1
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Tiong IS, Hiwase DK, Abro E, Bajel A, Palfreyman E, Beligaswatte A, Reynolds J, Anstee N, Nguyen T, Loo S, Chua CC, Ashby M, Wiltshire KM, Fleming S, Fong CY, Teh TC, Blombery P, Dillon R, Ivey A, Wei AH. Targeting Molecular Measurable Residual Disease and Low-Blast Relapse in AML With Venetoclax and Low-Dose Cytarabine: A Prospective Phase II Study (VALDAC). J Clin Oncol 2024; 42:2161-2173. [PMID: 38427924 PMCID: PMC11191043 DOI: 10.1200/jco.23.01599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/21/2023] [Accepted: 12/18/2023] [Indexed: 03/03/2024] Open
Abstract
PURPOSE A prospective phase II study examined the safety and efficacy of venetoclax combined with low-dose cytarabine (LDAC) in AML at first measurable residual disease (MRD) or oligoblastic relapse. METHODS Patients with either MRD (≥1 log10 rise) or oligoblastic relapse (blasts 5%-15%) received venetoclax 600 mg once daily D1-28 plus LDAC once daily D1-10 in 28-day cycles. The primary objective was MRD response in the MRD relapse cohort or complete remission (CR/CRh/CRi) in the oligoblastic relapse cohort. RESULTS Forty-eight adults with either MRD (n = 26) or oligoblastic (n = 22) relapse were enrolled. Median age was 67 years (range, 18-80) and 94% had received previous intensive chemotherapy. Patients received a median of four cycles of therapy; 17% completed ≥12 cycles. Patients with oligoblastic relapse had more grade ≥3 anemia (32% v 4%; P = .02) and infections (36% v 8%; P = .03), whereas grade 4 neutropenia (32 v 23%) or thrombocytopenia (27 v 15%) were comparable with the MRD relapse cohort. Markers of molecular MRD relapse included mutant NPM1 (77%), CBFB::MYH11 (4%), RUNX1::RUNX1T1 (4%), or KMT2A::MLLT3 (4%). Three patients with a log10 rise in IDH1/2 (12%) were included. By cycle 2 in the MRD relapse cohort, a log10 reduction in MRD was observed in 69%; 46% achieved MRD negative remission. In the oligoblastic relapse cohort, 73% achieved CR/CRh/CRi. Overall, 21 (44%) underwent hematopoietic cell transplantation. Median overall survival (OS) was not reached in either cohort. Estimated 2-year OS rate was 67% (95% CI, 50 to 89) in the MRD and 53% (95% CI, 34 to 84) in the oligoblastic relapse cohorts. CONCLUSION For AML in first remission and either MRD or oligoblastic relapse, venetoclax plus LDAC is well tolerated and highly effective.
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MESH Headings
- Humans
- Aged
- Middle Aged
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/mortality
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Neoplasm, Residual
- Cytarabine/administration & dosage
- Sulfonamides/administration & dosage
- Sulfonamides/adverse effects
- Adult
- Female
- Male
- Bridged Bicyclo Compounds, Heterocyclic/administration & dosage
- Bridged Bicyclo Compounds, Heterocyclic/adverse effects
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Antineoplastic Combined Chemotherapy Protocols/adverse effects
- Aged, 80 and over
- Prospective Studies
- Nucleophosmin
- Young Adult
- Adolescent
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Affiliation(s)
- Ing Soo Tiong
- The Alfred Hospital and Monash University, Melbourne, Australia
- Peter MacCallum Cancer Centre and The Royal Melbourne Hospital, Melbourne, Australia
| | - Devendra K. Hiwase
- Royal Adelaide Hospital, Adelaide, Australia
- University of Adelaide, Adelaide, Australia
- South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Emad Abro
- Princess Alexandra Hospital, Queensland, Australia
| | - Ashish Bajel
- Peter MacCallum Cancer Centre and The Royal Melbourne Hospital, Melbourne, Australia
- The University of Melbourne, Melbourne, Australia
| | | | - Ashanka Beligaswatte
- University of Adelaide, Adelaide, Australia
- Flinders Medical Centre, Bedford Park, Australia
| | - John Reynolds
- The Alfred Hospital and Monash University, Melbourne, Australia
| | - Natasha Anstee
- The University of Melbourne, Melbourne, Australia
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Tamia Nguyen
- Peter MacCallum Cancer Centre and The Royal Melbourne Hospital, Melbourne, Australia
- The University of Melbourne, Melbourne, Australia
| | - Sun Loo
- Peter MacCallum Cancer Centre and The Royal Melbourne Hospital, Melbourne, Australia
- The University of Melbourne, Melbourne, Australia
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- The Northern Hospital, Melbourne, Australia
| | - Chong Chyn Chua
- The Alfred Hospital and Monash University, Melbourne, Australia
- The University of Melbourne, Melbourne, Australia
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- The Northern Hospital, Melbourne, Australia
| | - Michael Ashby
- The Alfred Hospital and Monash University, Melbourne, Australia
| | | | - Shaun Fleming
- The Alfred Hospital and Monash University, Melbourne, Australia
| | - Chun Y. Fong
- Austin Health and Olivia Newton John Cancer Research Institute, Melbourne, Australia
| | - Tse-Chieh Teh
- The Alfred Hospital and Monash University, Melbourne, Australia
- Box Hill Hospital, Melbourne, Australia
| | - Piers Blombery
- Peter MacCallum Cancer Centre and The Royal Melbourne Hospital, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Richard Dillon
- Department of Medical and Molecular Genetics, King's College, London, United Kingdom
- Guy's Hospital, London, United Kingdom
| | - Adam Ivey
- The Alfred Hospital and Monash University, Melbourne, Australia
| | - Andrew H. Wei
- Peter MacCallum Cancer Centre and The Royal Melbourne Hospital, Melbourne, Australia
- The University of Melbourne, Melbourne, Australia
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
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2
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Oduro KA, Spivey T, Moore EM, Meyerson H, Yoest J, Tomlinson B, Beck R, Alouani D, Sadri N. Clonal Dynamics and Relapse Risk Revealed by High-Sensitivity FLT3-Internal Tandem Duplication Detection in Acute Myeloid Leukemia. Mod Pathol 2024; 37:100534. [PMID: 38852814 DOI: 10.1016/j.modpat.2024.100534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/21/2024] [Accepted: 05/27/2024] [Indexed: 06/11/2024]
Abstract
The ability to detect low-level disease is key to our understanding of clonal heterogeneity in acute myeloid leukemia (AML) and residual disease that elude conventional assays and seed relapse. We developed a high-sensitivity next-generation sequencing (HS-NGS) clinical assay, able to reliably detect low levels (1 × 10-5) of FLT3-ITD, a frequent, therapeutically targetable and prognostically relevant mutation in AML. By applying this assay to 289 longitudinal samples from 62 patients at initial diagnosis and/or clinical follow-up (mean follow-up of 22 months), we reveal the frequent occurrence of FLT3-ITD subclones at diagnosis and demonstrate a significantly decreased relapse risk when FLT3-ITD is cleared after induction or thereafter. We perform pairwise sequencing of diagnosis and relapse samples from 23 patients to uncover more detailed patterns of FLT3-ITD clonal evolution at relapse than is detectable by less-sensitive assays. Finally, we show that rising ITD level during consecutive biopsies is a harbinger of impending relapse. Our findings corroborate the emerging clinical utility of high-sensitivity FLT3-ITD testing and expands our understanding of clonal dynamics in FLT3-ITD-positive AML.
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Affiliation(s)
- Kwadwo Asare Oduro
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin; Department of Pathology and Laboratory Medicine, University Hospitals Cleveland Medical Center & Case Western Reserve University School of Medicine, Cleveland, Ohio.
| | - Theresa Spivey
- Department of Pathology and Laboratory Medicine, University Hospitals Cleveland Medical Center & Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Erika M Moore
- Department of Pathology and Laboratory Medicine, University Hospitals Cleveland Medical Center & Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Howard Meyerson
- Department of Pathology and Laboratory Medicine, University Hospitals Cleveland Medical Center & Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Jennifer Yoest
- Department of Pathology and Laboratory Medicine, University Hospitals Cleveland Medical Center & Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Benjamin Tomlinson
- Department of Hematology/Oncology, University Hospitals Cleveland Medical Center & Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Rose Beck
- Department of Pathology and Laboratory Medicine, University Hospitals Cleveland Medical Center & Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - David Alouani
- Department of Pathology and Laboratory Medicine, University Hospitals Cleveland Medical Center & Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Navid Sadri
- Department of Pathology and Laboratory Medicine, University Hospitals Cleveland Medical Center & Case Western Reserve University School of Medicine, Cleveland, Ohio.
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3
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Li EW, Tran NYK, McCulloch D, Krigstein M, Catalano A, Othman J, Abadir E, Smith C, Iland H. FLT3-TKD Measurable Residual Disease Detection Using Droplet Digital PCR and Clinical Applications in Acute Myeloid Leukemia. Int J Mol Sci 2024; 25:5771. [PMID: 38891959 PMCID: PMC11171966 DOI: 10.3390/ijms25115771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/18/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
The tyrosine kinase domain of the FMS-Like tyrosine kinase 3 (FLT3-TKD) is recurrently mutated in acute myeloid leukemia (AML). Common molecular techniques used in its detection include PCR and capillary electrophoresis, Sanger sequencing and next-generation sequencing with recognized sensitivity limitations. This study aims to validate the use of droplet digital PCR (ddPCR) in the detection of measurable residual disease (MRD) involving the common FLT3-TKD mutations (D835Y, D835H, D835V, D835E). Twenty-two diagnostic samples, six donor controls, and a commercial D835Y positive control were tested using a commercial Bio-rad® ddPCR assay. All known variants were identified, and no false positives were detected in the wild-type control (100% specificity and sensitivity). The assays achieved a limit of detection suitable for MRD testing at 0.01% variant allelic fraction. Serial samples from seven intensively-treated patients with FLT3-TKD variants at diagnosis were tested. Five patients demonstrated clearance of FLT3-TKD clones, but two patients had FLT3-TKD persistence in the context of primary refractory disease. In conclusion, ddPCR is suitable for the detection and quantification of FLT3-TKD mutations in the MRD setting; however, the clinical significance and optimal management of MRD positivity require further exploration.
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Affiliation(s)
- Eric Wenlong Li
- Institute of Hematology, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
- Molecular Hematology Laboratory, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia
| | - Ngoc Yen Kim Tran
- Molecular Hematology Laboratory, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
| | - Derek McCulloch
- Institute of Hematology, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
- Molecular Hematology Laboratory, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia
| | - Michael Krigstein
- Department of Hematology, St Vincent’s Hospital, Sydney, NSW 2010, Australia
| | - Alberto Catalano
- Molecular Hematology Laboratory, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
| | - Jad Othman
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia
- Department of Hematology, Royal North Shore Hospital, Sydney, NSW 2065, Australia
| | - Edward Abadir
- Institute of Hematology, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia
| | - Cheryl Smith
- Molecular Hematology Laboratory, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
| | - Harry Iland
- Institute of Hematology, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
- Molecular Hematology Laboratory, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia
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4
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Levis MJ, Hamadani M, Logan B, Jones RJ, Singh AK, Litzow M, Wingard JR, Papadopoulos EB, Perl AE, Soiffer RJ, Ustun C, Ueda Oshima M, Uy GL, Waller EK, Vasu S, Solh M, Mishra A, Muffly L, Kim HJ, Mikesch JH, Najima Y, Onozawa M, Thomson K, Nagler A, Wei AH, Marcucci G, Geller NL, Hasabou N, Delgado D, Rosales M, Hill J, Gill SC, Nuthethi R, King D, Wittsack H, Mendizabal A, Devine SM, Horowitz MM, Chen YB. Gilteritinib as Post-Transplant Maintenance for AML With Internal Tandem Duplication Mutation of FLT3. J Clin Oncol 2024; 42:1766-1775. [PMID: 38471061 PMCID: PMC11095884 DOI: 10.1200/jco.23.02474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 11/29/2023] [Accepted: 12/28/2023] [Indexed: 03/14/2024] Open
Abstract
PURPOSE Allogeneic hematopoietic cell transplantation (HCT) improves outcomes for patients with AML harboring an internal tandem duplication mutation of FLT3 (FLT3-ITD) AML. These patients are routinely treated with a FLT3 inhibitor after HCT, but there is limited evidence to support this. Accordingly, we conducted a randomized trial of post-HCT maintenance with the FLT3 inhibitor gilteritinib (ClinicalTrials.gov identifier: NCT02997202) to determine if all such patients benefit or if detection of measurable residual disease (MRD) could identify those who might benefit. METHODS Adults with FLT3-ITD AML in first remission underwent HCT and were randomly assigned to placebo or 120 mg once daily gilteritinib for 24 months after HCT. The primary end point was relapse-free survival (RFS). Secondary end points included overall survival (OS) and the effect of MRD pre- and post-HCT on RFS and OS. RESULTS Three hundred fifty-six participants were randomly assigned post-HCT to receive gilteritinib or placebo. Although RFS was higher in the gilteritinib arm, the difference was not statistically significant (hazard ratio [HR], 0.679 [95% CI, 0.459 to 1.005]; two-sided P = .0518). However, 50.5% of participants had MRD detectable pre- or post-HCT, and, in a prespecified subgroup analysis, gilteritinib was beneficial in this population (HR, 0.515 [95% CI, 0.316 to 0.838]; P = .0065). Those without detectable MRD showed no benefit (HR, 1.213 [95% CI, 0.616 to 2.387]; P = .575). CONCLUSION Although the overall improvement in RFS was not statistically significant, RFS was higher for participants with detectable FLT3-ITD MRD pre- or post-HCT who received gilteritinib treatment. To our knowledge, these data are among the first to support the effectiveness of MRD-based post-HCT therapy.
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Affiliation(s)
| | | | - Brent Logan
- CIBMTR/Medical College of Wisconsin, Milwaukee, WI
| | | | | | | | | | | | | | | | | | | | | | | | | | - Melhem Solh
- Northside Hospital Cancer Institute, Atlanta, GA
| | | | | | - Hee-Je Kim
- Catholic Hematology Hospital, Seoul St Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | | | - Yuho Najima
- Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
| | | | | | - Arnon Nagler
- Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Andrew H. Wei
- Peter MacCallum Cancer Centre, Royal Melbourne Hospital, Walter and Eliza Hill Institute of Medical Research and University of Melbourne, Melbourne, Australia
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5
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Latini S, Venafra V, Massacci G, Bica V, Graziosi S, Pugliese GM, Iannuccelli M, Frioni F, Minnella G, Marra JD, Chiusolo P, Pepe G, Helmer Citterich M, Mougiakakos D, Böttcher M, Fischer T, Perfetto L, Sacco F. Unveiling the signaling network of FLT3-ITD AML improves drug sensitivity prediction. eLife 2024; 12:RP90532. [PMID: 38564252 PMCID: PMC10987088 DOI: 10.7554/elife.90532] [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] [Indexed: 04/04/2024] Open
Abstract
Currently, the identification of patient-specific therapies in cancer is mainly informed by personalized genomic analysis. In the setting of acute myeloid leukemia (AML), patient-drug treatment matching fails in a subset of patients harboring atypical internal tandem duplications (ITDs) in the tyrosine kinase domain of the FLT3 gene. To address this unmet medical need, here we develop a systems-based strategy that integrates multiparametric analysis of crucial signaling pathways, and patient-specific genomic and transcriptomic data with a prior knowledge signaling network using a Boolean-based formalism. By this approach, we derive personalized predictive models describing the signaling landscape of AML FLT3-ITD positive cell lines and patients. These models enable us to derive mechanistic insight into drug resistance mechanisms and suggest novel opportunities for combinatorial treatments. Interestingly, our analysis reveals that the JNK kinase pathway plays a crucial role in the tyrosine kinase inhibitor response of FLT3-ITD cells through cell cycle regulation. Finally, our work shows that patient-specific logic models have the potential to inform precision medicine approaches.
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Affiliation(s)
- Sara Latini
- Cellular and Molecular Biology, Department of Biology, University of Rome Tor VergataRomeItaly
| | - Veronica Venafra
- Cellular and Molecular Biology, Department of Biology, University of Rome Tor VergataRomeItaly
| | | | - Valeria Bica
- Cellular and Molecular Biology, Department of Biology, University of Rome Tor VergataRomeItaly
| | - Simone Graziosi
- Cellular and Molecular Biology, Department of Biology, University of Rome Tor VergataRomeItaly
| | | | | | - Filippo Frioni
- Sezione di Ematologia, Dipartimento di Scienze Radiologiche ed Ematologiche, Università Cattolica del Sacro CuoreRomeItaly
| | - Gessica Minnella
- Dipartimento di Diagnostica per Immagini, Radioterapia Oncologica ed Ematologia, Fondazione Policlinico A. Gemelli IRCCSRomeItaly
| | - John Donald Marra
- Sezione di Ematologia, Dipartimento di Scienze Radiologiche ed Ematologiche, Università Cattolica del Sacro CuoreRomeItaly
| | - Patrizia Chiusolo
- Sezione di Ematologia, Dipartimento di Scienze Radiologiche ed Ematologiche, Università Cattolica del Sacro CuoreRomeItaly
| | - Gerardo Pepe
- Department of Biology, University of Rome Tor VergataRomeItaly
| | | | - Dimitros Mougiakakos
- Health Campus for Inflammation, Immunity and Infection (GCI3), Otto-von-Guericke University of MagdeburgMagdeburgGermany
- Department of Hematology and Oncology, Otto-von-Guericke University of MagdeburgMagdeburgGermany
| | - Martin Böttcher
- Health Campus for Inflammation, Immunity and Infection (GCI3), Otto-von-Guericke University of MagdeburgMagdeburgGermany
- Department of Hematology and Oncology, Otto-von-Guericke University of MagdeburgMagdeburgGermany
| | - Thomas Fischer
- Health Campus for Inflammation, Immunity and Infection (GCI3), Otto-von-Guericke University of MagdeburgMagdeburgGermany
- Institute of Molecular and Clinical Immunology, Otto-von-Guericke University of MagdeburgMagdeburgGermany
| | - Livia Perfetto
- Department of Biology, University of Rome Tor VergataRomeItaly
- Department of Biology, Fondazione Human TechnopoleMilanItaly
| | - Francesca Sacco
- Department of Biology, University of Rome Tor VergataRomeItaly
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
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6
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Reikvam H, Dillon R. Revisiting the role of measurable residual disease in FLT3 mutated acute myelogenous leukemia. Expert Rev Hematol 2024; 17:103-106. [PMID: 38654593 DOI: 10.1080/17474086.2024.2347303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/22/2024] [Indexed: 04/26/2024]
Affiliation(s)
- Håkon Reikvam
- K.G. Jebsen Center for Myeloid Blood Cancer, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Richard Dillon
- Department of Medical and Molecular Genetics, King's College, Guy's and St Thomas' NHS Foundation Trust, London, UK
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7
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Chea M, Rigolot L, Canali A, Vergez F. Minimal Residual Disease in Acute Myeloid Leukemia: Old and New Concepts. Int J Mol Sci 2024; 25:2150. [PMID: 38396825 PMCID: PMC10889505 DOI: 10.3390/ijms25042150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/01/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Minimal residual disease (MRD) is of major importance in onco-hematology, particularly in acute myeloid leukemia (AML). MRD measures the amount of leukemia cells remaining in a patient after treatment, and is an essential tool for disease monitoring, relapse prognosis, and guiding treatment decisions. Patients with a negative MRD tend to have superior disease-free and overall survival rates. Considerable effort has been made to standardize MRD practices. A variety of techniques, including flow cytometry and molecular methods, are used to assess MRD, each with distinct strengths and weaknesses. MRD is recognized not only as a predictive biomarker, but also as a prognostic tool and marker of treatment efficacy. Expected advances in MRD assessment encompass molecular techniques such as NGS and digital PCR, as well as optimization strategies such as unsupervised flow cytometry analysis and leukemic stem cell monitoring. At present, there is no perfect method for measuring MRD, and significant advances are expected in the future to fully integrate MRD assessment into the management of AML patients.
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Affiliation(s)
- Mathias Chea
- Laboratoire d’Hématologie Biologique, Institut Universitaire du Cancer de Toulouse Oncopole, Centre Hospitalier Universitaire de Toulouse, 31059 Toulouse, France; (M.C.); (L.R.); (A.C.)
| | - Lucie Rigolot
- Laboratoire d’Hématologie Biologique, Institut Universitaire du Cancer de Toulouse Oncopole, Centre Hospitalier Universitaire de Toulouse, 31059 Toulouse, France; (M.C.); (L.R.); (A.C.)
- School of Medicine, Université Toulouse III Paul Sabatier, 31062 Toulouse, France
| | - Alban Canali
- Laboratoire d’Hématologie Biologique, Institut Universitaire du Cancer de Toulouse Oncopole, Centre Hospitalier Universitaire de Toulouse, 31059 Toulouse, France; (M.C.); (L.R.); (A.C.)
- School of Medicine, Université Toulouse III Paul Sabatier, 31062 Toulouse, France
| | - Francois Vergez
- Laboratoire d’Hématologie Biologique, Institut Universitaire du Cancer de Toulouse Oncopole, Centre Hospitalier Universitaire de Toulouse, 31059 Toulouse, France; (M.C.); (L.R.); (A.C.)
- School of Medicine, Université Toulouse III Paul Sabatier, 31062 Toulouse, France
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8
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Turkalj S, Jakobsen NA, Groom A, Radtke FA, Vyas P. A protocol for simultaneous high-sensitivity genotyping and chromatin accessibility profiling in single cells. STAR Protoc 2023; 4:102641. [PMID: 37897733 PMCID: PMC10641301 DOI: 10.1016/j.xpro.2023.102641] [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: 08/11/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/30/2023] Open
Abstract
Single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq) resolves the heterogeneity of epigenetic states across cells but does not typically capture exonic mutations, which limits our knowledge of how somatic mutations alter chromatin landscapes. Here, we present a plate-based approach coupling high-sensitivity genotyping of genomic loci with high-content scATAC-seq libraries from the same single cells. We first describe steps for optimization of genotyping primers, followed by detailed guidance on the preparation of both scATAC-seq and single-cell genotyping libraries, fully automated on high-throughput liquid handling platforms. For complete details on the use and execution of this protocol, please refer to Turkalj, Jakobsen et al.1.
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Affiliation(s)
- Sven Turkalj
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
| | - Niels Asger Jakobsen
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Angus Groom
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Felix A Radtke
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Paresh Vyas
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
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9
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Bergeron J, Capo-Chichi JM, Tsui H, Mahe E, Berardi P, Minden MD, Brandwein JM, Schuh AC. The Clinical Utility of FLT3 Mutation Testing in Acute Leukemia: A Canadian Consensus. Curr Oncol 2023; 30:10410-10436. [PMID: 38132393 PMCID: PMC10742150 DOI: 10.3390/curroncol30120759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/02/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
FMS-like tyrosine kinase 3 (FLT3) mutations are detected in approximately 20-30% of patients with acute myeloid leukemia (AML), with the presence of a FLT3 internal tandem duplication (FLT3-ITD) mutation being associated with an inferior outcome. Assessment of FLT3 mutational status is now essential to define optimal upfront treatment in both newly diagnosed and relapsed AML, to support post-induction allogeneic hematopoietic stem cell transplantation (alloSCT) decision-making, and to evaluate treatment response via measurable (minimal) residual disease (MRD) evaluation. In view of its importance in AML diagnosis and management, the Canadian Leukemia Study Group/Groupe canadien d'étude sur la leucémie (CLSG/GCEL) undertook the development of a consensus statement on the clinical utility of FLT3 mutation testing, as members reported considerable inter-center variability across Canada with respect to testing availability and timing of use, methodology, and interpretation. The CLSG/GCEL panel identified key clinical and hematopathological questions, including: (1) which patients should be tested for FLT3 mutations, and when?; (2) which is the preferred method for FLT3 mutation testing?; (3) what is the clinical relevance of FLT3-ITD size, insertion site, and number of distinct FLT3-ITDs?; (4) is there a role for FLT3 analysis in MRD assessment?; (5) what is the clinical relevance of the FLT3-ITD allelic burden?; and (6) how should results of FLT3 mutation testing be reported? The panel followed an evidence-based approach, taken together with Canadian clinical and laboratory experience and expertise, to create a consensus document to facilitate a more uniform approach to AML diagnosis and treatment across Canada.
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Affiliation(s)
- Julie Bergeron
- CEMTL Installation Maisonneuve-Rosemont, Institut Universitaire d’Hématologie-Oncologie et de Thérapie Cellulaire, Université de Montréal, Montréal, QC H1T 2M4, Canada
| | - Jose-Mario Capo-Chichi
- Division of Clinical Laboratory Genetics, Department of Laboratory Medicine and Pathobiology, Laboratory Medicine Program, University Health Network, University of Toronto, Toronto, ON M5G 2C4, Canada;
| | - Hubert Tsui
- Division of Hematological Pathology, Department of Laboratory Medicine and Molecular Diagnostics, Precision Diagnostics and Therapeutics Program, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada;
- Department of Laboratory Medicine and Pathobiology, Department of Immunology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Etienne Mahe
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada;
- Division of Hematology and Hematological Malignancies, Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Philip Berardi
- Department of Pathology and Laboratory Medicine, The Ottawa Hospital/Eastern Ontario Regional Laboratory Association, Ottawa, ON K1H 8M2, Canada;
- Department of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Mark D. Minden
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada; (M.D.M.); (A.C.S.)
- Department of Medicine, University of Toronto, Toronto, ON M5S 3H2, Canada
| | - Joseph M. Brandwein
- Division of Hematology, Department of Medicine, University of Alberta, Edmonton, AB T6G 2G3, Canada;
| | - Andre C. Schuh
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada; (M.D.M.); (A.C.S.)
- Department of Medicine, University of Toronto, Toronto, ON M5S 3H2, Canada
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10
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Cloos J. Understanding differential technologies for detection of MRD and how to incorporate into clinical practice. HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2023; 2023:682-690. [PMID: 38066915 PMCID: PMC10727023 DOI: 10.1182/hematology.2023000454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Patient- and leukemia-specific factors assessed at diagnosis classify patients with acute myeloid leukemia (AML) in risk categories that are prognostic for outcome. The induction phase with intensive chemotherapy in fit patients aims to reach a complete remission (CR) of less than 5% blasts in bone marrow by morphology. To deepen and sustain the response, induction is followed by consolidation treatment. This postremission treatment of patients with AML is graduated in intensity based on this favorable, intermediate, or adverse risk group classification as defined in the European Leukemia Network (ELN) 2022 recommendations. The increment of evidence that measurable residual disease (MRD) after induction can be superimposed on risk group at diagnosis is instrumental in tailoring further treatment accordingly. Several techniques are applied to detect MRD such as multiparameter flow cytometry (MFC), quantitative (digital) polymerase chain reaction (PCR), and next-generation sequencing. The clinical implementation of MRD and the technique used differ among institutes, leading to the accumulation of a wide range of data, and therefore harmonization is warranted. Currently, evidence for MRD guidance is limited to the time point after induction using MFC or quantitative PCR for NPM1 and core binding factor abnormalities in intermediate-risk patients. The role of MRD in targeted or nonintensive therapies needs to be clarified, although some data show improved survival in patients achieving CR-MRD negativity. Potential application of MRD for selection of conditioning before stem cell transplantation, monitoring after consolidation, and use as an intermediate end point in clinical trials need further evaluation.
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Affiliation(s)
- Jacqueline Cloos
- Department of Hematology, Cancer Center Amsterdam, Amsterdam UMC, location VUMC, Amsterdam, the Netherlands
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11
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Hernández-Sánchez A, Bullinger L. Recent advances in precision medicine for acute myeloid leukemia. Curr Opin Oncol 2023; 35:581-588. [PMID: 37621173 DOI: 10.1097/cco.0000000000000965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
PURPOSE OF REVIEW Acute myeloid leukemia (AML) is a heterogeneous disease, in which treatment response and patient survival are highly conditioned by the leukemia biology. The aim of this review is to summarize recent advances in AML classification, risk stratification models, measurable residual disease (MRD) and the increasing number of treatment options that are paving the way towards precision medicine in AML. RECENT FINDINGS AML classification and risk stratification were recently updated by incorporating novel molecular markers that are important for diagnosis and outcome prediction. In addition, the impact of co-mutational patterns is under investigation and novel approaches using machine learning algorithms are starting to be used for individualized risk estimation. Molecular markers are also becoming useful in predicting response to non-intensive treatments. MRD informs of treatment response with high sensitivity, allowing dynamic patient risk assessment and early intervention. Finally, important advances were made in AML therapy, with an increasing number of targeted therapies becoming available and many novel treatment approaches being under development with promising early results. SUMMARY A better understanding of AML biology is leading to improved risk stratification and important advances in treatments, which are allowing the development of precision medicine in AML at an unprecedented pace.
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Affiliation(s)
- Alberto Hernández-Sánchez
- University Hospital of Salamanca
- Institute of Biomedical Research of Salamanca (IBSAL) , Salamanca, Spain
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12
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Othman J, Potter N, Mokretar K, Taussig D, Khan A, Krishnamurthy P, Latif AL, Cahalin P, Aries J, Amer M, Belsham E, Conneally E, Craddock C, Culligan D, Dennis M, Duncan C, Freeman SD, Furness C, Gilkes A, Gkreka P, Hodgson K, Ingram W, Jain M, King A, Knapper S, Kottaridis P, McMullin MF, Mohite U, Ngu L, O'Nions J, Patrick K, Rider T, Roberts W, Severinsen MT, Storrar N, Taylor T, Russell NH, Dillon R. FLT3 inhibitors as MRD-guided salvage treatment for molecular failure in FLT3 mutated AML. Leukemia 2023; 37:2066-2072. [PMID: 37558736 PMCID: PMC10539160 DOI: 10.1038/s41375-023-01994-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/17/2023] [Accepted: 08/02/2023] [Indexed: 08/11/2023]
Abstract
Patients with FLT3-mutated AML have a high relapse rate and suboptimal outcomes. Many have co-mutations suitable for measurable residual disease (MRD) monitoring by RT-qPCR and those destined to relapse can be identified by high or rising levels of MRD, called molecular failure. This provides a window for pre-emptive intervention, but there is little evidence to guide treatment. The use of FLT3 inhibitors (FLT3i) appears attractive but their use has not yet been evaluated. We identified 56 patients treated with FLT3i at molecular failure. The FLT3 mutation was an ITD in 52, TKD in 7 and both in 3. Over half of patients had previously received midostaurin. Molecular failure occurred at a median 9.2 months from diagnosis and was treated with gilteritinib (n = 38), quizartinib (n = 7) or sorafenib (n = 11). 60% achieved a molecular response, with 45% reaching MRD negativity. Haematological toxicity was low, and 22 patients were bridged directly to allogeneic transplant with another 6 to donor lymphocyte infusion. 2-year overall survival was 80% (95%CI 69-93) and molecular event-free survival 56% (95%CI 44-72). High-sensitivity next-generation sequencing for FLT3-ITD at molecular failure identified patients more likely to benefit. FLT3i monotherapy for molecular failure is a promising strategy which merits evaluation in prospective studies.
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Affiliation(s)
- Jad Othman
- Department of Medical and Molecular Genetics, King's College London, London, England, UK
- Guy's and St Thomas' NHS Foundation Trust, London, England, UK
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Nicola Potter
- Department of Medical and Molecular Genetics, King's College London, London, England, UK
| | | | - David Taussig
- The Royal Marsden NHS Foundation Trust, London, England, UK
| | - Anjum Khan
- Leeds Teaching Hospitals NHS Trust, Leeds, England, UK
| | | | | | - Paul Cahalin
- Blackpool Teaching Hospitals NHS Foundation Trust, Blackpool, England, UK
| | - James Aries
- Barts Cancer Institute, Queen Mary University of London, London, England, UK
| | - Mariam Amer
- University Hospital Southampton, Southampton, England, UK
| | | | | | | | | | - Mike Dennis
- The Christie NHS Foundation Trust, Manchester, England, UK
| | | | - Sylvie D Freeman
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, Scotland, UK
| | | | - Amanda Gilkes
- Department of Haematology, Cardiff University, Cardiff, Wales, UK
| | | | | | | | - Manish Jain
- Leeds Teaching Hospitals NHS Trust, Leeds, England, UK
| | - Andrew King
- Addenbrooke's Hospital, Cambridge, England, UK
| | - Steven Knapper
- School of Medicine, Cardiff University, Cardiff, Wales, UK
| | | | | | | | - Loretta Ngu
- Royal Devon & Exeter NHS Foundation Trust, Exeter, England, UK
| | - Jenny O'Nions
- University College London Hospital NHS Foundation Trust, London, England, UK
| | | | - Tom Rider
- The Royal Sussex County Hospital, Brighton and Hove, England, UK
| | - Wing Roberts
- Great North Children's Hospital, Newcastle upon Tyne, England, UK
| | - Marianne Tang Severinsen
- Department of Hematology, Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | | | - Tom Taylor
- Nottingham University Hospital, Nottingham, England, UK
| | - Nigel H Russell
- Guy's and St Thomas' NHS Foundation Trust, London, England, UK
| | - Richard Dillon
- Department of Medical and Molecular Genetics, King's College London, London, England, UK.
- Guy's and St Thomas' NHS Foundation Trust, London, England, UK.
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13
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Turkalj S, Jakobsen NA, Groom A, Metzner M, Riva SG, Gür ER, Usukhbayar B, Salazar MA, Hentges LD, Mickute G, Clark K, Sopp P, Davies JOJ, Hughes JR, Vyas P. GTAC enables parallel genotyping of multiple genomic loci with chromatin accessibility profiling in single cells. Cell Stem Cell 2023; 30:722-740.e11. [PMID: 37146586 DOI: 10.1016/j.stem.2023.04.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 02/23/2023] [Accepted: 04/12/2023] [Indexed: 05/07/2023]
Abstract
Understanding clonal evolution and cancer development requires experimental approaches for characterizing the consequences of somatic mutations on gene regulation. However, no methods currently exist that efficiently link high-content chromatin accessibility with high-confidence genotyping in single cells. To address this, we developed Genotyping with the Assay for Transposase-Accessible Chromatin (GTAC), enabling accurate mutation detection at multiple amplified loci, coupled with robust chromatin accessibility readout. We applied GTAC to primary acute myeloid leukemia, obtaining high-quality chromatin accessibility profiles and clonal identities for multiple mutations in 88% of cells. We traced chromatin variation throughout clonal evolution, showing the restriction of different clones to distinct differentiation stages. Furthermore, we identified switches in transcription factor motif accessibility associated with a specific combination of driver mutations, which biased transformed progenitors toward a leukemia stem cell-like chromatin state. GTAC is a powerful tool to study clonal heterogeneity across a wide spectrum of pre-malignant and neoplastic conditions.
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Affiliation(s)
- Sven Turkalj
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Niels Asger Jakobsen
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK; Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Angus Groom
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Marlen Metzner
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Simone G Riva
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - E Ravza Gür
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Batchimeg Usukhbayar
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Mirian Angulo Salazar
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Lance D Hentges
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Gerda Mickute
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Kevin Clark
- Flow Cytometry Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Paul Sopp
- Flow Cytometry Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - James O J Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK; Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Paresh Vyas
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK; Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
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14
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Perrone S, Ottone T, Zhdanovskaya N, Molica M. How acute myeloid leukemia (AML) escapes from FMS-related tyrosine kinase 3 (FLT3) inhibitors? Still an overrated complication? CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2023; 6:223-238. [PMID: 37457126 PMCID: PMC10344728 DOI: 10.20517/cdr.2022.130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 03/21/2023] [Accepted: 04/11/2023] [Indexed: 07/18/2023]
Abstract
FMS-related tyrosine kinase 3 (FLT3) mutations, present in about 25%-30% of acute myeloid leukemia (AML) patients, constitute one of the most frequently detected mutations in these patients. The binding of FLT3L to FLT3 activates the phosphatidylinositol 3-kinase (PI3K) and RAS pathways, producing increased cell proliferation and the inhibition of apoptosis. Two types of FLT3 mutations exist: FLT3-ITD and FLT3-TKD (point mutations in D835 and I836 or deletion of codon I836). A class of drugs, tyrosine-kinase inhibitors (TKI), targeting mutated FLT3, is already available with 1st and 2nd generation molecules, but only midostaurin and gilteritinib are currently approved. However, the emergence of resistance or the selection of clones not responding to FLT3 inhibitors has become an important clinical dilemma, as the duration of clinical responses is generally limited to a few months. This review analyzes the insights into mechanisms of resistance to TKI and poses a particular view on the clinical relevance of this phenomenon. Has resistance been overlooked? Indeed, FLT3 inhibitors have significantly contributed to reducing the negative impact of FLT3 mutations on the prognosis of AML patients who are no longer considered at high risk by the European LeukemiaNet (ELN) 2022. Finally, several ongoing efforts to overcome resistance to FLT3-inhibitors will be presented: new generation FLT3 inhibitors in monotherapy or combined with standard chemotherapy, hypomethylating drugs, or IDH1/2 inhibitors, Bcl2 inhibitors; novel anti-human FLT3 monoclonal antibodies (e.g., FLT3/CD3 bispecific antibodies); FLT3-CAR T-cells; CDK4/6 kinase inhibitor (e.g., palbociclib).
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Affiliation(s)
- Salvatore Perrone
- Hematology, Polo Universitario Pontino, S.M. Goretti Hospital, Latina 04100, Italy
| | - Tiziana Ottone
- Department of Biomedicine and Prevention, the University of Rome “Tor Vergata”, Rome 00100 Italy
- Neuro-Oncohematology, Santa Lucia Foundation, I.R.C.C.S., Rome 00100, Italy
| | - Nadezda Zhdanovskaya
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome 00161, Italy
| | - Matteo Molica
- Hematology Unit, S. Eugenio Hospital, ASL Roma 2, Rome 00144, Italy
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15
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Yokoyama S, Onozawa M, Yoshida S, Miyashita N, Kimura H, Takahashi S, Matsukawa T, Goto H, Fujisawa S, Miki K, Hidaka D, Hashiguchi J, Wakasa K, Ibata M, Takeda Y, Shigematsu A, Fujimoto K, Tsutsumi Y, Mori A, Ishihara T, Kakinoki Y, Kondo T, Hashimoto D, Teshima T. Subclinical minute FLT3-ITD clone can be detected in clinically FLT3-ITD-negative acute myeloid leukaemia at diagnosis. Br J Haematol 2023. [PMID: 37067758 DOI: 10.1111/bjh.18800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/18/2023]
Abstract
Recent advances in next-generation sequencing (NGS) have enabled the detection of subclinical minute FLT3-ITD. We selected 74 newly diagnosed, cytogenetically normal acute myeloid leukaemia (AML) samples in which FLT3-ITD was not detected by gel electrophoresis. We sequenced them using NGS and found minute FLT3-ITDs in 19 cases. We compared cases with clinically relevant FLT3-ITD (n = 37), cases with minute FLT3-ITD (n = 19) and cases without detectable FLT3-ITD (n = 55). Molecular characteristics (location and length) of minute FLT3-ITD were similar to those of clinically relevant FLT3-ITD. Survival of cases with minute FLT3-ITD was similar to that of cases without detectable FLT3-ITD, whereas the relapse rate within 1 year after onset was significantly higher in cases with minute FLT3-ITD. We followed 18 relapsed samples of cases with clinically FLT3-ITD-negative at diagnosis. Two of 3 cases with minute FLT3-ITD relapsed with progression to clinically relevant FLT3-ITD. Two of 15 cases in which FLT3-ITD was not detected by NGS relapsed with the emergence of minute FLT3-ITD, and one of them showed progression to clinically relevant FLT3-ITD at the second relapse. We revealed the clonal dynamics of subclinical minute FLT3-ITD in clinically FLT3-ITD-negative AML. Minute FLT3-ITD at the initial AML can expand to become a dominant clone at relapse.
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Affiliation(s)
- Shota Yokoyama
- Department of Hematology, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Masahiro Onozawa
- Department of Hematology, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Shota Yoshida
- Department of Hematology, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Naoki Miyashita
- Department of Hematology, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Hiroyuki Kimura
- Department of Hematology, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Shogo Takahashi
- Department of Hematology, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Toshihiro Matsukawa
- Department of Hematology, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Hideki Goto
- Department of Hematology, Hokkaido University Faculty of Medicine, Sapporo, Japan
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, Japan
| | - Shinichi Fujisawa
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, Japan
| | - Kosuke Miki
- Department of Hematology, Teine Keijinkai Hospital, Sapporo, Japan
| | - Daisuke Hidaka
- Department of Hematology, Sapporo Hokuyu Hospital, Sapporo, Japan
| | | | - Kentaro Wakasa
- Division of Hematology, Obihiro-Kosei General Hospital, Obihiro, Japan
| | - Makoto Ibata
- Department of Hematology, Sapporo-Kosei General Hospital, Sapporo, Japan
| | - Yukari Takeda
- Department of Hematology, Tonan Hospital, Sapporo, Japan
| | - Akio Shigematsu
- Department of Hematology, Kushiro Rosai Hospital, Kushiro, Japan
| | - Katsuya Fujimoto
- Department of Hematology, National Hospital Organization Hokkaido Cancer Center, Sapporo, Japan
| | - Yutaka Tsutsumi
- Department of Hematology, Hakodate Municipal Hospital, Hakodate, Japan
| | - Akio Mori
- Blood Disorders Center, Aiiku Hospital, Sapporo, Japan
| | | | | | - Takeshi Kondo
- Blood Disorders Center, Aiiku Hospital, Sapporo, Japan
| | - Daigo Hashimoto
- Department of Hematology, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Takanori Teshima
- Department of Hematology, Hokkaido University Faculty of Medicine, Sapporo, Japan
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, Japan
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16
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Tiong IS, Loo S. Targeting Measurable Residual Disease (MRD) in Acute Myeloid Leukemia (AML): Moving beyond Prognostication. Int J Mol Sci 2023; 24:4790. [PMID: 36902217 PMCID: PMC10003715 DOI: 10.3390/ijms24054790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 03/06/2023] Open
Abstract
Measurable residual disease (MRD) assessment in acute myeloid leukemia (AML) has an established role in disease prognostication, particularly in guiding decisions for hematopoietic cell transplantation in first remission. Serial MRD assessment is now routinely recommended in the evaluation of treatment response and monitoring in AML by the European LeukemiaNet. The key question remains, however, if MRD in AML is clinically actionable or "does MRD merely portend fate"? With a series of new drug approvals since 2017, we now have more targeted and less toxic therapeutic options for the potential application of MRD-directed therapy. Recent approval of NPM1 MRD as a regulatory endpoint is also foreseen to drastically transform the clinical trial landscape such as biomarker-driven adaptive design. In this article, we will review (1) the emerging molecular MRD markers (such as non-DTA mutations, IDH1/2, and FLT3-ITD); (2) the impact of novel therapeutics on MRD endpoints; and (3) how MRD might be used as a predictive biomarker to guide therapy in AML beyond its prognostic role, which is the focus of two large collaborative trials: AMLM26 INTERCEPT (ACTRN12621000439842) and MyeloMATCH (NCT05564390).
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Affiliation(s)
- Ing S. Tiong
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- The Alfred Hospital, Melbourne, VIC 3004, Australia
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC 3004, Australia
| | - Sun Loo
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- The Northern Hospital, Epping, VIC 3076, Australia
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17
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Lee S, Sun CH, Jang H, Kim D, Yoon SS, Koh Y, Na SC, Cho SI, Kim MJ, Seong MW, Byun JM, Yun H. ITDetect: a method to detect internal tandem duplication of FMS-like tyrosine kinase (FLT3) from next-generation sequencing data with high sensitivity and clinical application. BMC Bioinformatics 2023; 24:62. [PMID: 36823555 PMCID: PMC9951415 DOI: 10.1186/s12859-023-05173-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 02/03/2023] [Indexed: 02/25/2023] Open
Abstract
Internal tandem duplication (ITD) of the FMS-like tyrosine kinase (FLT3) gene is associated with poor clinical outcomes in patients with acute myeloid leukemia. Although recent methods for detecting FLT3-ITD from next-generation sequencing (NGS) data have replaced traditional ITD detection approaches such as conventional PCR or fragment analysis, their use in the clinical field is still limited and requires further information. Here, we introduce ITDetect, an efficient FLT3-ITD detection approach that uses NGS data. Our proposed method allows for more precise detection and provides more detailed information than existing in silico methods. Further, it enables FLT3-ITD detection from exome sequencing or targeted panel sequencing data, thereby improving its clinical application. We validated the performance of ITDetect using NGS-based and experimental ITD detection methods and successfully demonstrated that ITDetect provides the highest concordance with the experimental methods. The program and data underlying this study are available in a public repository.
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Affiliation(s)
- Sungyoung Lee
- grid.412484.f0000 0001 0302 820XDepartment of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea ,grid.412484.f0000 0001 0302 820XCenter for Precision Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Choong-Hyun Sun
- GenomeOpinion Inc., 117-3 Hoegiro, Dongdaemoon-gu, Seoul, Republic of Korea
| | - Heejun Jang
- grid.31501.360000 0004 0470 5905Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Daeyoon Kim
- grid.31501.360000 0004 0470 5905Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung-Soo Yoon
- grid.31501.360000 0004 0470 5905Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea ,grid.412484.f0000 0001 0302 820XDepartment of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Youngil Koh
- grid.31501.360000 0004 0470 5905Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea ,grid.412484.f0000 0001 0302 820XDepartment of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Seung Chan Na
- grid.412484.f0000 0001 0302 820XDepartment of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Sung Im Cho
- grid.412484.f0000 0001 0302 820XDepartment of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Man Jin Kim
- grid.412484.f0000 0001 0302 820XDepartment of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Moon-Woo Seong
- grid.412484.f0000 0001 0302 820XDepartment of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Ja Min Byun
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea. .,Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Hongseok Yun
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea. .,Center for Precision Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
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18
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Clinical Implications of the FLT3-ITD Allelic Ratio in Acute Myeloid Leukemia in the Context of an Allogeneic Stem Cell Transplantation. Cancers (Basel) 2023; 15:cancers15041312. [PMID: 36831653 PMCID: PMC9954047 DOI: 10.3390/cancers15041312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/07/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Although the presence of FLT3-ITD, as well as levels of the FLT3-ITD allelic ratio, have been described as prognostic factors in acute myeloid leukemia (AML), little is known about how the FLT3-ITD allelic ratio impacts patients' outcomes when receiving an allogeneic hematopoietic stem cell transplantation (HSCT). We analyzed 118 patients (median age at diagnosis 58.3, range 14.3-82.3 years) harboring FLT3-ITD, of whom 94 patients were consolidated with an allogeneic HSCT and included in outcome analyses. A high FLT3-ITD allelic ratio was associated with a higher white blood cell count, higher blood and bone marrow blasts, and worse ELN2017 risk at diagnosis. Patients with a high FLT3-ITD allelic ratio more often had NPM1 mutations, while patients with a low allelic ratio more often had FLT3-TKD mutations. Patients with a high FLT3-ITD allelic ratio were less likely to achieve a measurable residual disease (MRD)-negative remission prior to allogeneic HSCT and had a trend for a shorter time to relapse. However, there was no distinct cumulative incidence of relapse, non-relapse mortality, or overall survival according to the FLT3-ITD allelic ratio in transplanted patients. While co-mutated FLT3-TKD was associated with better outcomes, the MRD status at HSCT was the most significant factor for outcomes. While our data indicates that an allogeneic HSCT may mitigate the adverse effect of a high FLT3-ITD allelic ratio, comparative studies are needed to evaluate which FLT3-ITD mutated patients benefit from which consolidation strategy.
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Bystrom R, Levis MJ. An Update on FLT3 in Acute Myeloid Leukemia: Pathophysiology and Therapeutic Landscape. Curr Oncol Rep 2023; 25:369-378. [PMID: 36808557 DOI: 10.1007/s11912-023-01389-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2022] [Indexed: 02/21/2023]
Abstract
PURPOSE OF REVIEW This review aims to summarize the pathophysiology, clinical presentation, and management of acute myeloid leukemia (AML) with FMS-like tyrosine kinase-3 (FLT3) mutations. RECENT FINDINGS The recent European Leukemia Net (ELN2022) recommendations re-classified AML with FLT3 internal tandem duplications (FLT3-ITD) as intermediate risk regardless of Nucleophosmin 1 (NPM1) co-mutation or the FLT3 allelic ratio. Allogeneic hematopoietic cell transplantation (alloHCT) is now recommended for all eligible patients with FLT3-ITD AML. This review outlines the role of FLT3 inhibitors in induction and consolidation, as well as for post-alloHCT maintenance. It outlines the unique challenges and advantages of assessing FLT3 measurable residual disease (MRD) and discusses the pre-clinical basis for the combination of FLT3 and menin inhibitors. And, for the older or unfit patient ineligible for upfront intensive chemotherapy, it discusses the recent clinical trials incorporating FLT3 inhibitors into azacytidine- and venetoclax-based regimens. Finally, it proposes a rational sequential approach for integrating FLT3 inhibitors into less intensive regimens, with a focus on improved tolerability in the older and unfit patient population. The management of AML with FLT3 mutation remains a challenge in clinical practice. This review provides an update on the pathophysiology and therapeutic landscape of FLT3 AML, as well as a clinical management framework for managing the older or unfit patient ineligible for intensive chemotherapy.
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Affiliation(s)
- Rebecca Bystrom
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mark J Levis
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.
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20
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Krigstein M, Iland HJ, Wei AH. Applying molecular measurable residual disease testing in acute myeloid leukaemia. Pathology 2023; 55:1-7. [PMID: 36503638 DOI: 10.1016/j.pathol.2022.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/12/2022] [Accepted: 11/14/2022] [Indexed: 11/24/2022]
Abstract
Molecular testing in acute myeloid leukaemia (AML) has continued to dramatically advance in recent years, facilitating the ability to detect residual disease at exponentially lower levels. With the advent of the recently updated ELN consensus recommendations, there is increasing complexity to ordering and interpreting measurable residual disease (MRD) assays in AML. We outline the technology itself in conjunction with the relevant testing timepoints, clinically significant thresholds and potential prognostic and therapeutic significance of MRD testing for the major molecular targets in AML. This practical overview should assist haematologists in incorporating molecular MRD assays routinely into their personalised AML clinical management.
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Affiliation(s)
- Michael Krigstein
- Department of Haematology, St Vincent's Hospital, Sydney, NSW, Australia.
| | - Harry J Iland
- Department of Haematology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Andrew H Wei
- Department of Haematology, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Vic, Australia
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21
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Grob T, Sanders MA, Vonk CM, Kavelaars FG, Rijken M, Hanekamp DW, Gradowska PL, Cloos J, Fløisand Y, van Marwijk Kooy M, Manz MG, Ossenkoppele GJ, Tick LW, Havelange V, Löwenberg B, Jongen-Lavrencic M, Valk PJ. Prognostic Value of FLT3-Internal Tandem Duplication Residual Disease in Acute Myeloid Leukemia. J Clin Oncol 2023; 41:756-765. [PMID: 36315929 PMCID: PMC9901965 DOI: 10.1200/jco.22.00715] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
PURPOSE The applicability of FLT3-internal tandem duplications (FLT3-ITD) for assessing measurable residual disease (MRD) in acute myeloid leukemia (AML) in complete remission (CR) has been hampered by patient-specific duplications and potential instability of FLT3-ITD during relapse. Here, we comprehensively investigated the impact of next-generation sequencing (NGS)-based FLT3-ITD MRD detection on treatment outcome in a cohort of patients with newly diagnosed AML in relation to established prognostic factors at diagnosis and other MRD measurements, ie, mutant NPM1 and multiparameter flow cytometry. METHODS In 161 patients with de novo FLT3-ITD AML, NGS was performed at diagnosis and in CR after intensive remission induction treatment. FLT3-ITD MRD status was correlated with the cumulative incidence of relapse and overall survival (OS). RESULTS NGS-based FLT3-ITD MRD was present in 47 of 161 (29%) patients with AML. Presence of FLT3-ITD MRD was associated with increased risk of relapse (4-year cumulative incidence of relapse, 75% FLT3-ITD MRD v 33% no FLT3-ITD MRD; P < .001) and inferior OS (4-year OS, 31% FLT3-ITD MRD v 57% no FLT3-ITD MRD; P < .001). In multivariate analysis, detection of FLT3-ITD MRD in CR confers independent prognostic significance for relapse (hazard ratio, 3.55; P < .001) and OS (hazard ratio 2.51; P = .002). Strikingly, FLT3-ITD MRD exceeds the prognostic value of most generally accepted clinical and molecular prognostic factors, including the FLT3-ITD allelic ratio at diagnosis and MRD assessment by NGS-based mutant NPM1 detection or multiparameter flow cytometry. CONCLUSION NGS-based detection of FLT3-ITD MRD in CR identifies patients with AML with profound risk of relapse and death that outcompetes the significance of most established prognostic factors at diagnosis and during therapy, and furnishes support for FLT3-ITD as a clinically relevant biomarker for dynamic disease risk assessment in AML.
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Affiliation(s)
- Tim Grob
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Mathijs A. Sanders
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Christian M. Vonk
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Franҫois G. Kavelaars
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Melissa Rijken
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Diana W. Hanekamp
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands,Department of Hematology, Cancer Center Amsterdam, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Patrycja L. Gradowska
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Jacqueline Cloos
- Department of Hematology, Cancer Center Amsterdam, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Yngvar Fløisand
- Department of Hematology, Oslo University Hospital, Oslo, Norway
| | | | - Markus G. Manz
- Department of Medical Oncology and Hematology, Comprehensive Cancer Center Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Gert J. Ossenkoppele
- Department of Hematology, Cancer Center Amsterdam, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Lidwine W. Tick
- Department of Hematology, Maxima Medisch Centrum, Eindhoven, the Netherlands
| | - Violaine Havelange
- Department of Hematology, Cliniques universitaires Saint-Luc, Brussels, Belgium
| | - Bob Löwenberg
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Mojca Jongen-Lavrencic
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Peter J.M. Valk
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands,Peter J.M. Valk, PhD, Department of Hematology, Erasmus University Medical Center Rotterdam, Nc 806, Wytemaweg 80, 3015 CN Rotterdam Z-H, the Netherlands; e-mail:
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22
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Lee JM, Park S, Hwang I, Kang D, Cho BS, Kim HJ, Ahn A, Kim M, Kim Y. FLT3-ITD Measurable Residual Disease Monitoring in Acute Myeloid Leukemia Using Next-Generation Sequencing. Cancers (Basel) 2022; 14:6121. [PMID: 36551616 PMCID: PMC9776673 DOI: 10.3390/cancers14246121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/05/2022] [Accepted: 12/08/2022] [Indexed: 12/15/2022] Open
Abstract
The in-frame internal tandem duplication (ITD) of the FMS-like tyrosine kinase 3 (FLT3) gene is an important negative prognostic marker in acute myeloid leukemia (AML). FLT3-ITD monitoring is essential for patients at relapse or those receiving FLT3-targeted therapies. Fragment analysis (FA) is commonly used to detect and quantify FLT3-ITDs; however, detecting low-burden FLT3-ITDs after a treatment is challenging. We, therefore, developed a customized, next-generation sequencing (NGS)-based FLT3-ITD assay that includes a new ITD-tracing algorithm, "SEED", optimized for measurable residual disease (MRD) monitoring. NGS-SEED showed an enhanced sensitivity (0.001%) and has a superior performance over conventional fragment analysis. We further investigated the prognostic impact of MRD analyzed by NGS-SEED in AML patients who underwent allogeneic hematopoietic stem cell transplantation (HSCT). Our assay showed that the MRD assessed before and after HSCT were significantly associated with a risk of relapse and a poor overall survival, respectively, in a time-dependent analysis. Thus, this report highlighted the prognostic value of serial MRD monitoring using a sensitive method in a clinical setting of AML patients with FLT3-ITD.
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Affiliation(s)
- Jong-Mi Lee
- Department of Laboratory Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Catholic Genetic Laboratory Center, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Silvia Park
- Department of Hematology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Leukemia Research Institute, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Insik Hwang
- Dow Biomedica Inc., Seoul 05771, Republic of Korea
| | - Dain Kang
- Catholic Genetic Laboratory Center, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Byung Sik Cho
- Department of Hematology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Leukemia Research Institute, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Hee-Je Kim
- Department of Hematology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Leukemia Research Institute, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Ari Ahn
- Department of Laboratory Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Catholic Genetic Laboratory Center, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Myungshin Kim
- Department of Laboratory Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Catholic Genetic Laboratory Center, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Yonggoo Kim
- Department of Laboratory Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Catholic Genetic Laboratory Center, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
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23
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Loo S, Dillon R, Ivey A, Anstee NS, Othman J, Tiong IS, Potter N, Jovanovic J, Runglall M, Chong CC, Bajel A, Ritchie D, Gray K, Yeoh ZH, McBean M, Gilkes A, Thomas I, Johnson S, Russell NH, Wei AH. Pretransplant FLT3-ITD MRD assessed by high-sensitivity PCR-NGS determines posttransplant clinical outcome. Blood 2022; 140:2407-2411. [PMID: 35960851 PMCID: PMC10653044 DOI: 10.1182/blood.2022016567] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/26/2022] [Indexed: 11/20/2022] Open
Affiliation(s)
- Sun Loo
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Haematology, Peter MacCallum Cancer Centre, Royal Melbourne Hospital and University of Melbourne, Melbourne, Australia
- Department of Haematology, The Alfred Hospital, Melbourne, Australia
| | - Richard Dillon
- Guy’s and St Thomas Hospital, London, United Kingdom
- Department of Medical and Molecular Genetics, King’s College, London, United Kingdom
| | - Adam Ivey
- Department of Pathology, The Alfred Hospital, Melbourne, Australia
| | - Natasha S. Anstee
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Haematology, The Alfred Hospital, Melbourne, Australia
| | - Jad Othman
- Guy’s and St Thomas Hospital, London, United Kingdom
- Department of Medical and Molecular Genetics, King’s College, London, United Kingdom
| | - Ing Soo Tiong
- Department of Haematology, The Alfred Hospital, Melbourne, Australia
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Nicola Potter
- Department of Medical and Molecular Genetics, King’s College, London, United Kingdom
| | - Jelena Jovanovic
- Department of Medical and Molecular Genetics, King’s College, London, United Kingdom
| | - Manohursingh Runglall
- Department of Medical and Molecular Genetics, King’s College, London, United Kingdom
| | - Chyn Chua Chong
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Haematology, The Alfred Hospital, Melbourne, Australia
| | - Ashish Bajel
- Department of Haematology, Peter MacCallum Cancer Centre, Royal Melbourne Hospital and University of Melbourne, Melbourne, Australia
| | - David Ritchie
- Department of Haematology, Peter MacCallum Cancer Centre, Royal Melbourne Hospital and University of Melbourne, Melbourne, Australia
| | - Kelli Gray
- Department of Haematology, Peter MacCallum Cancer Centre, Royal Melbourne Hospital and University of Melbourne, Melbourne, Australia
| | - Zhi Han Yeoh
- Department of Haematology, Peter MacCallum Cancer Centre, Royal Melbourne Hospital and University of Melbourne, Melbourne, Australia
| | - Michelle McBean
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Amanda Gilkes
- Division of Cancer and Genetics, Cardiff University, Cardiff, United Kingdom
| | - Ian Thomas
- Centre for Trials Research, Cardiff University, Cardiff, United Kingdom
| | - Sean Johnson
- Centre for Trials Research, Cardiff University, Cardiff, United Kingdom
| | | | - Andrew H. Wei
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Haematology, Peter MacCallum Cancer Centre, Royal Melbourne Hospital and University of Melbourne, Melbourne, Australia
- Department of Haematology, The Alfred Hospital, Melbourne, Australia
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24
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Boudry A, Darmon S, Duployez N, Figeac M, Geffroy S, Bucci M, Celli-Lebras K, Duchmann M, Joudinaud R, Fenwarth L, Nibourel O, Goursaud L, Itzykson R, Dombret H, Hunault M, Preudhomme C, Salson M. Frugal alignment-free identification of FLT3-internal tandem duplications with FiLT3r. BMC Bioinformatics 2022; 23:448. [PMID: 36307762 PMCID: PMC9617311 DOI: 10.1186/s12859-022-04983-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 10/07/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Internal tandem duplications in the FLT3 gene, termed FLT3-ITDs, are useful molecular markers in acute myeloid leukemia (AML) for patient risk stratification and follow-up. FLT3-ITDs are increasingly screened through high-throughput sequencing (HTS) raising the need for robust and efficient algorithms. We developed a new algorithm, which performs no alignment and uses little resources, to identify and quantify FLT3-ITDs in HTS data. RESULTS Our algorithm (FiLT3r) focuses on the k-mers from reads covering FLT3 exons 14 and 15. We show that those k-mers bring enough information to accurately detect, determine the length and quantify FLT3-ITD duplications. We compare the performances of FiLT3r to state-of-the-art alternatives and to fragment analysis, the gold standard method, on a cohort of 185 AML patients sequenced with capture-based HTS. On this dataset FiLT3r is more precise (no false positive nor false negative) than the other software evaluated. We also assess the software on public RNA-Seq data, which confirms the previous results and shows that FiLT3r requires little resources compared to other software. CONCLUSION FiLT3r is a free software available at https://gitlab.univ-lille.fr/filt3r/filt3r . The repository also contains a Snakefile to reproduce our experiments. We show that FiLT3r detects FLT3-ITDs better than other software while using less memory and time.
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Affiliation(s)
- Augustin Boudry
- grid.410463.40000 0004 0471 8845Hematology Laboratory, Centre de Biologie Pathologie Génétique, CHU Lille, Lille, France ,grid.503422.20000 0001 2242 6780U1277 Cancer Heterogeneity Plasticity and Resistance to Therapies (CANTHER), University of Lille, INSERM, Lille, France
| | - Sasha Darmon
- grid.503422.20000 0001 2242 6780Univ. Lille, CNRS, Centrale Lille, UMR 9189 CRIStAL, F-59000 Lille, France ,grid.15140.310000 0001 2175 9188ENS Lyon, Lyon, France
| | - Nicolas Duployez
- grid.410463.40000 0004 0471 8845Hematology Laboratory, Centre de Biologie Pathologie Génétique, CHU Lille, Lille, France ,grid.503422.20000 0001 2242 6780U1277 Cancer Heterogeneity Plasticity and Resistance to Therapies (CANTHER), University of Lille, INSERM, Lille, France
| | - Martin Figeac
- grid.503422.20000 0001 2242 6780Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UMS 2014 - PLBS, F-59000 Lille, France
| | - Sandrine Geffroy
- grid.410463.40000 0004 0471 8845Hematology Laboratory, Centre de Biologie Pathologie Génétique, CHU Lille, Lille, France
| | - Maxime Bucci
- grid.410463.40000 0004 0471 8845Hematology Laboratory, Centre de Biologie Pathologie Génétique, CHU Lille, Lille, France
| | - Karine Celli-Lebras
- grid.413328.f0000 0001 2300 6614Department of Hematology, Saint Louis Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Matthieu Duchmann
- grid.508487.60000 0004 7885 7602INSERM/CNRS UMR 944/7212, Saint-Louis Research Institute, Paris Diderot University, Paris, France
| | - Romane Joudinaud
- grid.410463.40000 0004 0471 8845Hematology Laboratory, Centre de Biologie Pathologie Génétique, CHU Lille, Lille, France ,grid.503422.20000 0001 2242 6780U1277 Cancer Heterogeneity Plasticity and Resistance to Therapies (CANTHER), University of Lille, INSERM, Lille, France
| | - Laurène Fenwarth
- grid.410463.40000 0004 0471 8845Hematology Laboratory, Centre de Biologie Pathologie Génétique, CHU Lille, Lille, France ,grid.503422.20000 0001 2242 6780U1277 Cancer Heterogeneity Plasticity and Resistance to Therapies (CANTHER), University of Lille, INSERM, Lille, France
| | - Olivier Nibourel
- grid.410463.40000 0004 0471 8845Hematology Laboratory, Centre de Biologie Pathologie Génétique, CHU Lille, Lille, France
| | - Laure Goursaud
- grid.410463.40000 0004 0471 8845Hematology Department, CHU LILLE, Lille, France
| | - Raphael Itzykson
- grid.413328.f0000 0001 2300 6614Department of Hematology, Saint Louis Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France ,grid.508487.60000 0004 7885 7602INSERM/CNRS UMR 944/7212, Saint-Louis Research Institute, Paris Diderot University, Paris, France
| | - Hervé Dombret
- grid.413328.f0000 0001 2300 6614Department of Hematology, Saint Louis Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Mathilde Hunault
- grid.7252.20000 0001 2248 3363Univ Angers, Université de Nantes, CHU Angers, Inserm, CNRS, CRCI2NA, SFR ICAT, F-49000 Angers, France
| | - Claude Preudhomme
- grid.410463.40000 0004 0471 8845Hematology Laboratory, Centre de Biologie Pathologie Génétique, CHU Lille, Lille, France ,grid.503422.20000 0001 2242 6780U1277 Cancer Heterogeneity Plasticity and Resistance to Therapies (CANTHER), University of Lille, INSERM, Lille, France
| | - Mikaël Salson
- grid.503422.20000 0001 2242 6780Univ. Lille, CNRS, Centrale Lille, UMR 9189 CRIStAL, F-59000 Lille, France
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25
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Midostaurin plus intensive chemotherapy for younger and older Patients with AML and FLT3 internal tandem duplications. Blood Adv 2022; 6:5345-5355. [PMID: 35486475 PMCID: PMC9631686 DOI: 10.1182/bloodadvances.2022007223] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 04/13/2022] [Indexed: 11/20/2022] Open
Abstract
Midostaurin as adjunct to chemotherapy significantly improves outcome in younger and older patients with AML and FLT3-ITD. The data provide evidence for the use of midostaurin as the standard of care also for older patients with FLT3-mutated AML.
We conducted a single-arm, phase 2 trial (German-Austrian Acute Myeloid Leukemia Study Group [AMLSG] 16-10) to evaluate midostaurin with intensive chemotherapy followed by allogeneic hematopoietic-cell transplantation (HCT) and a 1-year midosta urin maintenance therapy in adult patients with acute myeloid leukemia (AML) and fms-related tyrosine kinase 3 (FLT3) internal tandem duplication (ITD). Patients 18 to 70 years of age with newly diagnosed FLT3-ITD-positive AML were eligible. Primary and key secondary endpoints were event-free survival (EFS) and overall survival (OS). Results were compared with a historical cohort of 415 patients treated on 5 prior AMLSG trials; statistical analysis was performed using a double-robust adjustment with propensity score weighting and covariate adjustment. Results were also compared with patients (18-59 years) treated on the placebo arm of the Cancer and Leukemia Group B (CALGB) 10603/RATIFY trial. The trial accrued 440 patients (18-60 years, n = 312; 61-70 years, n = 128). In multivariate analysis, EFS was significantly in favor of patients treated within the AMLSG 16-10 trial compared with the AMLSG control (hazard ratio [HR], 0.55; P < .001); both in younger (HR, 0.59; P < .001) and older patients (HR, 0.42; P < .001). Multivariate analysis also showed a significant beneficial effect on OS compared with the AMLSG control (HR, 0.57; P < .001) as well as to the CALGB 10603/RATIFY trial (HR, 0.71; P = .005). The treatment effect of midostaurin remained significant in sensitivity analysis including allogeneic HCT as a time-dependent covariate. Addition of midostaurin to chemotherapy was safe in younger and older patients. In comparison with historical controls, the addition of midostaurin to intensive therapy led to a significant improvement in outcome in younger and older patients with AML and FLT3-ITD. This trial is registered at clinicaltrialsregistry.eu as Eudra-CT number 2011-003168-63 and at clinicaltrials.gov as NCT01477606.
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26
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FLT3-inhibitor therapy for prevention and treatment of relapse after allogeneic hematopoietic cell transplantation. Int J Hematol 2022; 116:341-350. [PMID: 35460465 PMCID: PMC9392688 DOI: 10.1007/s12185-022-03352-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 02/05/2023]
Abstract
The curative potential of allogeneic hematopoietic cell transplantation (allo-HCT) for acute myeloid leukemia (AML) relies on the graft-versus-leukemia (GVL)-effect. Relapse after allo-HCT occurs in a considerable proportion of patients, and has a dismal prognosis with very limited curative potential, especially for patients with FLT-ITD-mutated AML. Since the first description of sorafenib for treatment of FLT3-ITD-mutated AML, several clinical trials have tried to determine the efficacy of FLT3 inhibitors for preventing and treating AML relapse after allo-HSCT, but many questions regarding differences among compounds and mechanisms of action remain unanswered. This review provides an overview on the established and evolving use of FLT3 inhibitors to prevent or treat relapse of AML in the context of allo-HCT, focusing on the recently discovered immunogenic potential of some FLT3 inhibitors and addressing the possible mechanisms of leukemia drug-escape.
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27
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FLT3 mutational analysis in acute myeloid leukemia: Advantages and pitfalls with different approaches. Blood Rev 2022; 54:100928. [DOI: 10.1016/j.blre.2022.100928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 12/17/2022]
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28
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Rücker FG, Du L, Luck TJ, Benner A, Krzykalla J, Gathmann I, Voso MT, Amadori S, Prior TW, Brandwein JM, Appelbaum FR, Medeiros BC, Tallman MS, Savoie L, Sierra J, Pallaud C, Sanz MA, Jansen JH, Niederwieser D, Fischer T, Ehninger G, Heuser M, Ganser A, Bullinger L, Larson RA, Bloomfield CD, Stone RM, Döhner H, Thiede C, Döhner K. Molecular landscape and prognostic impact of FLT3-ITD insertion site in acute myeloid leukemia: RATIFY study results. Leukemia 2022; 36:90-99. [PMID: 34316017 PMCID: PMC8727286 DOI: 10.1038/s41375-021-01323-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 05/27/2021] [Accepted: 06/03/2021] [Indexed: 12/20/2022]
Abstract
In acute myeloid leukemia (AML) internal tandem duplications of the FLT3 gene (FLT3-ITD) are associated with poor prognosis. Retrospectively, we investigated the prognostic and predictive impact of FLT3-ITD insertion site (IS) in 452 patients randomized within the RATIFY trial, which evaluated midostaurin additionally to intensive chemotherapy. Next-generation sequencing identified 908 ITDs, with 643 IS in the juxtamembrane domain (JMD) and 265 IS in the tyrosine kinase domain-1 (TKD1). According to IS, patients were categorized as JMDsole (n = 251, 55%), JMD and TKD1 (JMD/TKD1; n = 117, 26%), and TKD1sole (n = 84, 19%). While clinical variables did not differ among the 3 groups, NPM1 mutation was correlated with JMDsole (P = 0.028). Overall survival (OS) differed significantly, with estimated 4-year OS probabilities of 0.44, 0.50, and 0.30 for JMDsole, JMD/TKD1, and TKD1sole, respectively (P = 0.032). Multivariate (cause-specific) Cox models for OS and cumulative incidence of relapse using allogeneic hematopoietic cell transplantation (HCT) in first complete remission as a time-dependent variable identified TKD1sole as unfavorable and HCT as favorable factors. In addition, Midostaurin exerted a significant benefit only for JMDsole. Our results confirm the distinct molecular heterogeneity of FLT3-ITD and the negative prognostic impact of TKD1 IS in AML that was not overcome by midostaurin.
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Affiliation(s)
- Frank G Rücker
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Ling Du
- Novartis Pharmaceuticals, Cambridge, MA, USA
| | - Tamara J Luck
- Department of Hematology, Oncology and Tumor Immunology, Charité University, Berlin, Germany
| | - Axel Benner
- Division of Biostatistics, German Cancer Research Center, Heidelberg, Germany
| | - Julia Krzykalla
- Division of Biostatistics, German Cancer Research Center, Heidelberg, Germany
| | | | - Maria Teresa Voso
- Department of Biomedicine and Prevention, Università di Roma "Tor Vergata", Rome, Italy
| | - Sergio Amadori
- Department of Biomedicine and Prevention, Università di Roma "Tor Vergata", Rome, Italy
| | - Thomas W Prior
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | | | - Frederick R Appelbaum
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Bruno C Medeiros
- Division of Hematology, Stanford Comprehensive Cancer Center, Stanford University, Stanford, CA, USA
| | - Martin S Tallman
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY, USA
| | | | - Jorge Sierra
- Hematology Department, Hospital de la Santa Creu i Sant Pau and Jose Carreras Leukemia Research Institute, Autonomus University of Barcelona, Barcelona, Spain
| | | | - Miguel A Sanz
- Hospital Universitario la Fe, Hematology Department, Department of Medicine, University of Valencia, Valencia, Spain
| | - Joop H Jansen
- Radboud Institute Molecular Studies, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Thomas Fischer
- Department of Hematology and Oncology, Center of Internal Medicine, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Gerhard Ehninger
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus der TU Dresden, Dresden, Germany
| | - Michael Heuser
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Arnold Ganser
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Lars Bullinger
- Department of Hematology, Oncology and Tumor Immunology, Charité University, Berlin, Germany
| | - Richard A Larson
- Department of Medicine and Comprehensive Cancer Center, University of Chicago, Chicago, IL, USA
| | - Clara D Bloomfield
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Richard M Stone
- Department of Medical Oncology, Dana-Farber/Partners CancerCare, Boston, MA, USA
| | - Hartmut Döhner
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Christian Thiede
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus der TU Dresden, Dresden, Germany
| | - Konstanze Döhner
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany.
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29
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Vonk CM, Al Hinai ASA, Hanekamp D, Valk PJM. Molecular Minimal Residual Disease Detection in Acute Myeloid Leukemia. Cancers (Basel) 2021; 13:5431. [PMID: 34771594 PMCID: PMC8582498 DOI: 10.3390/cancers13215431] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 02/06/2023] Open
Abstract
Initial induction chemotherapy to eradicate the bulk of acute myeloid leukemia (AML) cells results in complete remission (CR) in the majority of patients. However, leukemic cells persisting in the bone marrow below the morphologic threshold remain unaffected and have the potential to proliferate and re-emerge as AML relapse. Detection of minimal/measurable residual disease (MRD) is a promising prognostic marker for AML relapse as it can assess an individual patients' risk profile and evaluate their response to treatment. With the emergence of molecular techniques, such as next generation sequencing (NGS), a more sensitive assessment of molecular MRD markers is available. In recent years, the detection of MRD by molecular assays and its association with AML relapse and survival has been explored and verified in multiple studies. Although most studies show that the presence of MRD leads to a worse clinical outcome, molecular-based methods face several challenges including limited sensitivity/specificity, and a difficult distinction between mutations that are representative of AML rather than clonal hematopoiesis. This review describes the studies that have been performed using molecular-based assays for MRD detection in the context of other MRD detection approaches in AML, and discusses limitations, challenges and opportunities.
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Affiliation(s)
- Christian M Vonk
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 CN Rotterdam, The Netherlands
| | - Adil S A Al Hinai
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 CN Rotterdam, The Netherlands
- National Genetic Center, Ministry of Health, Muscat 111, Oman
| | - Diana Hanekamp
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 CN Rotterdam, The Netherlands
- Department of Hematology, Cancer Center VU University Medical Center, Amsterdam University Medical Centers, 1081 HV Amsterdam, The Netherlands
| | - Peter J M Valk
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 CN Rotterdam, The Netherlands
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30
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Dai B, Yu H, Ma T, Lei Y, Wang J, Zhang Y, Lu J, Yan H, Jiang L, Chen B. The Application of Targeted RNA Sequencing for KMT2A-Partial Tandem Duplication Identification and Integrated Analysis of Molecular Characterization in Acute Myeloid Leukemia. J Mol Diagn 2021; 23:1478-1490. [PMID: 34384895 DOI: 10.1016/j.jmoldx.2021.07.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 07/12/2021] [Accepted: 07/26/2021] [Indexed: 12/25/2022] Open
Abstract
The partial tandem duplication of histone-lysine N-methyltransferase 2A (KMT2A-PTD) is an important genetic alteration in acute myeloid leukemia (AML) and is associated with poor clinical outcome. Accurate and rapid detection of KMT2A-PTD is important for outcome prediction and clinical management, but next-generation sequencing-based quantitative research is still lacking. In this study, we developed a targeted RNA-based next-generation sequencing panel, together with single primer enrichment and unique molecular identifiers, to identify KMT2A-PTD as well as AML-related gene fusions and other driver mutations. Our panel showed high sensitivity, accuracy, and reproducibility in detecting the fusion ratio of KMT2A-PTD. We characterized the mutation profile of KMT2A-PTD-positive patients with AML and found different distribution patterns of driver mutations according to KMT2A-PTD fusion ratio level. Survival analyses revealed that the fusion ratio of KMT2A-PTD did not affect clinical outcome, but a novel molecular combination, namely, KMT2A-PTD/DNMT3A/FMS-like tyrosine kinase 3-internal tandem duplication, was associated with poor prognosis. Finally, we proved that the dynamic changes in the KMT2A-PTD fusion ratio were consistent with the overall process of disease progression. In summary, we applied the unique molecular identifier-based RNA panel to quantitatively detect KMT2A-PTD and elucidate its clinical relevance, which complemented the integrative network of various genetic alterations in AML.
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Affiliation(s)
- Bing Dai
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hao Yu
- Jiangsu Key Laboratory of Zoonosis and Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonose, Yangzhou University, Yangzhou, China
| | - Tingting Ma
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yichen Lei
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiyue Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yunxiang Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Lu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Han Yan
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lu Jiang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Bing Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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31
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Tung JK, Suarez CJ, Chiang T, Zehnder JL, Stehr H. Accurate Detection and Quantification of FLT3 Internal Tandem Duplications in Clinical Hybrid Capture Next-Generation Sequencing Data. J Mol Diagn 2021; 23:1404-1413. [PMID: 34363960 DOI: 10.1016/j.jmoldx.2021.07.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 07/09/2021] [Accepted: 07/16/2021] [Indexed: 01/13/2023] Open
Abstract
FLT3 internal tandem duplications (ITDs) are found in approximately one-third of patients with acute myeloid leukemia and have important prognostic and therapeutic implications that have supported their assessment in routine clinical practice. Conventional methods for assessing FLT3-ITD status and allele burden have been primarily limited to PCR fragment size analysis because of the inherent difficulty in detecting large ITD variants by next-generation sequencing (NGS). In this study, we assess the performance of publicly available bioinformatic tools for the detection and quantification of FLT3-ITDs in clinical hybridization-capture NGS data. We found that FLT3_ITD_ext had the highest overall accuracy for detecting FLT3-ITDs and was able to accurately quantify allele burden. Although all other tools evaluated were able to detect FLT3-ITDs reasonably well, allele burden was consistently underestimated. We were able to significantly improve quantification of FLT3-ITD allelic burden independent of the detection method by utilizing soft-clipped reads and/or ITD junctional sequences. In addition, we show that identifying mutant reads by previously identified junctional sequences further improves the sensitivity of detecting FLT3-ITDs in post-treatment samples. Our results demonstrate that FLT3-ITDs can be reliably detected in clinical NGS data using available bioinformatic tools. We further describe how accurate quantification of FLT3-ITD allele burden can be added on to existing clinical NGS pipelines for routine assessment of FLT3-ITD status in patients with acute myeloid leukemia.
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Affiliation(s)
- Jack K Tung
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Carlos J Suarez
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Tsoyu Chiang
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Henning Stehr
- Department of Pathology, Stanford University School of Medicine, Stanford, California.
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32
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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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33
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Gilteritinib: potent targeting of FLT3 mutations in AML. Blood Adv 2021; 4:1178-1191. [PMID: 32208491 DOI: 10.1182/bloodadvances.2019000174] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 01/26/2020] [Indexed: 01/13/2023] Open
Abstract
Since the discovery of FMS-like tyrosine kinase-3 (FLT3)-activating mutations as genetic drivers in acute myeloid leukemia (AML), investigators have tried to develop tyrosine kinase inhibitors that could effectively target FLT3 and alter the disease trajectory. Giltertinib (formerly known as ASP2215) is a novel compound that entered the field late, but moved through the developmental process with remarkable speed. In many ways, this drug's rapid development was facilitated by the large body of knowledge gained over the years from efforts to develop other FLT3 inhibitors. Single-agent gilteritinib, a potent and selective oral FLT3 inhibitor, improved the survival of patients with relapsed or refractory FLT3-mutated AML compared with standard chemotherapy. This continues to validate the approach of targeting FLT3 itself and establishes a new backbone for testing combination regimens. This review will frame the preclinical and clinical development of gilteritinib in the context of the lessons learned from its predecessors.
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34
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Engen C, Hellesøy M, Grob T, Al Hinai A, Brendehaug A, Wergeland L, Bedringaas SL, Hovland R, Valk PJM, Gjertsen BT. FLT3-ITD mutations in acute myeloid leukaemia - molecular characteristics, distribution and numerical variation. Mol Oncol 2021; 15:2300-2317. [PMID: 33817952 PMCID: PMC8410560 DOI: 10.1002/1878-0261.12961] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/02/2021] [Accepted: 04/01/2021] [Indexed: 11/07/2022] Open
Abstract
Recurrent somatic internal tandem duplications (ITD) in the FMS-like tyrosine kinase 3 (FLT3) gene characterise approximately one third of patients with acute myeloid leukaemia (AML), and FLT3-ITD mutation status guides risk-adapted treatment strategies. The aim of this work was to characterise FLT3-ITD variant distribution in relation to molecular and clinical features, and overall survival in adult AML patients. We performed two parallel retrospective cohort studies investigating FLT3-ITD length and expression by cDNA fragment analysis, followed by Sanger sequencing in a subset of samples. In the two cohorts, a total of 139 and 172 mutant alleles were identified in 111 and 123 patients, respectively, with 22% and 28% of patients presenting with more than one mutated allele. Further, 15% and 32% of samples had a FLT3-ITD total variant allele frequency (VAF) < 0.3, while 24% and 16% had a total VAF ≥ 0.7. Most of the assessed clinical features did not significantly correlate to FLT3-ITD numerical variation nor VAF. Low VAF was, however, associated with lower white blood cell count, while increasing VAF correlated with inferior overall survival in one of the cohorts. In the other cohort, ITD length above 50 bp was identified to correlate with inferior overall survival. Our report corroborates the poor prognostic association with high FLT3-ITD disease burden, as well as extensive inter- and intrapatient heterogeneity in the molecular features of FLT3-ITD. We suggest that future use of FLT3-targeted therapy could be accompanied with thorough molecular diagnostics and follow-up to better predict optimal therapy responders.
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Affiliation(s)
- Caroline Engen
- Department of Clinical Science, Centre for Cancer Biomarkers CCBIO, University of Bergen, Norway
| | - Monica Hellesøy
- Haematology Section, Department of Medicine, Haukeland University Hospital, Helse Bergen HF, Norway
| | - Tim Grob
- Department of Haematology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Adil Al Hinai
- Department of Haematology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Atle Brendehaug
- Department of Medical Genetics, Haukeland University Hospital, Helse Bergen HF, Norway
| | - Line Wergeland
- Department of Clinical Science, Centre for Cancer Biomarkers CCBIO, University of Bergen, Norway
| | - Siv Lise Bedringaas
- Department of Clinical Science, Centre for Cancer Biomarkers CCBIO, University of Bergen, Norway
| | - Randi Hovland
- Department of Medical Genetics, Haukeland University Hospital, Helse Bergen HF, Norway.,Department of Biosciences, University of Bergen, Norway
| | - Peter J M Valk
- Department of Haematology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Bjørn T Gjertsen
- Department of Clinical Science, Centre for Cancer Biomarkers CCBIO, University of Bergen, Norway.,Haematology Section, Department of Medicine, Haukeland University Hospital, Helse Bergen HF, Norway
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35
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Yuan D, He X, Han X, Yang C, Liu F, Zhang S, Luan H, Li R, He J, Duan X, Wang D, Zhou Q, Gao S, Niu B. Comprehensive review and evaluation of computational methods for identifying FLT3-internal tandem duplication in acute myeloid leukaemia. Brief Bioinform 2021; 22:6225087. [PMID: 33851200 DOI: 10.1093/bib/bbab099] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 02/15/2021] [Accepted: 03/06/2021] [Indexed: 12/25/2022] Open
Abstract
Internal tandem duplication (ITD) of FMS-like tyrosine kinase 3 (FLT3-ITD) constitutes an independent indicator of poor prognosis in acute myeloid leukaemia (AML). AML with FLT3-ITD usually presents with poor treatment outcomes, high recurrence rate and short overall survival. Currently, polymerase chain reaction and capillary electrophoresis are widely adopted for the clinical detection of FLT3-ITD, whereas the length and mutation frequency of ITD are evaluated using fragment analysis. With the development of sequencing technology and the high incidence of FLT3-ITD mutations, a multitude of bioinformatics tools and pipelines have been developed to detect FLT3-ITD using next-generation sequencing data. However, systematic comparison and evaluation of the methods or software have not been performed. In this study, we provided a comprehensive review of the principles, functionality and limitations of the existing methods for detecting FLT3-ITD. We further compared the qualitative and quantitative detection capabilities of six representative tools using simulated and biological data. Our results will provide practical guidance for researchers and clinicians to select the appropriate FLT3-ITD detection tools and highlight the direction of future developments in this field. Availability: A Docker image with several programs pre-installed is available at https://github.com/niu-lab/docker-flt3-itd to facilitate the application of FLT3-ITD detection tools.
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Affiliation(s)
- Danyang Yuan
- Computer Network Information Center, Chinese Academy of Sciences. She is mainly engaged in leukaemia-related bioinformatics and cancer genomics research. Her affiliation is with Computer Network Information Center, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Beijing 100190, China
| | - Xiaoyu He
- Computer Network Information Center, Chinese Academy of Sciences. She is mainly engaged in research related to the cancer genome and construction of the Chinese Cancer Genome Database. Her affiliation is with Computer Network Information Center, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Beijing 100190, China
| | - Xinyin Han
- Computer Network Information Center, Chinese Academy of Sciences. He is mainly engaged in cancer genomics research focusing on the precise detection of tumour immunotherapy biomarkers. His affiliation is with Computer Network Information Center, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Beijing 100190, China
| | - Chunyan Yang
- Vice Director of the Laboratory of ChosenMed Technology (Beijing) Co., Ltd. She is mainly engaged in research regarding solid tumours and haematologic malignancy using multiple approaches, including next-generation sequencing. Her affiliation is with ChosenMed Technology (Beijing) Co., Ltd., Beijing 100176, China
| | - Fei Liu
- bioinformatics analysis engineer of ChosenMed Technology (Beijing) Co., Ltd. She is mainly engaged in the collection of biological information and analysis of genomic and cancer data or other biological information. Her affiliation is with ChosenMed Technology (Beijing) Co., Ltd., Beijing 100176, China
| | - Shuying Zhang
- Computer Network Information Center, Chinese Academy of Sciences. Her research mainly focuses on the cancer genome and bioinformatics. Her affiliation is with Computer Network Information Center, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Beijing 100190, China
| | - Haijing Luan
- Computer Network Information Center, Chinese Academy of Sciences. She is mainly engaged in researching cancers of unknown primary sites (CUP) based on deep learning. Her affiliation is with Computer Network Information Center, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Beijing 100190, China
| | - Ruilin Li
- Computer Network Information Center, Chinese Academy of Sciences. Her research interests include high-performance computing and bioinformatics. Her affiliation is with Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Jiayin He
- George Washington University. She is currently researching at the Computer Network Information Center, Chinese Academy of Sciences. Her research interests include biostatistics and computational statistics. Her affiliation is with Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Xiaohong Duan
- Laboratory of ChosenMed Technology (Beijing) Co., Ltd. She is mainly engaged in the research of solid tumours and haematologic malignancies using multiple approaches, including next-generation sequencing. Her affiliation is with ChosenMed Technology (Beijing) Co., Ltd., Beijing 100176, China
| | - Dongliang Wang
- Harbin Medical University. He is now the Chief Medical Officer of ChosenMed Technology (Beijing). His research mainly focuses on the mining and verification of molecular markers for tumour therapy. His affiliation is with ChosenMed Technology (Beijing) Co., Ltd., Beijing 100176, China
| | - Qiming Zhou
- CTO of ChosenMed Technology (Beijing) Co., Ltd. He is mainly engaged in the development of new molecular diagnostics technologies in genetic testing. His affiliation is with ChosenMed Technology (Beijing) Co., Ltd., Beijing 100176, China
| | - Sujun Gao
- Department of Haematology, The First Hospital of Jilin University. Her research mainly focuses on the experimental and clinical research of malignant haematological disorders and haematopoietic stem cell transplantation. Her affiliation is with Department of Haematology, The First Hospital of Jilin University, Changchun 130021, China
| | - Beifang Niu
- Computer Network Information Center, Chinese Academy of Sciences. His research interests include cancer genomics, metagenomics, and the development of computational tools for working with data from next-generation sequencing technologies. His affiliation is with Computer Network Information Center, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Beijing 100190, China, ChosenMed Technology (Beijing) Co., Ltd., Beijing 100176, China
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36
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Abstract
Aberrant FLT3 receptor signaling is common in acute myeloid leukemia (AML) and has important implications for the biology and clinical management of the disease. Patients with FLT3-mutated AML frequently present with critical illness, are more likely to relapse after treatment, and have worse clinical outcomes than their FLT3 wild type counterparts. The clinical management of FLT3-mutated AML has been transformed by the development of FLT3 inhibitors, which are now in use in the frontline and relapsed/refractory settings. However, many questions regarding the optimal approach to the treatment of these patients remain. In this paper, we will review the rationale for targeting the FLT3 receptor in AML, the impact of FLT3 mutation on patient prognosis, the current standard of care approaches to FLT3-mutated AML management, and the diverse array of FLT3 inhibitors in use and under investigation. We will also explore new opportunities and strategies for targeting the FLT3 receptor. These include targeting the receptor in patients with non-canonical FLT3 mutations or wild type FLT3, pairing FLT3 inhibitors with other novel therapies, using minimal residual disease (MRD) testing to guide the targeting of FLT3, and novel immunotherapeutic approaches.
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Affiliation(s)
- Alexander J Ambinder
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mark Levis
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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37
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Carlsen ED, Aggarwal N, Bailey NG. Molecular methods for measurable residual disease in acute myeloid leukemia: where are we and where are we going? J Hematop 2021. [DOI: 10.1007/s12308-020-00440-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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38
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Patkar N, Kakirde C, Shaikh AF, Salve R, Bhanshe P, Chatterjee G, Rajpal S, Joshi S, Chaudhary S, Kodgule R, Ghoghale S, Deshpande N, Shetty D, Khizer SH, Jain H, Bagal B, Menon H, Khattry N, Sengar M, Tembhare P, Subramanian P, Gujral S. Clinical impact of panel-based error-corrected next generation sequencing versus flow cytometry to detect measurable residual disease (MRD) in acute myeloid leukemia (AML). Leukemia 2021; 35:1392-1404. [PMID: 33558666 PMCID: PMC8102181 DOI: 10.1038/s41375-021-01131-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/30/2020] [Accepted: 01/07/2021] [Indexed: 01/30/2023]
Abstract
We accrued 201 patients of adult AML treated with conventional therapy, in morphological remission, and evaluated MRD using sensitive error-corrected next generation sequencing (NGS-MRD) and multiparameter flow cytometry (FCM-MRD) at the end of induction (PI) and consolidation (PC). Nearly 71% of patients were PI NGS-MRD+ and 40.9% PC NGS-MRD+ (median VAF 0.76%). NGS-MRD+ patients had a significantly higher cumulative incidence of relapse (p = 0.003), inferior overall survival (p = 0.001) and relapse free survival (p < 0.001) as compared to NGS-MRD- patients. NGS-MRD was predictive of inferior outcome in intermediate cytogenetic risk and demonstrated potential in favorable cytogenetic risk AML. PI NGS-MRD- patients had a significantly improved survival as compared to patients who became NGS-MRD- subsequently indicating that kinetics of NGS-MRD clearance was of paramount importance. NGS-MRD identified over 80% of cases identified by flow cytometry at PI time point whereas FCM identified 49.3% identified by NGS. Only a fraction of cases were NGS-MRD- but FCM-MRD+. NGS-MRD provided additional information of the risk of relapse when compared to FCM-MRD. We demonstrate a widely applicable, scalable NGS-MRD approach that is clinically informative and synergistic to FCM-MRD in AML treated with conventional therapies. Maximum clinical utility may be leveraged by combining FCM and NGS-MRD modalities.
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Affiliation(s)
- Nikhil Patkar
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,grid.450257.10000 0004 1775 9822Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Chinmayee Kakirde
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Anam Fatima Shaikh
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Rakhi Salve
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Prasanna Bhanshe
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Gaurav Chatterjee
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,grid.450257.10000 0004 1775 9822Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Sweta Rajpal
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,grid.450257.10000 0004 1775 9822Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Swapnali Joshi
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Shruti Chaudhary
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Rohan Kodgule
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Sitaram Ghoghale
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Nilesh Deshpande
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Dhanalaxmi Shetty
- grid.410869.20000 0004 1766 7522Dept of Cytogenetics, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Syed Hasan Khizer
- grid.410869.20000 0004 1766 7522Dept of Cytogenetics, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,grid.410871.b0000 0004 1769 5793Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Hasmukh Jain
- grid.410869.20000 0004 1766 7522Dept of Cytogenetics, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,grid.410871.b0000 0004 1769 5793Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Bhausaheb Bagal
- grid.450257.10000 0004 1775 9822Homi Bhabha National Institute (HBNI), Mumbai, India ,grid.410871.b0000 0004 1769 5793Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Hari Menon
- Haemato-Oncology, CyteCare Cancer Hospital, Bangalore, India
| | - Navin Khattry
- grid.410869.20000 0004 1766 7522Dept of Cytogenetics, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,Haemato-Oncology, CyteCare Cancer Hospital, Bangalore, India
| | - Manju Sengar
- grid.450257.10000 0004 1775 9822Homi Bhabha National Institute (HBNI), Mumbai, India ,grid.410871.b0000 0004 1769 5793Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Prashant Tembhare
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,grid.450257.10000 0004 1775 9822Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Papagudi Subramanian
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,grid.450257.10000 0004 1775 9822Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Sumeet Gujral
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,grid.450257.10000 0004 1775 9822Homi Bhabha National Institute (HBNI), Mumbai, India
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Altman JK, Perl AE, Hill JE, Rosales M, Bahceci E, Levis MJ. The impact of FLT3 mutation clearance and treatment response after gilteritinib therapy on overall survival in patients with FLT3 mutation-positive relapsed/refractory acute myeloid leukemia. Cancer Med 2020; 10:797-805. [PMID: 33340276 PMCID: PMC7897940 DOI: 10.1002/cam4.3652] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 10/01/2020] [Accepted: 11/21/2020] [Indexed: 01/08/2023] Open
Abstract
The FLT3 inhibitor gilteritinib has clinical activity in patients with FLT3‐mutated (FLT3mut+) relapsed/refractory (R/R) acute myeloid leukemia (AML). The impact of FLT3 mutation clearance and the achievement of composite complete remission (CRc) and complete remission/complete remission with partial hematologic recovery (CR/CRh) on overall survival (OS) in patients with FLT3mut+ R/R AML treated with single‐agent gilteritinib in a phase 1/2 trial were evaluated. Using next‐generation sequencing, a FLT3‐ITD variant allele frequency of ≤10−4 was used to define FLT3‐ITD clearance in patients with no morphologic leukemia (ie, CRc). A total of 108 patients with FLT3‐ITD‐positive (FLT3‐ITD+) R/R AML were analyzed; 95 of these patients had received ≥80‐mg/day gilteritinib. Ten of the 95 patients had FLT3‐ITD clearance; eight of these 10 patients achieved CRc and were considered negative for measurable residual disease. There was a trend toward longer OS in patients who attained CRc with FLT3‐ITD clearance (131.4 weeks) versus those who achieved CRc and did not have FLT3‐ITD clearance (n = 41; 43.3 weeks; HR = 0.416; p = 0.066). Among patients treated with ≥80‐mg/day gilteritinib who achieved CR/CRh (n = 24), seven had FLT3‐ITD clearance. Among patients who received 120‐mg/day gilteritinib, those who achieved CR/CRh had a longer median OS (70.6 weeks) and higher 52‐week survival probability (66.7%) than patients who did not achieve CR/CRh (n = 71; median OS, 41.7 weeks; 52‐week survival probability, 20.2%). Overall, these data suggest that gilteritinib can induce deep molecular responses in patients with FLT3‐ITD+ R/R AML, and in the setting of CRc or CR/CRh, these responses may be associated with prolonged survival.
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Affiliation(s)
- Jessica K Altman
- Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
| | - Alexander E Perl
- Abramson Comprehensive Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | | | - Mark J Levis
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
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40
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Molecular Mechanisms of Resistance to FLT3 Inhibitors in Acute Myeloid Leukemia: Ongoing Challenges and Future Treatments. Cells 2020; 9:cells9112493. [PMID: 33212779 PMCID: PMC7697863 DOI: 10.3390/cells9112493] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/07/2020] [Accepted: 11/13/2020] [Indexed: 12/17/2022] Open
Abstract
Treatment of FMS-like tyrosine kinase 3 (FLT3)-internal tandem duplication (ITD)-positive acute myeloid leukemia (AML) remains a challenge despite the development of novel FLT3-directed tyrosine kinase inhibitors (TKI); the relapse rate is still high even after allogeneic stem cell transplantation. In the era of next-generation FLT3-inhibitors, such as midostaurin and gilteritinib, we still observe primary and secondary resistance to TKI both in monotherapy and in combination with chemotherapy. Moreover, remissions are frequently short-lived even in the presence of continuous treatment with next-generation FLT3 inhibitors. In this comprehensive review, we focus on molecular mechanisms underlying the development of resistance to relevant FLT3 inhibitors and elucidate how this knowledge might help to develop new concepts for improving the response to FLT3-inhibitors and reducing the development of resistance in AML. Tailored treatment approaches that address additional molecular targets beyond FLT3 could overcome resistance and facilitate molecular responses in AML.
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41
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Bewersdorf JP, Shallis RM, Boddu PC, Wood B, Radich J, Halene S, Zeidan AM. The minimal that kills: Why defining and targeting measurable residual disease is the “Sine Qua Non” for further progress in management of acute myeloid leukemia. Blood Rev 2020; 43:100650. [DOI: 10.1016/j.blre.2019.100650] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 12/04/2019] [Accepted: 12/13/2019] [Indexed: 12/13/2022]
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42
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Freeman SD, Hourigan CS. MRD evaluation of AML in clinical practice: are we there yet? HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2019; 2019:557-569. [PMID: 31808906 PMCID: PMC6913462 DOI: 10.1182/hematology.2019000060] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
MRD technologies increase our ability to measure response in acute myeloid leukemia (AML) beyond the limitations of morphology. When applied in clinical trials, molecular and immunophenotypic MRD assays have improved prognostic precision, providing a strong rationale for their use to guide treatment, as well as to measure its effectiveness. Initiatives such as those from the European Leukemia Network now provide a collaborative knowledge-based framework for selection and implementation of MRD assays most appropriate for defined genetic subgroups. For patients with mutated-NPM1 AML, quantitative polymerase chain reaction (qPCR) monitoring of mutated-NPM1 transcripts postinduction and sequentially after treatment has emerged as a highly sensitive and specific tool to predict relapse and potential benefit from allogeneic transplant. Flow cytometric MRD after induction is prognostic across genetic risk groups and can identify those patients in the wild-type NPM1 intermediate AML subgroup with a very high risk for relapse. In parallel with these data, advances in genetic profiling have extended understanding of the etiology and the complex dynamic clonal nature of AML, as well as created the opportunity for MRD monitoring using next-generation sequencing (NGS). NGS AML MRD detection can stratify outcomes and has potential utility in the peri-allogeneic transplant setting. However, there remain challenges inherent in the NGS approach of multiplex quantification of mutations to track AML MRD. Although further development of this methodology, together with orthogonal testing, will clarify its relevance for routine clinical use, particularly for patients lacking a qPCR genetic target, established validated MRD assays can already provide information to direct clinical practice.
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Affiliation(s)
- Sylvie D Freeman
- Clinical Immunology Service, Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom; and
| | - Christopher S Hourigan
- Laboratory of Myeloid Malignancies, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
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43
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Ghannam J, Dillon LW, Hourigan CS. Next-generation sequencing for measurable residual disease detection in acute myeloid leukaemia. Br J Haematol 2019; 188:77-85. [PMID: 31804716 DOI: 10.1111/bjh.16362] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Acute myeloid leukaemia (AML) is a blood cancer characterized by acquired genetic mutations. There is great interest in accurately establishing measurable residual disease (MRD) burden in AML patients in remission after treatment but at risk of relapse. However, inter- and intrapatient genetic diversity means that, unlike in the chronic myeloid and acute promyelocytic leukaemias, no single genetic abnormality is pathognomonic for all cases of AML MRD. Next-generation sequencing offers the opportunity to test broadly and deeply for potential genetic evidence of residual AML, and while not currently accepted for such use clinically, is likely to be increasingly used for AML MRD testing in the future.
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Affiliation(s)
- Jack Ghannam
- Laboratory of Myeloid Malignancies, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Laura W Dillon
- Laboratory of Myeloid Malignancies, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Christopher S Hourigan
- Laboratory of Myeloid Malignancies, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
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44
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A DNA pool of FLT3-ITD positive DNA samples can be used efficiently for analytical evaluation of NGS-based FLT3-ITD quantitation - Testing several different ITD sequences and rates, simultaneously. J Biotechnol 2019; 303:25-29. [PMID: 31302157 DOI: 10.1016/j.jbiotec.2019.06.305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/31/2019] [Accepted: 06/03/2019] [Indexed: 12/16/2022]
Abstract
Internal tandem duplication (ITD) in the fms-like tyrosine kinase 3 (FLT3) gene is one of the most frequent genetic alteration in acute myeloid leukemia (AML), and it is associated with worse clinical outcome. Not only the presence but also the size, localization and the rate of this variant or the presence of multiple ITDs has prognostic information. The traditional PCR based diagnostic methods cannot provide information about all of these parameters in one assay, however the application of next generation sequencing (NGS) technique can be a reliable solution for this diagnostic problem. In order to evaluate the analytical properties of an NGS-based FLT3-ITD detection assay a quality control sample was prepared from DNA of AML patients containing 19 different FLT3-ITD variants identified by NGS. The higher the total read count was in a certain sample of the NGS run, the more ITD variant types could be detected. The maximal sensitivity of FLT3-ITD detection by NGS technique was as low as 0.007% FLT3-ITD/total allele rate, however, below 0.1% rate, the reproducibility of the quantitation was poor (CV > 25%). DNA pools with several FLT3-ITDs can be used efficiently for analytical evaluation of NGS-based FLT3-ITD quantitation testing several different ITD sequences and rates, simultaneously.
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