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Sala-Torra O, Reddy S, Hung LH, Beppu L, Wu D, Radich J, Yeung KY, Yeung CCS. Rapid detection of myeloid neoplasm fusions using single-molecule long-read sequencing. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0002267. [PMID: 37699001 PMCID: PMC10497132 DOI: 10.1371/journal.pgph.0002267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 07/17/2023] [Indexed: 09/14/2023]
Abstract
Recurrent gene fusions are common drivers of disease pathophysiology in leukemias. Identifying these structural variants helps stratify disease by risk and assists with therapy choice. Precise molecular diagnosis in low-and-middle-income countries (LMIC) is challenging given the complexity of assays, trained technical support, and the availability of reliable electricity. Current fusion detection methods require a long turnaround time (7-10 days) or advance knowledge of the genes involved in the fusions. Recent technology developments have made sequencing possible without a sophisticated molecular laboratory, potentially making molecular diagnosis accessible to remote areas and low-income settings. We describe a long-read sequencing DNA assay designed with CRISPR guides to select and enrich for recurrent leukemia fusion genes, that does not need a priori knowledge of the abnormality present. By applying rapid sequencing technology based on nanopores, we sequenced long pieces of genomic DNA and successfully detected fusion genes in cell lines and primary specimens (e.g., BCR::ABL1, PML::RARA, CBFB::MYH11, KMT2A::AFF1) using cloud-based bioinformatics workflows with novel custom fusion finder software. We detected fusion genes in 100% of cell lines with the expected breakpoints and confirmed the presence or absence of a recurrent fusion gene in 12 of 14 patient cases. With our optimized assay and cloud-based bioinformatics workflow, these assays and analyses could be performed in under 8 hours. The platform's portability, potential for adaptation to lower-cost devices, and integrated cloud analysis make this assay a candidate to be placed in settings like LMIC to bridge the need of bedside rapid molecular diagnostics.
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Affiliation(s)
- Olga Sala-Torra
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- University of Washington, Seattle, Washington, United States of America
| | - Shishir Reddy
- University of Washington, Seattle, Washington, United States of America
| | - Ling-Hong Hung
- University of Washington, Seattle, Washington, United States of America
| | - Lan Beppu
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - David Wu
- School of Engineering and Technology, University of Washington Tacoma, Tacoma, Washington, United States of America
| | - Jerald Radich
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- School of Engineering and Technology, University of Washington Tacoma, Tacoma, Washington, United States of America
| | - Ka Yee Yeung
- University of Washington, Seattle, Washington, United States of America
| | - Cecilia C. S. Yeung
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- School of Engineering and Technology, University of Washington Tacoma, Tacoma, Washington, United States of America
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2
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Matsuo T, Tashiro H, Sumiyoshi R, Saito S, Shirasaki R, Shirafuji N. Functional expression cloning of molecules inducing CD34 expression in bone marrow-derived stromal myofibroblasts. Biochem Biophys Res Commun 2020; 533:1283-1289. [PMID: 33066959 DOI: 10.1016/j.bbrc.2020.10.006] [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: 09/29/2020] [Accepted: 10/03/2020] [Indexed: 01/01/2023]
Abstract
We have previously shown a fraction of stromal fibroblasts/myofibroblasts (Fibs) from leukemic bone marrow cells expresses leukemia-specific transcripts along with hematopoietic and Fib-related markers. Normal bone marrow-derived Fibs (nFibs) do not express CD34 or CD45; however, nFibs may express hematopoietic markers with some specific stimulations. CD34 expression was detected in nFib cultures following the addition of a culture supernatant of blood mononuclear cells stimulated with phytohemagglutinin (PHA)-P. To identify the molecules responsible for inducing CD34 expression in nFibs, cDNA clones were isolated using functional expression cloning with a library constructed from PHA-P-stimulated human blood mononuclear cells. Positive clones inducing CD34 transcription in nFibs were selected. We confirmed that an isolated positive cDNA clone encoded human interleukin (IL)-1 beta (β). CD34 expression was observed in the nFib cultures with recombinant human (rh) IL-1β protein. And CD34 transcription was suppressed when a rhIL-1β neutralizing antibody was added to the IL-1β-stimulated nFib cultures. nFibs expressed gp130 and IL-6 receptors, and CD45 expression was detected in nFibs cultured with rhIL-1β and rhIL-6. Chronic myelogenous leukemia (CML) cells reportedly respond well to IL-1β. When CML-derived Fibs were cultured with rhIL-1β and rhIL-6, CD45-positive cells increased in number. Cell fate may be influenced by an external specific stimulation without gene introduction.
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Affiliation(s)
- Takuji Matsuo
- Department of Hematology/Oncology, Teikyo University School of Medicine, 2-11-1, Kaga, Itabashi-ku, Tokyo, 173-8606, Japan
| | - Haruko Tashiro
- Department of Hematology/Oncology, Teikyo University School of Medicine, 2-11-1, Kaga, Itabashi-ku, Tokyo, 173-8606, Japan
| | - Ritsu Sumiyoshi
- Department of Hematology/Oncology, Teikyo University School of Medicine, 2-11-1, Kaga, Itabashi-ku, Tokyo, 173-8606, Japan
| | - Sumiko Saito
- Department of Hematology/Oncology, Teikyo University School of Medicine, 2-11-1, Kaga, Itabashi-ku, Tokyo, 173-8606, Japan
| | - Ryosuke Shirasaki
- Department of Hematology/Oncology, Teikyo University School of Medicine, 2-11-1, Kaga, Itabashi-ku, Tokyo, 173-8606, Japan
| | - Naoki Shirafuji
- Department of Hematology/Oncology, Teikyo University School of Medicine, 2-11-1, Kaga, Itabashi-ku, Tokyo, 173-8606, Japan.
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3
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Cumbo C, Anelli L, Specchia G, Albano F. Monitoring of Minimal Residual Disease (MRD) in Chronic Myeloid Leukemia: Recent Advances. Cancer Manag Res 2020; 12:3175-3189. [PMID: 32440215 PMCID: PMC7211966 DOI: 10.2147/cmar.s232752] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 04/23/2020] [Indexed: 12/14/2022] Open
Abstract
Chronic myeloid leukemia (CML) is a myeloproliferative neoplasm caused by the BCR-ABL1 fusion gene generation as a consequence of the t(9;22)(q34;q11) rearrangement. The identification of the BCR-ABL1 transcript was of critical importance for both CML diagnosis and minimal residual disease (MRD) monitoring. In this review, we report the recent advances in the CML MRD monitoring based on RNA, DNA and protein analysis. The detection of the BCR-ABL1 transcript by the quantitative reverse-transcriptase polymerase chain reaction is the gold standard method, but other systems based on digital PCR or on GeneXpert technology have been developed. In the last years, DNA-based assays showed high sensitivity and specificity, and flow cytometric approaches for the detection of the BCR-ABL1 fusion protein have also been tested. Recently, new MRD monitoring systems based on the detection of molecular markers other than the BCR-ABL1 fusion were proposed. These approaches, such as the identification of CD26+ leukemic stem cells, microRNAs and mitochondrial DNA mutations, just remain preliminary and need to be implemented. In the precision medicine era, the constant improvement of the CML MRD monitoring practice could allow clinicians to choose the best therapeutic algorithm and a more accurate selection of CML patients eligible for the tyrosine kinase inhibitors discontinuation.
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Affiliation(s)
- Cosimo Cumbo
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, Bari 70124, Italy
| | - Luisa Anelli
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, Bari 70124, Italy
| | - Giorgina Specchia
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, Bari 70124, Italy
| | - Francesco Albano
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, Bari 70124, Italy
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Krumbholz M, Goerlitz K, Albert C, Lawlor J, Suttorp M, Metzler M. Large amplicon droplet digital PCR for DNA-based monitoring of pediatric chronic myeloid leukaemia. J Cell Mol Med 2019; 23:4955-4961. [PMID: 31199062 PMCID: PMC6653534 DOI: 10.1111/jcmm.14321] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 02/27/2019] [Accepted: 03/25/2019] [Indexed: 12/16/2022] Open
Abstract
Quantification of tumour‐specific molecular markers at the RNA and DNA level for treatment response monitoring is crucial for risk‐adapted stratification and guidance of individualized therapy in leukaemia and other malignancies. Most pediatric leukaemias and solid tumours of mesenchymal origin are characterized by a relatively low mutation burden at the single nucleotide level and the presence of recurrent chromosomal translocations. The genomic fusion sites resulting from translocations are stable molecular tumour markers; however, repeat‐rich DNA sequences flanking intronic breakpoints limit the design of high sensitivity PCR assays for minimal residual disease (MRD) monitoring. Here, we quantitatively evaluated the impact of repeat elements on assay selection and the feasibility of using extended amplicons (≤1330 bp) amplified by droplet digital PCR to monitor pediatric chronic myeloid leukaemia (CML). Molecular characterization of 178 genomic BCR‐ABL1 fusion sites showed that 64% were located within sequence repeat elements, impeding optimal primer/probe design. Comparative quantification of DNA and RNA BCR‐ABL1 copy numbers in 687 specimens from 55 pediatric patients revealed that their levels were highly correlated. The combination of droplet digital PCR, double quenched probes and extended amplicons represents a valuable tool for sensitive MRD assessment in CML and may be adapted to other translocation‐positive tumours.
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Affiliation(s)
- Manuela Krumbholz
- Department of Pediatrics, University Hospital Erlangen, Erlangen, Germany
| | - Katharina Goerlitz
- Department of Pediatrics, University Hospital Erlangen, Erlangen, Germany
| | - Christian Albert
- Department of Pediatrics, University Hospital Erlangen, Erlangen, Germany
| | - Jennifer Lawlor
- Department of Pediatrics, University Hospital Erlangen, Erlangen, Germany.,Department of Biology, Division of Genetics, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Meinolf Suttorp
- Medical Faculty, Pediatric Hemato-Oncology, Technical University, Dresden, Germany
| | - Markus Metzler
- Department of Pediatrics, University Hospital Erlangen, Erlangen, Germany
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5
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Huang M, Wei S. Overview of Molecular Testing of Cytology Specimens. Acta Cytol 2019; 64:136-146. [PMID: 30917368 DOI: 10.1159/000497187] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 01/23/2019] [Indexed: 12/15/2022]
Abstract
OBJECTIVE Utilizing cytology specimens for molecular testing has attracted increasing attention in the era of personalized medicine. Cytology specimens are clinically easier to access. The samples can be quickly and completely fixed in a very short time of fixation before tissue degradation occurs, compared to hours or days of fixation in surgical pathology specimens. In addition, cytology specimens can be fixed without formalin, which can significantly damage DNA and RNA. All these factors contribute to the superb quality of DNA and RNA in cytology specimens for molecular tests. STUDY DESIGN We summarize the most pertinent information in the literature regarding molecular testing in the field of cytopathology. RESULTS The first part focuses on the types of cytological specimens that can be used for molecular testing, including the advantages and limitations. The second section describes the common molecular tests and their clinical application. CONCLUSION Various types of cytology specimens are suitable for many molecular tests, which may require additional clinical laboratory validation.
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Affiliation(s)
- Min Huang
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Shuanzeng Wei
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA,
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6
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Colorimetric determination of BCR/ABL fusion genes using a nanocomposite consisting of Au@Pt nanoparticles covered with a PAMAM dendrimer and acting as a peroxidase mimic. Mikrochim Acta 2018; 185:401. [DOI: 10.1007/s00604-018-2940-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 07/30/2018] [Indexed: 12/22/2022]
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7
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Cumbo C, Impera L, Minervini CF, Orsini P, Anelli L, Zagaria A, Coccaro N, Tota G, Minervini A, Casieri P, Brunetti C, Rossi AR, Parciante E, Specchia G, Albano F. Genomic BCR-ABL1 breakpoint characterization by a multi-strategy approach for "personalized monitoring" of residual disease in chronic myeloid leukemia patients. Oncotarget 2018. [PMID: 29541390 PMCID: PMC5834283 DOI: 10.18632/oncotarget.23971] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
For monitoring minimal residual disease (MRD) in chronic myeloid leukemia (CML) the most recommended method is quantitative RT-PCR (RT-qPCR) for measuring BCR-ABL1 transcripts. Several studies reported that a DNA-based assay enhances the sensitivity of detection of the BCR-ABL1 genomic rearrangement, even if its characterization results difficult. We developed a DNA-based method for detecting and quantifying residual BCR-ABL1 positive leukemic stem cells in CML patients. We propose two alternative approaches: the first one is a fluorescence in situ hybridization (FISH)-based step followed by Sanger sequencing; the second one employs MinION, a single molecule sequencer based on nanopore technology. Finally, after defining the BCR-ABL1 genomic junction, we performed the target CML patient–specific quantification, using droplet digital PCR (ddPCR). FISH and MinION steps, respectively, together with ddPCR analysis, greatly reduce the complexity that has impeded the use of “personalized monitoring” of CML in clinical practice. Our report suggests a feasible pipeline, in terms of costs and reproducibility, aimed at characterizing and quantifying the genomic BCR-ABL1 rearrangement during MRD monitoring in CML patients.
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Affiliation(s)
- Cosimo Cumbo
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Luciana Impera
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | | | - Paola Orsini
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Luisa Anelli
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Antonella Zagaria
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Nicoletta Coccaro
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Giuseppina Tota
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Angela Minervini
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Paola Casieri
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Claudia Brunetti
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Antonella Russo Rossi
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Elisa Parciante
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Giorgina Specchia
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Francesco Albano
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
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8
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Abstract
In chronic myeloid leukemia (CML), the BCR-ABL fusion gene is both the therapeutic target of tyrosine kinase inhibitors and the indisputable direct marker of disease burden. Thus, sensitive assays for BCR-ABL now drive therapeutic options and are good surrogates for short- and long-term outcomes. Because CML is such an ideal model, new methods are arising that should make testing in CML faster, more reliable, and reach a greater sensitivity. These methods should be able to be transferred to other hematological malignancies that have mutation markers.
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Affiliation(s)
- Cecilia C S Yeung
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave North, G7-910, Seattle, WA, 98109, USA.
| | - Daniel Egan
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave North, G7-910, Seattle, WA, 98109, USA
| | - Jerald Radich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave North, G7-910, Seattle, WA, 98109, USA
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9
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Monitoring of childhood ALL using BCR-ABL1 genomic breakpoints identifies a subgroup with CML-like biology. Blood 2017; 129:2771-2781. [PMID: 28331056 DOI: 10.1182/blood-2016-11-749978] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 03/17/2017] [Indexed: 12/20/2022] Open
Abstract
We used the genomic breakpoint between BCR and ABL1 genes for the DNA-based monitoring of minimal residual disease (MRD) in 48 patients with childhood acute lymphoblastic leukemia (ALL). Comparing the results with standard MRD monitoring based on immunoglobulin/T-cell receptor (Ig/TCR) gene rearrangements and with quantification of IKZF1 deletion, we observed very good correlation for the methods in a majority of patients; however, >20% of children (25% [8/32] with minor and 12.5% [1/8] with major-BCR-ABL1 variants in the consecutive cohorts) had significantly (>1 log) higher levels of BCR-ABL1 fusion than Ig/TCR rearrangements and/or IKZF1 deletion. We performed cell sorting of the diagnostic material and assessed the frequency of BCR-ABL1-positive cells in various hematopoietic subpopulations; 12% to 83% of non-ALL B lymphocytes, T cells, and/or myeloid cells harbored the BCR-ABL1 fusion in patients with discrepant MRD results. The multilineage involvement of the BCR-ABL1-positive clone demonstrates that in some patients diagnosed with BCR-ABL1-positive ALL, a multipotent hematopoietic progenitor is affected by the BCR-ABL1 fusion. These patients have BCR-ABL1-positive clonal hematopoiesis resembling a chronic myeloid leukemia (CML)-like disease manifesting in "lymphoid blast crisis." The biological heterogeneity of BCR-ABL1-positive ALL may impact the patient outcomes and optimal treatment (early stem cell transplantation vs long-term administration of tyrosine-kinase inhibitors) as well as on MRD testing. Therefore, we recommend further investigations on CML-like BCR-ABL1-positive ALL.
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10
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Egan D, Radich J. Making the diagnosis, the tools, and risk stratification: More than just BCR-ABL. Best Pract Res Clin Haematol 2016; 29:252-263. [PMID: 27839566 DOI: 10.1016/j.beha.2016.10.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 10/10/2016] [Indexed: 10/20/2022]
Abstract
The implementation of cytogenetic and molecular techniques into standard clinical practice has improved our ability to more accurately diagnose and monitor CML. Routine peripheral blood BCR-ABL transcript testing can help monitor response, predict outcome, and detect early resistance or poor adherence to TKI therapy. The widely-used Sokal, Hasford and EUTOS clinical risk stratification scores were developed in patients receiving chemotherapy, interferon and imatinib, respectively; their predictive ability in patients receiving next-generation tyrosine kinase inhibitors (TKIs) remains to be established. Newer more sensitive molecular techniques are being developed that may aid in the expanding emphasis on discontinuing therapy in patients with a deep and consistent molecular response.
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Affiliation(s)
- Daniel Egan
- Clinical Research Division, Fred Hutchinson Cancer Research Center, United States.
| | - Jerald Radich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, United States.
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11
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Marum JE, Branford S. Current developments in molecular monitoring in chronic myeloid leukemia. Ther Adv Hematol 2016; 7:237-251. [PMID: 27695615 PMCID: PMC5026293 DOI: 10.1177/2040620716657994] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Molecular monitoring plays an essential role in the clinical management of chronic myeloid leukemia (CML) patients, and now guides clinical decision making. Quantitative reverse-transcriptase-polymerase-chain-reaction (qRT-PCR) assessment of BCR-ABL1 transcript levels has become the standard of care protocol in CML. However, further developments are required to assess leukemic burden more efficiently, monitor minimal residual disease (MRD), detect mutations that drive resistance to tyrosine kinase inhibitor (TKI) therapy and identify predictors of response to TKI therapy. Cartridge-based BCR-ABL1 quantitation, digital PCR and next generation sequencing are examples of technologies which are currently being explored, evaluated and translated into the clinic. Here we review the emerging molecular methods/technologies currently being developed to advance molecular monitoring in CML.
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Affiliation(s)
- Justine Ellen Marum
- Centre for Cancer Biology, SA Pathology, Adelaide, Australia
- Division of Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Susan Branford
- Centre for Cancer Biology, SA Pathology, Adelaide, Australia
- School of Pharmacy and Medical Science, University of South Australia, Adelaide, SA, Australia
- School of Medicine, University of Adelaide, SA, Adelaide, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
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12
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Yeung CCS, Egan D, Radich JP. Molecular monitoring of chronic myeloid leukemia: present and future. Expert Rev Mol Diagn 2016; 16:1083-1091. [PMID: 27552202 DOI: 10.1080/14737159.2016.1227243] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
INTRODUCTION Fusion of BCR-ABL1 genes causes chronic myeloid leukemia (CML). As a reliable marker of disease burden, it also serves as the target of tyrosine kinase inhibitors (TKIs). New more sensitive molecular diagnostic tools for BCR-ABL1 can contribute to therapeutic decision-making, especially in considering drug discontinuation for patients enjoying prolonged deep molecular response. Areas covered: Several novel platforms are transforming CML molecular diagnostics to enable faster point-of-care devices, better understanding of clonal diversity and resistance mutations. Here, we review these molecular platforms, knowing implementation in other hematological malignancies will ensue. Expert commentary: Treatment with TKI in CML is the first example of a highly effective targeted therapy. Monitoring of BCR-ABL1 mRNA is standard in assessing disease burden being highly predictive of outcomes recommended by both European LeukemiaNet (ELN) and National Comprehensive Cancer Network (NCCN); however, studies has demonstrated poor adherence to these recommendations. In both clinical practice and assay performance, further optimizing of BCR-ABL1 monitoring can be envisioned including point-of-care methods for increased availability of rapid, standardized testing and increasingly sensitive molecular assays that allow for quantification of MRD and detecting resistance mutations.
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Affiliation(s)
- Cecilia Ching Sze Yeung
- a Clinical Research Division , Fred Hutchinson Cancer Research Center Ringgold standard institution , Seattle , WA , USA.,b Pathology , University of Washington School of Medicine Ringgold standard institution , Seattle , WA , USA
| | - Daniel Egan
- a Clinical Research Division , Fred Hutchinson Cancer Research Center Ringgold standard institution , Seattle , WA , USA
| | - Jerald P Radich
- c Fred Hutchinson Cancer Research Center , Seattle , WA , USA
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13
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Soverini S, De Benedittis C, Mancini M, Martinelli G. Present and future of molecular monitoring in chronic myeloid leukaemia. Br J Haematol 2016; 173:337-49. [PMID: 26947577 DOI: 10.1111/bjh.13966] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Currently, physicians treating chronic myeloid leukaemia (CML) patients can rely on a wide spectrum of therapeutic options: the best use of such options is essential to achieve excellent clinical outcomes and, possibly, treatment-free remission (TFR). To accomplish this, proper integration of expert clinical and laboratory monitoring of CML patients is fundamental. Molecular response (MR) monitoring of patients at defined time points has emerged as an important success factor for optimal disease management and BCR-ABL1 kinase domain mutation screening is useful to guide therapeutic reassessment in patients who do not achieve optimal responses to tyrosine kinase inhibitor therapy. Deeper MRs might be associated with improved long-term survival outcomes. More importantly, they are considered a gateway to TFR. In molecular biology, novel procedures and technologies are continually being developed. More sophisticated molecular tools and automated analytical solutions are emerging as CML treatment endpoints and expectations become more and more ambitious. Here we provide a critical overview of current and novel methodologies, present their strengths and pitfalls and discuss what their present and future role might be.
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Affiliation(s)
- Simona Soverini
- Department of Experimental, Diagnostic and Specialty Medicine, Haematology/Oncology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy
| | - Caterina De Benedittis
- Department of Experimental, Diagnostic and Specialty Medicine, Haematology/Oncology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy
| | - Manuela Mancini
- Department of Experimental, Diagnostic and Specialty Medicine, Haematology/Oncology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy
| | - Giovanni Martinelli
- Department of Experimental, Diagnostic and Specialty Medicine, Haematology/Oncology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy
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14
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Is cure for chronic myeloid leukemia possible in the tyrosine kinase inhibitors era? Curr Opin Hematol 2016; 23:115-20. [DOI: 10.1097/moh.0000000000000224] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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15
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Alikian M, Ellery P, Forbes M, Gerrard G, Kasperaviciute D, Sosinsky A, Mueller M, Whale AS, Milojkovic D, Apperley J, Huggett JF, Foroni L, Reid AG. Next-Generation Sequencing-Assisted DNA-Based Digital PCR for a Personalized Approach to the Detection and Quantification of Residual Disease in Chronic Myeloid Leukemia Patients. J Mol Diagn 2016; 18:176-89. [PMID: 26857065 DOI: 10.1016/j.jmoldx.2015.09.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 08/31/2015] [Accepted: 09/17/2015] [Indexed: 01/06/2023] Open
Abstract
Recent studies indicate that 40% of chronic myeloid leukemia patients who achieve sustained undetectable BCR-ABL1 transcripts on tyrosine kinase inhibitor therapy remain disease-free after drug discontinuation. In contrast, 60% experience return of detectable disease and have to restart treatment, thus highlighting the need for an improved method of identifying patients with the lowest likelihood of relapse. Here we describe the validation of a personalized DNA-based digital PCR (dPCR) approach for quantifying very low levels of residual disease, which involves the rapid identification of t(9;22) fusion junctions using targeted next-generation sequencing coupled with the use of a dPCR platform. t(9;22) genomic breakpoints were successfully mapped in samples from 32 of 32 patients with early stage disease. Disease quantification by DNA-based dPCR was performed using the Fluidigm BioMark platform on 46 follow-up samples from 6 of the 32 patients, including 36 samples that were in deep molecular remission. dPCR detected persistent disease in 81% of molecular-remission samples, outperforming both RT-dPCR (25%) and DNA-based quantitative PCR (19%). We conclude that dPCR for BCR-ABL1 DNA is the most sensitive available method of residual-disease detection in chronic myeloid leukemia and may prove useful in the management of tyrosine kinase inhibitor withdrawal.
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Affiliation(s)
- Mary Alikian
- Imperial Molecular Pathology, Imperial Healthcare Trust, Hammersmith Hospital, London, United Kingdom; Centre for Haematology, Faculty of Medicine, Imperial College London, London, United Kingdom.
| | - Peter Ellery
- Imperial Molecular Pathology, Imperial Healthcare Trust, Hammersmith Hospital, London, United Kingdom
| | - Martin Forbes
- Centre for Haematology, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Gareth Gerrard
- Imperial Molecular Pathology, Imperial Healthcare Trust, Hammersmith Hospital, London, United Kingdom; Centre for Haematology, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Dalia Kasperaviciute
- Clinical Genome Informatics Facility, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Alona Sosinsky
- Clinical Genome Informatics Facility, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Michael Mueller
- Clinical Genome Informatics Facility, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Alexandra S Whale
- Molecular & Cell Biology, LGC Limited, Queens Road, Teddington, United Kingdom
| | - Dragana Milojkovic
- Clinical Haematology, Imperial College Healthcare National Health Institute Trust, London, United Kingdom
| | - Jane Apperley
- Centre for Haematology, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Jim F Huggett
- Molecular & Cell Biology, LGC Limited, Queens Road, Teddington, United Kingdom
| | - Letizia Foroni
- Imperial Molecular Pathology, Imperial Healthcare Trust, Hammersmith Hospital, London, United Kingdom; Centre for Haematology, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Alistair G Reid
- Imperial Molecular Pathology, Imperial Healthcare Trust, Hammersmith Hospital, London, United Kingdom; Centre for Haematology, Faculty of Medicine, Imperial College London, London, United Kingdom
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16
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Latham S, Bartley PA, Budgen B, Ross DM, Hughes E, Branford S, White D, Hughes TP, Morley AA. BCR-ABL1 expression, RT-qPCR and treatment decisions in chronic myeloid leukaemia. J Clin Pathol 2016; 69:817-21. [PMID: 26837312 DOI: 10.1136/jclinpath-2015-203538] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 01/13/2016] [Indexed: 11/03/2022]
Abstract
AIMS RT-qPCR is used to quantify minimal residual disease (MRD) in chronic myeloid leukaemia (CML) in order to make decisions on treatment, but its results depend on the level of BCR-ABL1 expression as well as leukaemic cell number. The aims of the study were to quantify inter-individual differences in expression level, to determine the relationship between expression level and response to treatment, and to investigate the effect of expression level on interpretation of the RT-qPCR result. METHODS BCR-ABL1 expression was studied in 248 samples from 65 patients with CML by determining the difference between MRD quantified by RT-qPCR and DNA-qPCR. The results were analysed statistically and by simple indicative modelling. RESULTS Inter-individual levels of expression approximated a normal distribution with an SD of 0.36 log. Expression at diagnosis correlated with expression during treatment. Response to treatment, as measured by the number of leukaemic cells after 3, 6 or 12 months of treatment, was not related to the level of expression. Indicative modelling suggested that interpretation of RT-qPCR results in relation to treatment guidelines could be affected by variation in expression when MRD was around 10% at 3 months and by both expression variation and Poisson variation when MRD was around or below the limit of detection of RT-qPCR. CONCLUSIONS Variation between individuals in expression of BCR-ABL1 can materially affect interpretation of the RT-qPCR when this test is used to make decisions on treatment.
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Affiliation(s)
- Susan Latham
- Department of Haematology & Genetic Pathology, School of Medicine, Flinders University and Medical Centre, Bedford Park, South Australia, Australia
| | - Paul A Bartley
- Department of Haematology & Genetic Pathology, School of Medicine, Flinders University and Medical Centre, Bedford Park, South Australia, Australia
| | - Bradley Budgen
- Department of Haematology & Genetic Pathology, School of Medicine, Flinders University and Medical Centre, Bedford Park, South Australia, Australia
| | - David M Ross
- Department of Haematology & Genetic Pathology, School of Medicine, Flinders University and Medical Centre, Bedford Park, South Australia, Australia Haematology Division, SA Pathology, Adelaide, South Australia, Australia
| | - Elizabeth Hughes
- Department of Haematology & Genetic Pathology, School of Medicine, Flinders University and Medical Centre, Bedford Park, South Australia, Australia
| | - Susan Branford
- Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
| | - Deborah White
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Timothy P Hughes
- Haematology Division, SA Pathology, Adelaide, South Australia, Australia
| | - Alexander A Morley
- Department of Haematology & Genetic Pathology, School of Medicine, Flinders University and Medical Centre, Bedford Park, South Australia, Australia Monoquant Pty Ltd, Adelaide, South Australia, Australia
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17
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Crampe M, Langabeer SE. Comment on: Technical Issues Behind Molecular Monitoring in Chronic Myeloid Leukemia. Mol Diagn Ther 2015. [PMID: 26224625 DOI: 10.1007/s40291-015-0151-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Mireille Crampe
- Cancer Molecular Diagnostics, Central Pathology Laboratory, St. James's Hospital, Dublin 8, Ireland
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