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Burmeister T, Gröger D, Gökbuget N, Spriewald B, Starck M, Elmaagacli A, Hoelzer D, Keller U, Schwartz S. Molecular characterization of TCF3::PBX1 chromosomal breakpoints in acute lymphoblastic leukemia and their use for measurable residual disease assessment. Sci Rep 2023; 13:15167. [PMID: 37704696 PMCID: PMC10499895 DOI: 10.1038/s41598-023-42294-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 09/07/2023] [Indexed: 09/15/2023] Open
Abstract
The translocation t(1;19)(q23;p13) with the resulting chimeric TCF3::PBX1 gene is the third most prevalent recurrent chromosomal translocation in acute lymphoblastic leukemia and accounts for 3-5% of cases. The molecular background of this translocation has been incompletely studied, especially in adult cases. We characterized the chromosomal breakpoints of 49 patients with TCF3::PBX1 and the corresponding reciprocal PBX1::TCF3 breakpoints in 15 cases at the molecular level, thus providing an extensive molecular overview of this translocation in a well-defined study patient population. Breakpoints were found to be remarkably clustered not only in TCF3 but also in PBX1. No association with DNA repeats or putative cryptic recombination signal sequence sites was observed. A simplified detection method for breakpoint identification was developed and the feasibility of patient-specific chromosomal break sites as molecular markers for detecting measurable residual disease (MRD) was explored. A highly sensitive generic real-time PCR for MRD assessment using these breakpoint sequences was established that could serve as a useful alternative to the classical method utilizing rearranged immune gene loci. This study provides the first extensive molecular data set on the chromosomal breakpoints of the t(1;19)/TCF3::PBX1 aberration in adult ALL. Based on the obtained data a generic MRD method was developed that has several theoretical advantages, including an on average higher sensitivity and a greater stability of the molecular marker in the course of disease.
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Affiliation(s)
- Thomas Burmeister
- Department of Hematology, Oncology and Tumor Immunology, CVK, Charité - Universitätsmedizin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
| | - Daniela Gröger
- Department of Hematology, Oncology and Tumor Immunology, CBF, Charité - Universitätsmedizin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nicola Gökbuget
- Medical Department 2, Goethe-Universität, Frankfurt, Germany
| | - Bernd Spriewald
- Department of Internal Medicine 5, Hematology and Oncology, University Hospital Erlangen, Erlangen, Germany
| | - Michael Starck
- I. Medical Department, München Klinik Schwabing, Munich, Germany
| | - Ahmet Elmaagacli
- Department of Hematology, Oncology, Asklepios Klinik St. Georg, Hamburg, Germany
| | - Dieter Hoelzer
- Medical Department 2, Goethe-Universität, Frankfurt, Germany
| | - Ulrich Keller
- Department of Hematology, Oncology and Tumor Immunology, CBF, Charité - Universitätsmedizin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Stefan Schwartz
- Department of Hematology, Oncology and Tumor Immunology, CBF, Charité - Universitätsmedizin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
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Lim HJ, Lee JH, Lee SY, Choi HW, Choi HJ, Kee SJ, Shin JH, Shin MG. Diagnostic Validation of a Clinical Laboratory-Oriented Targeted RNA Sequencing System for Detecting Gene Fusions in Hematologic Malignancies. J Mol Diagn 2021; 23:1015-1029. [PMID: 34082071 DOI: 10.1016/j.jmoldx.2021.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 04/30/2021] [Accepted: 05/10/2021] [Indexed: 10/21/2022] Open
Abstract
Targeted RNA sequencing (RNA-seq) is a highly accurate method for sequencing transcripts of interest with a high resolution and throughput. However, RNA-seq has not been widely performed in clinical molecular laboratories because of the complexity of data processing and interpretation. We developed and validated a customized RNA-seq panel and data processing protocol for fusion detection using 4 analytical validation samples and 51 clinical samples, covering seven types of hematologic malignancies. Analytical validation showed that the results for target gene coverage and between- and within-run precision and linearity tests were reliable. Using clinical samples, RNA-seq based on filtering and prioritization strategies detected all 25 known fusions previously found by multiplex reverse transcriptase-PCR and fluorescence in situ hybridization. It also detected nine novel fusions. Known fusions detected by RNA-seq included two IGH rearrangements supported by expression analysis. Novel fusions included six that targeted just one partner gene. In addition, 18 disease- and drug resistance-associated transcript variants in ABL1, GATA2, IKZF1, JAK2, RUNX1, and WT1 were designated simultaneously. Expression analysis showed distinct clustering according to subtype and lineage. In conclusion, this study showed that our customized RNA-seq system had a reliable and stable performance for fusion detection, with enhanced diagnostic yield for hematologic malignancies in a clinical diagnostic setting.
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Affiliation(s)
- Ha Jin Lim
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Republic of Korea
| | - Jun Hyung Lee
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Republic of Korea
| | - Seung Yeob Lee
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Republic of Korea
| | - Hyun-Woo Choi
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Republic of Korea
| | - Hyun-Jung Choi
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Republic of Korea
| | - Seung-Jung Kee
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Republic of Korea
| | - Jong Hee Shin
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Republic of Korea
| | - Myung Geun Shin
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Republic of Korea; Brain Korea 21 Plus Project, Chonnam National University Medical School, Gwangju, Republic of Korea.
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Pettersson L, Johansson Alm S, Almstedt A, Chen Y, Orrsjö G, Shah-Barkhordar G, Zhou L, Kotarsky H, Vidovic K, Asp J, Lazarevic V, Saal LH, Fogelstrand L, Ehinger M. Comparison of RNA- and DNA-based methods for measurable residual disease analysis in NPM1-mutated acute myeloid leukemia. Int J Lab Hematol 2021; 43:664-674. [PMID: 34053184 DOI: 10.1111/ijlh.13608] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 05/02/2021] [Accepted: 05/06/2021] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Reverse transcriptase quantitative PCR (RT-qPCR) is considered the method of choice for measurable residual disease (MRD) assessment in NPM1-mutated acute myeloid leukemia (AML). MRD can also be determined with DNA-based methods offering certain advantages. We here compared the DNA-based methods quantitative PCR (qPCR), droplet digital PCR (ddPCR), and targeted deep sequencing (deep seq) with RT-qPCR. METHODS Of 110 follow-up samples from 30 patients with NPM1-mutated AML were analyzed by qPCR, ddPCR, deep seq, and RT-qPCR. To select DNA MRD cutoffs for bone marrow, we performed receiver operating characteristic analyses for each DNA method using prognostically relevant RT-qPCR cutoffs. RESULTS The DNA-based methods showed strong intermethod correlation, but were less sensitive than RT-qPCR. A bone marrow cutoff at 0.1% leukemic DNA for qPCR or 0.05% variant allele frequency for ddPCR and deep seq offered optimal sensitivity and specificity with respect to 3 log10 reduction of NPM1 transcripts and/or 2% mutant NPM1/ABL. With these cutoffs, MRD results agreed in 95% (191/201) of the analyses. Although more sensitive, RT-qPCR failed to detect leukemic signals in 10% of samples with detectable leukemic DNA. CONCLUSION DNA-based MRD techniques may complement RT-qPCR for assessment of residual leukemia. DNA-based methods offer high positive and negative predictive values with respect to residual leukemic NPM1 transcripts at levels of importance for response to treatment. However, moving to DNA-based MRD methods will miss a proportion of patients with residual leukemic RNA, but on the other hand some MRD samples with detectable leukemic DNA can be devoid of measurable leukemic RNA.
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Affiliation(s)
- Louise Pettersson
- Department of Clinical Sciences, Division of Pathology, Lund University, Skane University Hospital, Lund, Sweden.,Department of Pathology, Halland Hospital Halmstad, Region Halland, Halmstad, Sweden
| | - Sofie Johansson Alm
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Alvar Almstedt
- SciLife Clinical Genomics Gothenburg, Gothenburg, Sweden
| | - Yilun Chen
- Department of Clinical Sciences, Division of Oncology, Faculty of Medicine, Lund University, Lund, Sweden
| | - Gustav Orrsjö
- Section for Hematology and Coagulation, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Giti Shah-Barkhordar
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Li Zhou
- Klinisk Patologi, Region Laboratories, Region Skåne, Lund, Sweden
| | - Heike Kotarsky
- Klinisk Patologi, Region Laboratories, Region Skåne, Lund, Sweden
| | - Karina Vidovic
- Department of Clinical Sciences, Division of Pathology, Lund University, Skane University Hospital, Lund, Sweden
| | - Julia Asp
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Vladimir Lazarevic
- Department of Hematology, Oncology and Radiation Physics, Lund University, Skane University Hospital, Lund, Sweden
| | - Lao H Saal
- Department of Clinical Sciences, Division of Oncology, Faculty of Medicine, Lund University, Lund, Sweden.,Lund University Cancer Center, Medicon Village, Lund, Sweden
| | - Linda Fogelstrand
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Mats Ehinger
- Department of Clinical Sciences, Division of Pathology, Lund University, Skane University Hospital, Lund, Sweden.,Klinisk Patologi, Region Laboratories, Region Skåne, Lund, Sweden
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Identification of Fusion Gene Breakpoints is Feasible and Facilitates Accurate Sensitive Minimal Residual Disease Monitoring on Genomic Level in Patients With PML-RARA, CBFB-MYH11, and RUNX1-RUNX1T1. Hemasphere 2020; 4:e489. [PMID: 33204999 PMCID: PMC7665249 DOI: 10.1097/hs9.0000000000000489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/23/2020] [Indexed: 11/26/2022] Open
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Next-generation sequencing-based minimal residual disease monitoring in patients receiving allogeneic hematopoietic stem cell transplantation for acute myeloid leukemia or myelodysplastic syndrome. Curr Opin Hematol 2019; 25:425-432. [PMID: 30281033 DOI: 10.1097/moh.0000000000000464] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
PURPOSE OF REVIEW The monitoring of minimal residual disease (MRD) has important clinical implications in both the pre and postallogeneic stem cell transplant (SCT) setting in acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). Next-generation sequencing (NGS) is a rapidly improving technology whose application to the monitoring of MRD is an active area of research. We aim to describe existing methods of MRD in AML and MDS, with a focus on the utility of NGS in patients undergoing SCT. RECENT FINDINGS Flow cytometry and quantitative PCR have been recommended by the European Leukemia Net as the preferred methods of MRD in AML and MDS, but these methods have limitations in cases without a disease-defining phenotype and genotype. Clinical trials are currently ongoing to assess the use of NGS in the setting of SCT for MDS and AML. Few studies have so far assessed the optimal method of MRD monitoring in the posttransplant setting. SUMMARY The optimal method for the monitoring of MRD in AML and MDS both pre and post transplant may require more than one technology. NGS holds great promise for the monitoring of MRD, with prospective trials currently ongoing to evaluate its efficacy in this regard.
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Hoffmann J, Krumbholz M, Gutiérrez HP, Fillies M, Szymansky A, Bleckmann K, Zur Stadt U, Köhler R, Kuiper RP, Horstmann M, von Stackelberg A, Eckert C, Metzler M. High sensitivity and clonal stability of the genomic fusion as single marker for response monitoring in ETV6-RUNX1-positive acute lymphoblastic leukemia. Pediatr Blood Cancer 2019; 66:e27780. [PMID: 31034759 DOI: 10.1002/pbc.27780] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 03/21/2019] [Accepted: 04/09/2019] [Indexed: 11/08/2022]
Abstract
BACKGROUND Assessment of minimal residual disease (MRD) is an integral component for response monitoring and treatment stratification in acute lymphoblastic leukemia (ALL). We aimed to evaluate the genomic ETV6-RUNX1 fusion sites as a single marker for MRD quantification. PROCEDURE In a representative, uniformly treated cohort of pediatric relapsed ALL patients (n = 52), ETV6-RUNX1 fusion sites were compared to the current gold standard, immunoglobulin/T-cell receptor (Ig/TCR) gene rearrangements. RESULTS Primer/probe sets designed to ETV6-RUNX1 fusions achieved significantly more frequent a sensitivity and a quantitative range of at least 10-4 compared to the gold standard with 100% and 73% versus 76% and 47%, respectively. The breakpoint sequence was identical at diagnosis and relapse in all tested cases. There was a high degree of concordance between quantitative MRD results assessed using ETV6-RUNX1 and the highest Ig/TCR marker (Spearman's 0.899, P < .01) with differences >½ log-step in only 6% of patients. A high proportion of ETV6-RUNX1-positive ALL relapses (40%) in our cohort showed a poor response to induction treatment at relapse, and therefore had an indication for hematopoietic stem cell transplantation, demonstrating the need of accurate identification of this subgroup. CONCLUSIONS ETV6-RUNX1 fusion sites are highly sensitive and reliable MRD markers. Our data confirm that they are unaffected by clonal evolution and selection during front-line and second-line chemotherapy in contrast to Ig/TCR rearrangements, which require several markers per patient to compensate for the observed loss of target clones. In future studies, the genomic ETV6-RUNX1 fusion can be used as single MRD marker.
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Affiliation(s)
- Jana Hoffmann
- Pediatric Oncology/Hematology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Manuela Krumbholz
- Pediatric Oncology/Hematology, University Hospital Erlangen, Erlangen, Germany
| | | | - Marion Fillies
- Pediatric Oncology/Hematology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Annabell Szymansky
- Pediatric Oncology/Hematology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Kirsten Bleckmann
- Department of Pediatrics, University of Schleswig-Holstein, Kiel, Germany
| | - Udo Zur Stadt
- Center for Diagnostics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Rolf Köhler
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Roland P Kuiper
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Martin Horstmann
- Research Institute Children's Cancer Center, Hamburg, Germany.,Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Arend von Stackelberg
- Pediatric Oncology/Hematology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Cornelia Eckert
- Pediatric Oncology/Hematology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Markus Metzler
- Pediatric Oncology/Hematology, University Hospital Erlangen, Erlangen, Germany
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Abstract
Increasing evidence supports the prognostic significance of measurable residual disease (MRD) in acute myeloid leukemia (AML). Dynamic MRD assessment for patients with AML complements baseline patient risk assessment factors in determining patient prognosis. MRD status may also be helpful in informing therapeutic decisions. The European Leukemia Net MRD working party recently issued consensus recommendations for the use of MRD in AML. The Food and Drug Administration also issued advice for using MRD in trials of hematologic malignancies. This article discusses MRD testing, highlights the challenges in adopting MRD testing in clinical practice, and provides insights into the future of the field.
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8
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Ehinger M, Pettersson L. Measurable residual disease testing for personalized treatment of acute myeloid leukemia. APMIS 2019; 127:337-351. [PMID: 30919505 DOI: 10.1111/apm.12926] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 12/28/2018] [Indexed: 12/13/2022]
Abstract
This review summarizes - with the practicing hematologist in mind - the methods used to determine measurable residual disease (MRD) in everyday practice with some future perspectives, and the current knowledge about the prognostic impact of MRD on outcome in acute myeloid leukemia (AML), excluding acute promyelocytic leukemia. Possible implications for choice of MRD method, timing of MRD monitoring, and guidance of therapy are discussed in general and in some detail for certain types of leukemia with specific molecular markers to monitor, including core binding factor (CBF)-leukemias and NPM1-mutated leukemias.
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Affiliation(s)
- Mats Ehinger
- Department of Clinical Sciences, Pathology, Skane University Hospital, Lund University, Lund, Sweden
| | - Louise Pettersson
- Department of Pathology, Halland Hospital Halmstad, Region Halland, Halmstad, Sweden.,Faculty of Medicine, Division of Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
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Onecha E, Linares M, Rapado I, Ruiz-Heredia Y, Martinez-Sanchez P, Cedena T, Pratcorona M, Oteyza JP, Herrera P, Barragan E, Montesinos P, Vela JAG, Magro E, Anguita E, Figuera A, Riaza R, Martinez-Barranco P, Sanchez-Vega B, Nomdedeu J, Gallardo M, Martinez-Lopez J, Ayala R. A novel deep targeted sequencing method for minimal residual disease monitoring in acute myeloid leukemia. Haematologica 2018; 104:288-296. [PMID: 30093399 PMCID: PMC6355493 DOI: 10.3324/haematol.2018.194712] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 08/08/2018] [Indexed: 12/11/2022] Open
Abstract
A high proportion of patients with acute myeloid leukemia who achieve minimal residual disease negative status ultimately relapse because a fraction of pathological clones remains undetected by standard methods. We designed and validated a high-throughput sequencing method for minimal residual disease assessment of cell clonotypes with mutations of NPM1, IDH1/2 and/or FLT3-single nucleotide variants. For clinical validation, 106 follow-up samples from 63 patients in complete remission were studied by sequencing, evaluating the level of mutations detected at diagnosis. The predictive value of minimal residual disease status by sequencing, multiparameter flow cytometry, or quantitative polymerase chain reaction analysis was determined by survival analysis. The sequencing method achieved a sensitivity of 10−4 for single nucleotide variants and 10−5 for insertions/deletions and could be used in acute myeloid leukemia patients who carry any mutation (86% in our diagnostic data set). Sequencing–determined minimal residual disease positive status was associated with lower disease-free survival (hazard ratio 3.4, P=0.005) and lower overall survival (hazard ratio 4.2, P<0.001). Multivariate analysis showed that minimal residual disease positive status determined by sequencing was an independent factor associated with risk of death (hazard ratio 4.54, P=0.005) and the only independent factor conferring risk of relapse (hazard ratio 3.76, P=0.012). This sequencing-based method simplifies and standardizes minimal residual disease evaluation, with high applicability in acute myeloid leukemia. It is also an improvement upon flow cytometry- and quantitative polymerase chain reaction-based prediction of outcomes of patients with acute myeloid leukemia and could be incorporated in clinical settings and clinical trials.
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Affiliation(s)
- Esther Onecha
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid.,Hematological Malignancies Clinical Research Unit, CNIO, Madrid
| | - Maria Linares
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid.,Hematological Malignancies Clinical Research Unit, CNIO, Madrid
| | - Inmaculada Rapado
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid.,Hematological Malignancies Clinical Research Unit, CNIO, Madrid.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid
| | - Yanira Ruiz-Heredia
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid.,Hematological Malignancies Clinical Research Unit, CNIO, Madrid
| | | | - Teresa Cedena
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid.,Hematological Malignancies Clinical Research Unit, CNIO, Madrid.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid.,Complutense University, Madrid
| | - Marta Pratcorona
- Hematology Department, Hospital Santa Creu i Sant Pau, Barcelona
| | | | - Pilar Herrera
- Hematology Department, Hospital Universitario Ramon y Cajal, Madrid
| | - Eva Barragan
- Complutense University, Madrid.,Hematology Department, Hospital Universitario La Fe, Valencia
| | - Pau Montesinos
- Complutense University, Madrid.,Hematology Department, Hospital Universitario La Fe, Valencia
| | | | - Elena Magro
- Hematology Department, Hospital Universitario Principe de Asturias, Madrid
| | - Eduardo Anguita
- Hematology Department, Hospital Clínico San Carlos, IdISSC, UCM, Madrid
| | - Angela Figuera
- Hematology Department, Hospital Universitario de la Princesa, Madrid
| | - Rosalia Riaza
- Hematology Department, Hospital Universitario Severo Ochoa, Madrid
| | | | - Beatriz Sanchez-Vega
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid.,Hematological Malignancies Clinical Research Unit, CNIO, Madrid
| | - Josep Nomdedeu
- Hematology Department, Hospital Santa Creu i Sant Pau, Barcelona
| | - Miguel Gallardo
- Hematological Malignancies Clinical Research Unit, CNIO, Madrid
| | - Joaquin Martinez-Lopez
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid.,Hematological Malignancies Clinical Research Unit, CNIO, Madrid.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid.,Complutense University, Madrid
| | - Rosa Ayala
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid .,Hematological Malignancies Clinical Research Unit, CNIO, Madrid.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid.,Complutense University, Madrid
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Molecular Minimal Residual Disease Testing in Acute Myeloid Leukemia: A Review for the Practicing Clinician. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2018; 18:636-647. [PMID: 30006258 DOI: 10.1016/j.clml.2018.06.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/12/2018] [Accepted: 06/19/2018] [Indexed: 11/21/2022]
Abstract
Minimal residual disease (MRD) testing in acute myeloid leukemia is increasingly being used to assess treatment response and stratify the risk of relapse for individual patients. Molecular methods for MRD testing began with PCR-based assays for individual recurrent mutations. To date, there is robust evidence for testing NPM1, CBFB-MYH11, and RUNX1/RUNXT1 mutations using this approach, though the best timing and threshold level for each mutation varies. More recent approaches have been with PCR-based multigene panels, occasionally combined with flow cytometric techniques, and next-generation sequencing techniques. This review outlines the various techniques used in molecular approaches to MRD, the evidence behind individual mutation testing, and the novel approaches for evaluating multigene MRD so that clinicians can understand and incorporate these evaluations into their practice.
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11
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Selim AG, Moore AS. Molecular Minimal Residual Disease Monitoring in Acute Myeloid Leukemia. J Mol Diagn 2018; 20:389-397. [DOI: 10.1016/j.jmoldx.2018.03.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 02/22/2018] [Accepted: 03/27/2018] [Indexed: 01/22/2023] Open
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12
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Spirin P, Lebedev T, Orlova N, Morozov A, Poymenova N, Dmitriev SE, Buzdin A, Stocking C, Kovalchuk O, Prassolov V. Synergistic suppression of t(8;21)-positive leukemia cell growth by combining oridonin and MAPK1/ERK2 inhibitors. Oncotarget 2017; 8:56991-57002. [PMID: 28915648 PMCID: PMC5593619 DOI: 10.18632/oncotarget.18503] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 04/18/2017] [Indexed: 01/03/2023] Open
Abstract
One of the most common chromosomal translocations in acute myeloid leukemia is t(8;21)(q22;q22), which results in the appearance of abnormal transcripts encoding for the fusion protein RUNX1-ETO. Therefore, this oncoprotein is considered to be a pertinent and promising target for treating t(8;21) leukemia. Previously, we have shown that downregulation of RUNX1-ETO leads to activation of intracellular signaling pathways enhancing cell survival and determined that the protein ERK2 can mediate activation of most of these pathways. Here we used a combination of oridonin (natural tetracycline diterpenoid), which has been shown to exhibit anti-RUNX1-ETO activity, and ERK2 kinase inhibitors. We found that treatment of leukemic t(8;21)-positive Kasumi-1 cells with oridonin cause decrease of phosphorylated ERK1/2. Treatment of these cells with ERK2 inhibitors makes them more sensitive to RUNX1-ETO inhibition with oridonin. Therefore we postulate that simultaneous inhibition of RUNX1-ETO and ERK2 cause synergistic effect on survival of leukemic cells.
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Affiliation(s)
- Pavel Spirin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Timofey Lebedev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Natalia Orlova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexey Morozov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Nadezhda Poymenova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Sergey E Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Anton Buzdin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.,Dmitry Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow 117997, Russia.,National Research Centre "Kurchatov Institute", Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, Moscow 123182, Russia
| | - Carol Stocking
- Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Olga Kovalchuk
- OncoFinder Ltd, Lethbridge, AB T1K7×8, Canada.,Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K3M4, Canada
| | - Vladimir Prassolov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
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13
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Clinical Relevance of RUNX1 and CBFB Alterations in Acute Myeloid Leukemia and Other Hematological Disorders. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 962:175-199. [PMID: 28299658 DOI: 10.1007/978-981-10-3233-2_12] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The translocation t(8;21), leading to a fusion between the RUNX1 gene and the RUNX1T1 locus, was the first chromosomal translocation identified in cancer. Since the first description of this balanced rearrangement in a patient with acute myeloid leukemia (AML) in 1973, RUNX1 translocations and point mutations have been found in various myeloid and lymphoid neoplasms. In this chapter, we summarize the currently available data on the clinical relevance of core binding factor gene alterations in hematological disorders. In the first section, we discuss the prognostic implications of the core binding factor translocations RUNX1-RUNX1T1 and CBFB-MYH11 in AML patients. We provide an overview of the cooperating genetic events in patients with CBF-rearranged AML and their clinical implications, and review current treatment approaches for CBF AML and the utility of minimal residual disease monitoring. In the next sections, we summarize the available data on rare RUNX1 rearrangements in various hematologic neoplasms and the role of RUNX1 translocations in therapy-related myeloid neoplasia. The final three sections of the chapter cover the spectrum and clinical significance of RUNX1 point mutations in AML and myelodysplastic syndromes, in familial platelet disorder with associated myeloid malignancy, and in acute lymphoblastic leukemia.
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Life after transplant: are we becoming high maintenance in AML? Bone Marrow Transplant 2016; 51:1423-1430. [DOI: 10.1038/bmt.2016.160] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 04/25/2016] [Indexed: 01/11/2023]
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Latysheva NS, Babu MM. Discovering and understanding oncogenic gene fusions through data intensive computational approaches. Nucleic Acids Res 2016; 44:4487-503. [PMID: 27105842 PMCID: PMC4889949 DOI: 10.1093/nar/gkw282] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 03/24/2016] [Indexed: 12/21/2022] Open
Abstract
Although gene fusions have been recognized as important drivers of cancer for decades, our understanding of the prevalence and function of gene fusions has been revolutionized by the rise of next-generation sequencing, advances in bioinformatics theory and an increasing capacity for large-scale computational biology. The computational work on gene fusions has been vastly diverse, and the present state of the literature is fragmented. It will be fruitful to merge three camps of gene fusion bioinformatics that appear to rarely cross over: (i) data-intensive computational work characterizing the molecular biology of gene fusions; (ii) development research on fusion detection tools, candidate fusion prioritization algorithms and dedicated fusion databases and (iii) clinical research that seeks to either therapeutically target fusion transcripts and proteins or leverages advances in detection tools to perform large-scale surveys of gene fusion landscapes in specific cancer types. In this review, we unify these different-yet highly complementary and symbiotic-approaches with the view that increased synergy will catalyze advancements in gene fusion identification, characterization and significance evaluation.
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Affiliation(s)
- Natasha S Latysheva
- MRC Laboratory of Molecular Biology, Francis Crick Ave, Cambridge CB2 0QH, United Kingdom
| | - M Madan Babu
- MRC Laboratory of Molecular Biology, Francis Crick Ave, Cambridge CB2 0QH, United Kingdom
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Hokland P, Ommen HB, Mulé MP, Hourigan CS. Advancing the Minimal Residual Disease Concept in Acute Myeloid Leukemia. Semin Hematol 2015; 52:184-92. [PMID: 26111465 DOI: 10.1053/j.seminhematol.2015.04.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The criteria to evaluate response to treatment in acute myeloid leukemia (AML) have changed little in the past 60 years. It is now possible to use higher sensitivity tools to measure residual disease burden in AML. Such minimal or measurable residual disease (MRD) measurements provide a deeper understanding of current patient status and allow stratification for risk of subsequent clinical relapse. Despite these obvious advantages, and after over a decade of laboratory investigation and preclinical validation, MRD measurements are not currently routinely used for clinical decision-making or drug development in non-acute promyelocytic leukemia (non-APL) AML. We review here some potential constraints that may have delayed adoption, including a natural hesitancy of end users, economic impact concerns, misperceptions regarding the meaning of and need for assay sensitivity, the lack of one single MRD solution for all AML patients, and finally the need to involve patients in decision-making based on such correlates. It is our opinion that none of these issues represent insurmountable barriers and our hope is that by providing potential solutions we can help map a path forward to a future where our patients will be offered personalized treatment plans based on the amount of AML they have left remaining to treat.
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Affiliation(s)
- Peter Hokland
- Department of Hematology, Aarhus University Hospital, Denmark
| | - Hans B Ommen
- Department of Hematology, Aarhus University Hospital, Denmark
| | - Matthew P Mulé
- Myeloid Malignancies Section, Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Christopher S Hourigan
- Myeloid Malignancies Section, Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD.
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Duployez N, Willekens C, Marceau-Renaut A, Boudry-Labis E, Preudhomme C. Prognosis and monitoring of core-binding factor acute myeloid leukemia: current and emerging factors. Expert Rev Hematol 2014; 8:43-56. [PMID: 25348871 DOI: 10.1586/17474086.2014.976551] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Core-binding factor acute myeloid leukemia (CBF-AML) - including AML with t(8;21) and AML with inv(16) - accounts for about 15% of adult AML and is associated with a relatively favorable prognosis. Nonetheless, relapse incidence may reach 40% in these patients. In this context, identification of prognostic markers is considered of great interest. Due to similarities between their molecular and prognostic features, t(8;21) and inv(16)-AML are usually grouped and reported together in clinical studies. However, considerable experimental evidences have highlighted that they represent two distinct entities and should be considered separately for further studies. This review summarizes recent laboratory and clinical findings in this particular subset of AML and how they could be used to improve management of patients in routine practice.
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Affiliation(s)
- Nicolas Duployez
- Hematology Laboratory, Biology and Pathology Center, Lille University Hospital, Lille, France
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