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Branford S, Apperley JF. Measurable residual disease in chronic myeloid leukemia. Haematologica 2022; 107:2794-2809. [PMID: 36453517 PMCID: PMC9713565 DOI: 10.3324/haematol.2022.281493] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Indexed: 12/03/2022] Open
Abstract
Chronic myeloid leukemia is characterized by a single genetic abnormality resulting in a fusion gene whose mRNA product is easily detected and quantified by reverse-transcriptase polymerase chain reaction analysis. Measuring residual disease was originally introduced to identify patients relapsing after allogeneic stem cell transplantation but rapidly adopted to quantify responses to tyrosine kinase inhibitors. Real-time quantitative polymerase chain reaction is now an essential tool for the management of patients and is used to influence treatment decisions. In this review we track this development including the international collaboration to standardize results, discuss the integration of molecular monitoring with other factors that affect patients' management, and describe emerging technology. Four case histories describe varying scenarios in which the accurate measurement of residual disease identified patients at risk of disease progression and allowed appropriate investigations and timely clinical intervention.
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Affiliation(s)
- Susan Branford
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, Australia,School of Medicine, University of Adelaide, Adelaide, Australia,Clinical and Health Sciences, University of South Australia, Adelaide, Australia,S. Branford
| | - Jane F. Apperley
- Department of Haematology, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UK,Centre for Haematology, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, UK
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Shanmuganathan N, Branford S. Multiplex technologies for the assessment of minimal residual disease and low-level mutation detection in leukaemia: mass spectrometry versus next-generation sequencing. Br J Haematol 2021; 196:19-30. [PMID: 34124782 DOI: 10.1111/bjh.17623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/10/2021] [Accepted: 05/17/2021] [Indexed: 01/07/2023]
Abstract
With the focus of leukaemia management shifting to the implications of low-level disease burden, increasing attention is being paid on the development of highly sensitive methodologies required for detection. There are various techniques capable of identification of measurable residual disease (MRD) either evidencing as relevant mutation detection [e.g. nucleophosmin 1 (NPM1) mutation] or trace levels of leukaemic clonal populations. The vast majority of these methods only permit detection of a single clone or mutation. However, mass spectrometry and next-generation sequencing enable the interrogation of multiple genes simultaneously, facilitating a more complete genomic profile. In the present review, we explore the methodologies of both techniques in conjunction with the important advantages and limitations associated with each assay. We also highlight the evidence and the various instances where either technique has been used and propose future strategies for MRD detection.
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Affiliation(s)
- Naranie Shanmuganathan
- Department of Haematology, Royal Adelaide Hospital and SA Pathology, Adelaide, South Australia, Australia.,Department of Genetics and Molecular Pathology and Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia.,Precision Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia.,School of Pharmacy and Medical Science, University of South Australia, Adelaide, South Australia, Australia.,School of Medicine, University of Adelaide, Adelaide, South Australia, Australia
| | - Susan Branford
- Department of Genetics and Molecular Pathology and Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia.,Precision Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia.,School of Pharmacy and Medical Science, University of South Australia, Adelaide, South Australia, Australia.,School of Medicine, University of Adelaide, Adelaide, South Australia, Australia
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3
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Benjamin ESB, Ravindra N, Rajamani BM, Anandan S, Kausalya B, Veldore V, Mathews V, Velayudhan SR, Balasubramanian P. BCR-ABL1 kinase domain mutation analysis by next generation sequencing detected additional mutations in chronic myeloid leukemia patients with suboptimal response to imatinib. Leuk Lymphoma 2021; 62:1528-1531. [PMID: 33478278 PMCID: PMC7611165 DOI: 10.1080/10428194.2021.1872074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 12/28/2020] [Indexed: 10/22/2022]
Affiliation(s)
| | | | | | | | | | | | - Vikram Mathews
- Department of Hematology, Christian Medical College, Vellore, India
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Prospective assessment of NGS-detectable mutations in CML patients with nonoptimal response: the NEXT-in-CML study. Blood 2020; 135:534-541. [PMID: 31877211 DOI: 10.1182/blood.2019002969] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 12/03/2019] [Indexed: 12/20/2022] Open
Abstract
In chronic myeloid leukemia (CML) patients, tyrosine kinase inhibitors (TKIs) may select for drug-resistant BCR-ABL1 kinase domain (KD) mutants. Although Sanger sequencing (SS) is considered the gold standard for BCR-ABL1 KD mutation screening, next-generation sequencing (NGS) has recently been assessed in retrospective studies. We conducted a prospective, multicenter study (NEXT-in-CML) to assess the frequency and clinical relevance of low-level mutations and the feasibility, cost, and turnaround times of NGS-based BCR-ABL1 mutation screening in a routine setting. A series of 236 consecutive CML patients with failure (n = 124) or warning (n = 112) response to TKI therapy were analyzed in parallel by SS and NGS in 1 of 4 reference laboratories. Fifty-one patients (22 failure, 29 warning) who were negative for mutations by SS had low-level mutations detectable by NGS. Moreover, 29 (27 failure, 2 warning) of 60 patients who were positive for mutations by SS showed additional low-level mutations. Thus, mutations undetectable by SS were identified in 80 out of 236 patients (34%), of whom 42 (18% of the total) had low-level mutations somehow relevant for clinical decision making. Prospective monitoring of mutation kinetics demonstrated that TKI-resistant low-level mutations are invariably selected if the patients are not switched to another TKI or if they are switched to a inappropriate TKI or TKI dose. The NEXT-in-CML study provides for the first time robust demonstration of the clinical relevance of low-level mutations, supporting the incorporation of NGS-based BCR-ABL1 KD mutation screening results in the clinical decision algorithms.
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Trojani A, Pungolino E, Rossi G, D’Adda M, Lodola M, Camillo BD, Perego A, Turrini M, Orlandi E, Borin L, Iurlo A, Malato S, Spina F, Latargia ML, Lanza F, Artale S, Anghilieri M, Carraro MC, Canal GD, Morra E, Cairoli R. Wide-transcriptome analysis and cellularity of bone marrow CD34+/lin- cells of patients with chronic-phase chronic myeloid leukemia at diagnosis vs. 12 months of first-line nilotinib treatment. Cancer Biomark 2017; 21:41-53. [DOI: 10.3233/cbm-170209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Alessandra Trojani
- Division of Hematology, ASST Grande Ospedale Metropolitano Niguarda, Milano, Italy
| | - Ester Pungolino
- Division of Hematology, ASST Grande Ospedale Metropolitano Niguarda, Milano, Italy
| | - Giuseppe Rossi
- Department of Hematology, ASST Spedali Civili, Brescia, Italy
| | - Mariella D’Adda
- Department of Hematology, ASST Spedali Civili, Brescia, Italy
| | - Milena Lodola
- Division of Hematology, ASST Grande Ospedale Metropolitano Niguarda, Milano, Italy
| | - Barbara Di Camillo
- Department of Information Engineering, University of Padova, Padova, Italy
| | | | - Mauro Turrini
- Division of Hematology, Department of Internal Medicine, Valduce Hospital, Como, Italy
| | - Ester Orlandi
- Hematology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Lorenza Borin
- Hematology Division, San Gerardo Hospital, Monza, Italy
| | - Alessandra Iurlo
- Oncohematology Division, IRCCS Ca’ Granda – Maggiore Policlinico Hospital Foundation, Milano, Italy
| | - Simona Malato
- Hematology and Bone Marrow Transplantation Unit, San Raffaele Scientific Institute, Milano, Italy
| | - Francesco Spina
- Division of Hematology – Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | | | | | | | | | | | - Gabriella De Canal
- Pathology Department, Cytogenetics, ASST Grande Ospedale Metropolitano Niguarda, Milano, Italy
| | - Enrica Morra
- Executive Committee, Rete Ematologia Lombarda, Italy
| | - Roberto Cairoli
- Division of Hematology, ASST Grande Ospedale Metropolitano Niguarda, Milano, Italy
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6
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Minervini CF, Cumbo C, Orsini P, Anelli L, Zagaria A, Impera L, Coccaro N, Brunetti C, Minervini A, Casieri P, Tota G, Russo Rossi A, Specchia G, Albano F. Mutational analysis in BCR - ABL1 positive leukemia by deep sequencing based on nanopore MinION technology. Exp Mol Pathol 2017; 103:33-37. [DOI: 10.1016/j.yexmp.2017.06.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 05/22/2017] [Accepted: 06/25/2017] [Indexed: 01/11/2023]
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Treatment-free remission in patients with chronic myeloid leukemia. Int J Hematol 2017; 108:355-364. [PMID: 28689264 DOI: 10.1007/s12185-017-2295-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 05/01/2017] [Indexed: 01/09/2023]
Abstract
Clinical trials have formally demonstrated that in chronic myeloid leukemia (CML), patients treated with tyrosine kinase inhibitors (TKI) who achieved and maintained deep molecular responses could discontinue their treatment after several years without facing overt signs of disease relapse in approximately 50% of the cases. In patients with a molecular relapse, prompt re-introduction of TKI therapy was able to rapidly restore deep molecular responses. The concept of a lifelong therapy with TKI has thus been challenged and treatment-free remission (TFR) strategies will soon integrate clinical practice, providing that safe recommendations will be established. In this article, we give an update on TKI discontinuation studies in CML and we also provide an overview of upcoming TFR clinical and biological challenges.
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The impact of multiple low-level BCR-ABL1 mutations on response to ponatinib. Blood 2016; 127:1870-80. [PMID: 26773037 DOI: 10.1182/blood-2015-09-666214] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 01/05/2016] [Indexed: 12/25/2022] Open
Abstract
The third-generation tyrosine kinase inhibitor (TKI) ponatinib shows activity against all common BCR-ABL1 single mutants, including the highly resistant BCR-ABL1-T315I mutant, improving outcome for patients with refractory chronic myeloid leukemia (CML). However, responses are variable, and causal baseline factors have not been well-studied. The type and number of low-level BCR-ABL1 mutations present after imatinib resistance has prognostic significance for subsequent treatment with nilotinib or dasatinib as second-line therapy. We therefore investigated the impact of low-level mutations detected by sensitive mass-spectrometry before ponatinib initiation (baseline) on treatment response in 363 TKI-resistant patients enrolled in the PONATINIB for Chronic Myeloid Leukemia Evaluation and Ph(+)Acute Lymphoblastic Leukemia trial, including 231 patients in chronic phase (CP-CML). Low-level mutations were detected in 53 patients (15%, including low-level T315I in 14 patients); most, however, did not undergo clonal expansion during ponatinib treatment and, moreover, no specific individual mutations were associated with inferior outcome. We demonstrate however, that the number of mutations detectable by mass spectrometry after TKI resistance is associated with response to ponatinib treatment and could be used to refine the therapeutic approach. Although CP-CML patients with T315I (63/231, 27%) had superior responses overall, those with multiple mutations detectable by mass spectrometry (20, 32%) had substantially inferior responses compared with those with T315I as the sole mutation detected (43, 68%). In contrast, for CP-CML patients without T315I, the inferior responses previously observed with nilotinib/dasatinib therapy for imatinib-resistant patients with multiple mutations were not seen with ponatinib treatment, suggesting that ponatinib may prove to be particularly advantageous for patients with multiple mutations detectable by mass spectrometry after TKI resistance.
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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.
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Szankasi P, Schumacher JA, Kelley TW. Detection of BCR-ABL1 mutations that confer tyrosine kinase inhibitor resistance using massively parallel, next generation sequencing. Ann Hematol 2015; 95:201-10. [PMID: 26555285 DOI: 10.1007/s00277-015-2539-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 10/25/2015] [Indexed: 12/19/2022]
Abstract
Detection of BCR-ABL1 mutations that confer resistance to tyrosine kinase inhibitors is important for management of patients with t(9;22);BCR-ABL1-positive (Ph+) leukemias. Testing is often performed using Sanger sequencing (SS) which has relatively poor sensitivity. Given the widespread adoption of next generation sequencing (NGS), we sought to reevaluate the testing in the context of NGS methods. We developed an NGS-based BCR-ABL1 mutation test on the Ion Torrent Personal Genome Machine (PGM) to test for resistance mutations, primarily in the kinase domain in BCR-ABL1. We analyzed 508 clinical samples from patients with Ph+ leukemias. In a subset of these samples (n = 97), we conducted a comparison of the NGS results to a classical SS-based test. NGS facilitated detection of low-level mutations (<20 % allele frequency) that were not detectable by SS. In a subset of cases with multiple mutations, NGS was also able to determine if two mutations were on the same molecule (compound) or on separate molecules (polyclonal) but this was limited by the distance between mutated positions and by the effects of apparent distance-dependent PCR recombination. We found 22 compound mutations that centered on one or two key residues including two novel compound mutants: Q252H/Y253H and F311Y/F359I. The advantages of NGS make it a superior method for inventorying BCR-ABL1 resistance mutations. However, data analysis may be complicated by short read lengths and the effects of PCR recombination.
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Affiliation(s)
| | | | - Todd W Kelley
- Department of Pathology, University of Utah, Salt Lake City, UT, 84112, USA.
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Zerumbone induces mitochondria-mediated apoptosis via increased calcium, generation of reactive oxygen species and upregulation of soluble histone H2AX in K562 chronic myelogenous leukemia cells. Tumour Biol 2015; 36:8479-89. [DOI: 10.1007/s13277-015-3583-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 05/18/2015] [Indexed: 11/25/2022] Open
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Capuozzo M, Ottaiano A, Nava E, Cascone S, Cinque C, Vercellone A, Scognamiglio C, Palumbo E, Iaffaioli RV. Nilotinib for the Frontline Treatment of Chronic Myeloid Leukemia Carrying the p230 Transcript: Dream or Reality? Front Oncol 2014; 4:17. [PMID: 24551597 PMCID: PMC3910244 DOI: 10.3389/fonc.2014.00017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 01/22/2014] [Indexed: 11/13/2022] Open
Affiliation(s)
- Maurizio Capuozzo
- Department of Pharmacy, Local Sanitary Agency (LSA) Naples 3 South , Naples , Italy
| | - Alessandro Ottaiano
- Department of Colorectal Oncology, National Cancer Institute "G. Pascale" Foundation , Naples , Italy
| | - Eduardo Nava
- Department of Pharmacy, Local Sanitary Agency (LSA) Naples 3 South , Naples , Italy
| | - Stefania Cascone
- Department of Pharmacy, Local Sanitary Agency (LSA) Naples 3 South , Naples , Italy
| | - Claudia Cinque
- Local Sanitary Agency (LSA) Naples 1 Center , Naples , Italy
| | - Adriano Vercellone
- Department of Pharmacy, Local Sanitary Agency (LSA) Naples 3 South , Naples , Italy
| | - Corinne Scognamiglio
- Department of Pharmacy, Local Sanitary Agency (LSA) Naples 3 South , Naples , Italy
| | - Emilia Palumbo
- Department of Pharmacy, Local Sanitary Agency (LSA) Naples 3 South , Naples , Italy
| | - Rosario V Iaffaioli
- Department of Colorectal Oncology, National Cancer Institute "G. Pascale" Foundation , Naples , Italy
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Inhibition of PI3K/mTOR overcomes nilotinib resistance in BCR-ABL1 positive leukemia cells through translational down-regulation of MDM2. PLoS One 2013; 8:e83510. [PMID: 24349524 PMCID: PMC3859659 DOI: 10.1371/journal.pone.0083510] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 11/04/2013] [Indexed: 02/05/2023] Open
Abstract
Chronic myeloid leukemia (CML) is a cytogenetic disorder resulting from formation of the Philadelphia chromosome (Ph), that is, the t(9;22) chromosomal translocation and the formation of the BCR-ABL1 fusion protein. Tyrosine kinase inhibitors (TKI), such as imatinib and nilotinib, have emerged as leading compounds with which to treat CML. t(9;22) is not restricted to CML, 20-30% of acute lymphoblastic leukemia (ALL) cases also carry the Ph. However, TKIs are not as effective in the treatment of Ph+ ALL as in CML. In this study, the Ph+ cell lines JURL-MK2 and SUP-B15 were used to investigate TKI resistance mechanisms and the sensitization of Ph+ tumor cells to TKI treatment. The annexin V/PI (propidium iodide) assay revealed that nilotinib induced apoptosis in JURL-MK2 cells, but not in SUP-B15 cells. Since there was no mutation in the tyrosine kinase domain of BCR-ABL1 in cell line SUP-B15, the cells were not generally unresponsive to TKI, as evidenced by dephosphorylation of the BCR-ABL1 downstream targets, Crk-like protein (CrkL) and Grb-associated binder-2 (GAB2). Resistance to apoptosis after nilotinib treatment was accompanied by the constitutive and nilotinib unresponsive activation of the phosphoinositide 3-kinase (PI3K) pathway. Treatment of SUP-B15 cells with the dual PI3K/mammalian target of rapamycin (mTOR) inhibitor BEZ235 alone induced apoptosis in a low percentage of cells, while combining nilotinib and BEZ235 led to a synergistic effect. The main role of PI3K/mTOR inhibitor BEZ235 and the reason for apoptosis in the nilotinib-resistant cells was the block of the translational machinery, leading to the rapid downregulation of the anti-apoptotic protein MDM2 (human homolog of the murine double minute-2). These findings highlight MDM2 as a potential therapeutic target to increase TKI-mediated apoptosis and imply that the combination of PI3K/mTOR inhibitor and TKI might form a novel strategy to combat TKI-resistant BCR-ABL1 positive leukemia.
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