine, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Liang-Tsai Hsiao
- Faculty of Medicine, National Yang-Ming University, Taipei, Taiwan.,Division of Hematology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Tzeon-Jye Chiou
- Division of Transfusion Medicine, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan.,Faculty of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Jyh-Pyng Gau
- Faculty of Medicine, National Yang-Ming University, Taipei, Taiwan.,Division of Hematology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Muh-Hwa Yang
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan.,Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chun-Yu Liu
- Division of Transfusion Medicine, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan.,Faculty of Medicine, National Yang-Ming University, Taipei, Taiwan.,Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
| |
Collapse
|
5
|
ABL1 tyrosine kinase domain mutations in chronic myeloid leukemia treatment resistance. Mol Biol Rep 2019; 46:3747-3754. [PMID: 31025148 DOI: 10.1007/s11033-019-04816-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 04/12/2019] [Indexed: 12/15/2022]
Abstract
The development of mutations in the BCR-ABL1 fusion gene transcript causes resistance to tyrosine kinase inhibitors (TKIs) based therapy in chronic myeloid leukemia (CML). Thereby, screening for BCR-ABL1 mutations is advised especially in patients undergoing poor response to treatment. In the current study the authors investigated 43 patients with CML that failed or had suboptimal response to TKIs treatment. Blood samples were collected from patients that were treated with TKIs. The analysis of genetic mutations was performed using a semi-nested PCR assay, followed by Sanger sequencing. The analysis revealed 15 mutations (32.55%): 14 point mutations and an exon 7 deletion. In roughly 30% of cases, mutations in the BCR-ABL1 fusion gene are common causes for treatment resistance.
Collapse
|
6
|
Wang BD, Lee NH. Aberrant RNA Splicing in Cancer and Drug Resistance. Cancers (Basel) 2018; 10:E458. [PMID: 30463359 PMCID: PMC6266310 DOI: 10.3390/cancers10110458] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 11/15/2018] [Accepted: 11/15/2018] [Indexed: 12/22/2022] Open
Abstract
More than 95% of the 20,000 to 25,000 transcribed human genes undergo alternative RNA splicing, which increases the diversity of the proteome. Isoforms derived from the same gene can have distinct and, in some cases, opposing functions. Accumulating evidence suggests that aberrant RNA splicing is a common and driving event in cancer development and progression. Moreover, aberrant splicing events conferring drug/therapy resistance in cancer is far more common than previously envisioned. In this review, aberrant splicing events in cancer-associated genes, namely BCL2L1, FAS, HRAS, CD44, Cyclin D1, CASP2, TMPRSS2-ERG, FGFR2, VEGF, AR and KLF6, will be discussed. Also highlighted are the functional consequences of aberrant splice variants (BCR-Abl35INS, BIM-γ, IK6, p61 BRAF V600E, CD19-∆2, AR-V7 and PIK3CD-S) in promoting resistance to cancer targeted therapy or immunotherapy. To overcome drug resistance, we discuss opportunities for developing novel strategies to specifically target the aberrant splice variants or splicing machinery that generates the splice variants. Therapeutic approaches include the development of splice variant-specific siRNAs, splice switching antisense oligonucleotides, and small molecule inhibitors targeting splicing factors, splicing factor kinases or the aberrant oncogenic protein isoforms.
Collapse
Affiliation(s)
- Bi-Dar Wang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Eastern Shore, Princess Anne, MD 21853, USA.
| | - Norman H Lee
- Department of Pharmacology and Physiology, School of Medicine and Health Sciences, George Washington University, GW Cancer Center, Washington, DC 20037, USA.
| |
Collapse
|
7
|
Mikhailov I. BCR-ABL exon 7 deletion and novel point mutation in patient with chronic myelogenous leukemia and TKI resistance. Clin Case Rep 2018; 6:2057-2060. [PMID: 30455891 PMCID: PMC6230594 DOI: 10.1002/ccr3.1794] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 07/28/2018] [Accepted: 08/14/2018] [Indexed: 11/18/2022] Open
Abstract
I report a novel BCR-ABL point mutation c.844G>C p.E282Q and a case of combination of two BCR-ABL point mutations (p.E282Q and p.L298R) and exon 7 deletion (del. c.1086-1270) in TKI-resistant patient. These point mutations were present only in a truncated transcript and were absent in "wild-type" BCR-ABL transcript.
Collapse
Affiliation(s)
- Ilya Mikhailov
- Faculty of Fundamental MedicineLomonosov Moscow State UniversityMoscowRussian Federation
| |
Collapse
|
8
|
Yuda J, Miyamoto T, Odawara J, Ohkawa Y, Semba Y, Hayashi M, Miyamura K, Tanimoto M, Yamamoto K, Taniwaki M, Akashi K. Persistent detection of alternatively spliced BCR-ABL variant results in a failure to achieve deep molecular response. Cancer Sci 2017; 108:2204-2212. [PMID: 28801986 PMCID: PMC5666036 DOI: 10.1111/cas.13353] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/07/2017] [Accepted: 08/08/2017] [Indexed: 01/04/2023] Open
Abstract
Treatment with tyrosine kinase inhibitors (TKI) may sequentially induce TKI‐resistant BCR‐ABL mutants in chronic myeloid leukemia (CML). Conventional PCR monitoring of BCR‐ABL is an important indicator to determine therapeutic intervention for preventing disease progression. However, PCR cannot separately quantify amounts of BCR‐ABL and its mutants, including alternatively spliced BCR‐ABL with an insertion of 35 intronic nucleotides (BCR‐ABLIns35bp) between ABL exons 8 and 9, which introduces the premature termination and loss of kinase activity. To assess the clinical impact of BCR‐ABL mutants, we performed deep sequencing analysis of BCR‐ABL transcripts of 409 samples from 37 patients with suboptimal response to frontline imatinib who were switched to nilotinib. At baseline, TKI‐resistant mutations were documented in 3 patients, whereas BCR‐ABLIns35bp was detected in all patients. After switching to nilotinib, both BCR‐ABL and BCR‐ABLIns35bp became undetectable in 3 patients who attained complete molecular response (CMR), whereas in the remaining all 34 patients, BCR‐ABLIns35bp was persistently detected, and minimal residual disease (MRD) fluctuated at low but detectable levels. PCR monitoring underestimated molecular response in 5 patients whose BCR‐ABLIns35bp was persisted, although BCR‐ABLIns35bp does not definitively mark TKI resistance. Therefore, quantification of BCR‐ABLIns35bp is useful for evaluating “functional” MRD and determining the effectiveness of TKI with accuracy.
Collapse
Affiliation(s)
- Junichiro Yuda
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan
| | - Toshihiro Miyamoto
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan
| | - Jun Odawara
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan.,Department of Advanced Medical Initiatives, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yasuyuki Ohkawa
- Department of Advanced Medical Initiatives, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yuichiro Semba
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan.,Department of Advanced Medical Initiatives, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masayasu Hayashi
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan.,Department of Advanced Medical Initiatives, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Koichi Miyamura
- Department of Hematology, Japanese Red Cross Nagoya Daiichi Hospital, Nagoya, Japan
| | - Mitsune Tanimoto
- Department of Hematology, Oncology and Respiratory Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Science, Okayama, Japan
| | - Kazuhito Yamamoto
- Department of Clinical Research and Department of Hematology and Cell Therapy, Aichi Cancer Center, Nagoya, Japan
| | - Masafumi Taniwaki
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Koichi Akashi
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan
| |
Collapse
|
9
|
Pan J, Tan YH, Zhao JX, Chen XH, Xu ZF, Xu J, Chang JM, Xue F, Zhang N, Ren FG, Zhang YF, Wang XJ, Wang HW. [Discovery of a novel spliceosome of ABL gene (ABL(Δexon7+35INS)) and its association with TKIs resistance in chronic myeloid leukemia]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2016; 37:503-6. [PMID: 27431076 PMCID: PMC7348335 DOI: 10.3760/cma.j.issn.0253-2727.2016.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Indexed: 11/05/2022]
Abstract
OBJECTIVE To explore whether the ABL(Δexon7) and ABL(35INS) spliceosome contributed to TKIs resistance. METHODS Screening ABL(Δexon7) and ABL(35INS) in 74 normal people and 76 CML patients (53 patients in remission and 23 patients with TKIs resistance) by using polyacrylamide gel electrophoresis combined with cloning sequencing. RESULTS A novel spliceosome ABL(Δexon7+ 35INS) (ABL(Δexon7) and ABL(3)5INS existed at the same time) was identified and the mutation was detected in 8 (10.8%) of 74 normal people, 4 (7.5%) of 53 remission patients and 2 (8.7%) of 23 resistant patients. While 47 (63.5%) cases expressed ABL(Δexon7) and 8 (10.8% ) cases expressed ABL(35INS) in 74 healthy people, 30 (56.6%) cases expressed ABL(Δexon7) and 5 (9.4% ) cases expressed ABL(35INS) in 53 remission patients, 12 (52.2%) cases expressed ABL(Δexon7) and 3(13.0%) cases expressed ABL(35INS) in 23 resistant patients. Three kinds of spliceosome in all groups had no statistical difference. CONCLUSION ABL(Δexon7+ 35INS), ABL(Δexon7) and ABL(35INS) may be not uncommon in ABL gene and were unrelated to resistance in CML with TKIs treatment. ABL(35INS) were often accompanying with exon 7 deletion.
Collapse
Affiliation(s)
- J Pan
- Department of Hematology, the Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Molecular Diagnosis and Treatment of Blood Diseases, Taiyuan 030001, China
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Patkar N, Ghodke K, Joshi S, Chaudhary S, Mascerhenas R, Dusseja S, Mahadik S, Gaware S, Tembhare P, Gujral S, Kabre S, Kadam-Amare P, Jain H, Dangi U, Bagal B, Khattry N, Sengar M, Arora B, Narula G, Banavali S, Menon H, Subramanian PG. Characteristics ofBCR-ABLkinase domain mutations in chronic myeloid leukemia from India: not just missense mutations but insertions and deletions are also associated with TKI resistance. Leuk Lymphoma 2016; 57:2653-60. [DOI: 10.3109/10428194.2016.1157868] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
|
11
|
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.
Collapse
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.
| |
Collapse
|
12
|
Compound mutations in BCR-ABL1 are not major drivers of primary or secondary resistance to ponatinib in CP-CML patients. Blood 2015; 127:703-12. [PMID: 26603839 DOI: 10.1182/blood-2015-08-660977] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 11/10/2015] [Indexed: 12/14/2022] Open
Abstract
BCR-ABL1 kinase domain mutations can confer resistance to first- and second-generation tyrosine kinase inhibitors (TKIs) in chronic myeloid leukemia (CML). In preclinical studies, clinically achievable concentrations of the third-generation BCR-ABL1 TKI ponatinib inhibit T315I and all other single BCR-ABL1 mutants except T315M, which generates a single amino acid exchange, but requires 2 sequential nucleotide exchanges. In addition, certain compound mutants (containing ≥2 mutations in cis) confer resistance. Initial analyses based largely on conventional Sanger sequencing (SS) have suggested that the preclinical relationship between BCR-ABL1 mutation status and ponatinib efficacy is generally recapitulated in patients receiving therapy. Thus far, however, such analyses have been limited by the inability of SS to definitively identify compound mutations or mutations representing less than ~20% of total alleles (referred to as "low-level mutations"), as well as limited patient follow-up. Here we used next-generation sequencing (NGS) to define the baseline BCR-ABL1 mutation status of 267 heavily pretreated chronic phase (CP)-CML patients from the PACE trial, and used SS to identify clonally dominant mutants that may have developed on ponatinib therapy (30.1 months median follow-up). Durable cytogenetic and molecular responses were observed irrespective of baseline mutation status and included patients with compound mutations. No single or compound mutation was identified that consistently conferred primary and/or secondary resistance to ponatinib in CP-CML patients. Ponatinib is effective in CP-CML irrespective of baseline mutation status.
Collapse
|
13
|
Cavelier L, Ameur A, Häggqvist S, Höijer I, Cahill N, Olsson-Strömberg U, Hermanson M. Clonal distribution of BCR-ABL1 mutations and splice isoforms by single-molecule long-read RNA sequencing. BMC Cancer 2015; 15:45. [PMID: 25880391 PMCID: PMC4335374 DOI: 10.1186/s12885-015-1046-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 01/27/2015] [Indexed: 12/17/2022] Open
Abstract
Background The evolution of mutations in the BCR-ABL1 fusion gene transcript renders CML patients resistant to tyrosine kinase inhibitor (TKI) based therapy. Thus screening for BCR-ABL1 mutations is recommended particularly in patients experiencing poor response to treatment. Herein we describe a novel approach for the detection and surveillance of BCR-ABL1 mutations in CML patients. Methods To detect mutations in the BCR-ABL1 transcript we developed an assay based on the Pacific Biosciences (PacBio) sequencing technology, which allows for single-molecule long-read sequencing of BCR-ABL1 fusion transcript molecules. Samples from six patients with poor response to therapy were analyzed both at diagnosis and follow-up. cDNA was generated from total RNA and a 1,6 kb fragment encompassing the BCR-ABL1 transcript was amplified using long range PCR. To estimate the sensitivity of the assay, a serial dilution experiment was performed. Results Over 10,000 full-length BCR-ABL1 sequences were obtained for all samples studied. Through the serial dilution analysis, mutations in CML patient samples could be detected down to a level of at least 1%. Notably, the assay was determined to be sufficiently sensitive even in patients harboring a low abundance of BCR-ABL1 levels. The PacBio sequencing successfully identified all mutations seen by standard methods. Importantly, we identified several mutations that escaped detection by the clinical routine analysis. Resistance mutations were found in all but one of the patients. Due to the long reads afforded by PacBio sequencing, compound mutations present in the same molecule were readily distinguished from independent alterations arising in different molecules. Moreover, several transcript isoforms of the BCR-ABL1 transcript were identified in two of the CML patients. Finally, our assay allowed for a quick turn around time allowing samples to be reported upon within 2 days. Conclusions In summary the PacBio sequencing assay can be applied to detect BCR-ABL1 resistance mutations in both diagnostic and follow-up CML patient samples using a simple protocol applicable to routine diagnosis. The method besides its sensitivity, gives a complete view of the clonal distribution of mutations, which is of importance when making therapy decisions.
Collapse
Affiliation(s)
- Lucia Cavelier
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| | - Adam Ameur
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| | - Susana Häggqvist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| | - Ida Höijer
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| | - Nicola Cahill
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| | | | - Monica Hermanson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| |
Collapse
|
14
|
Al-Dewik NI, Jewell AP, Yassin MA, El-Ayoubi HR, Morsi HM. Studying the impact of presence of point mutation, insertion mutation and additional chromosomal abnormalities in chronic myeloid leukemia patients treated with imatinib mesylate in the State of Qatar. QSCIENCE CONNECT 2014. [DOI: 10.5339/connect.2014.13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Nader I Al-Dewik
- 1National Center for Cancer Care and Research (NCCCR), Hamad Medical Corporation (HMC), Doha, Qatar
- 2Faculty of Health and Social Care Sciences, Kingston University and St George's University of London, United Kingdom
| | - Andrew P Jewell
- 2Faculty of Health and Social Care Sciences, Kingston University and St George's University of London, United Kingdom
- 3Medical Research Centre, HMC, Doha, Qatar
| | - Mohammed A Yassin
- 1National Center for Cancer Care and Research (NCCCR), Hamad Medical Corporation (HMC), Doha, Qatar
| | - Hanadi R El-Ayoubi
- 1National Center for Cancer Care and Research (NCCCR), Hamad Medical Corporation (HMC), Doha, Qatar
| | - Hisham M Morsi
- 2Faculty of Health and Social Care Sciences, Kingston University and St George's University of London, United Kingdom
- 3Medical Research Centre, HMC, Doha, Qatar
| |
Collapse
|
15
|
Zhang XZ, Yin AH, Zhu XY, Ding Q, Wang CH, Chen YX. Using an exon microarray to identify a global profile of gene expression and alternative splicing in K562 cells exposed to sodium valproate. Oncol Rep 2011; 27:1258-65. [PMID: 22200904 PMCID: PMC3583465 DOI: 10.3892/or.2011.1601] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 12/12/2011] [Indexed: 12/22/2022] Open
Abstract
To investigate the effect of valproate treatment on the K562 cell line, a model for chronic myelogenous leukaemia, the growth and survival of the K562 cell line were investigated using the Annexin-V/PI dual staining method, and global profiles of gene expression and alternative splicing in K562 cells were assessed using exon microarrays. A significant increase in cell apoptosis was observed in valproate-exposed K562 cells using flow cytometry. A total of 628 transcripts were identified as being significantly differentially expressed. The number of genes demonstrating increased expression levels was greater than the number of genes demonstrating decreased expression levels (445 genes vs. 183 genes, respectively). The significant enrichment analysis of GO terms for the differentially expressed genes revealed that these genes are involved in many important biological processes such as apoptosis. Six of the genes observed to be differentially expressed that might be involved in apoptosis were selected to undergo qRT-PCR validation. In total, 198 candidates of alternative splicing variants were identified. Among them, three alternative splicing events were selected for validation, and CBLC and TBX1 were confirmed to be alternatively spliced by semi-nested PCR. In conclusion, valproate exposure facilitated cell apoptosis, altered mRNA expression and alternative splicing events in the K562 cell line.
Collapse
Affiliation(s)
- Xiang-Zhong Zhang
- Department of Hematology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, PR China
| | | | | | | | | | | |
Collapse
|
16
|
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]
|
17
|
The BCR-ABL35INS insertion/truncation mutant is kinase-inactive and does not contribute to tyrosine kinase inhibitor resistance in chronic myeloid leukemia. Blood 2011; 118:5250-4. [PMID: 21908430 DOI: 10.1182/blood-2011-05-349191] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Chronic myeloid leukemia is effectively treated with imatinib, but reactivation of BCR-ABL frequently occurs through acquisition of kinase domain mutations. The additional approved ABL tyrosine kinase inhibitors (TKIs) nilotinib and dasatinib, along with investigational TKIs such as ponatinib (AP24534) and DCC-2036, support the possibility that mutation-mediated resistance in chronic myeloid leukemia can be fully controlled; however, the molecular events underlying resistance in patients lacking BCR-ABL point mutations are largely unknown. We previously reported on an insertion/truncation mutant, BCR-ABL(35INS), in which structural integrity of the kinase domain is compromised and all ABL sequence beyond the kinase domain is eliminated. Although we speculated that BCR-ABL(35INS) is kinase-inactive, recent reports propose this mutant contributes to ABL TKI resistance. We present cell-based and biochemical evidence establishing that BCR-ABL(35INS) is kinase-inactive and does not contribute to TKI resistance, and we find that detection of BCR-ABL(35INS) does not consistently track with or explain resistance in clinical samples from chronic myeloid leukemia patients.
Collapse
|
18
|
Shieh MP, Mitsuhashi M, Lilly M. Moving on up: Second-Line Agents as Initial Treatment for Newly-Diagnosed Patients with Chronic Phase CML. Clin Med Insights Oncol 2011; 5:185-99. [PMID: 21792346 PMCID: PMC3140277 DOI: 10.4137/cmo.s6416] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The treatment of chronic myelogenous leukemia (CML) was revolutionized by the development of imatinib mesylate, a small molecule inhibitor of several protein tyrosine kinases, including the ABL1 protein tyrosine kinase. The current second generation of FDA-approved ABL tyrosine kinase inhibitors, dasatinib and nilotinib, are more potent inhibitors of BCR-ABL1 kinase in vitro. Originally approved for the treatment of patients who were refractory to or intolerant of imatinib, dasatinib and nilotinib are now also FDA approved in the first-line setting. The choice of tyrosine kinase inhibitor (ie, standard or high dose imatinib, dasatinib, nilotinib) to use for initial therapy in chronic-phase CML (CML-CP) will not always be obvious. Therapy selection will depend on both clinical and molecular factors, which we will discuss in this review.
Collapse
Affiliation(s)
- Marie P Shieh
- Division of Hematology-Oncology, Department of Medicine, and Chao Family Comprehensive Cancer Center, University of California, Irvine, CA, USA
| | | | | |
Collapse
|