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Álvarez N, Martín A, Dorado S, Colmenares R, Rufián L, Rodríguez M, Giménez A, Carneros L, Sanchez R, Carreño G, Rapado I, Heredia Y, Martínez-López J, Barrio S, Ayala R. Detection of minimal residual disease in acute myeloid leukemia: evaluating utility and challenges. Front Immunol 2024; 15:1252258. [PMID: 38938565 PMCID: PMC11210172 DOI: 10.3389/fimmu.2024.1252258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 04/29/2024] [Indexed: 06/29/2024] Open
Abstract
This study discusses the importance of minimal residual disease (MRD) detection in acute myeloid leukemia (AML) patients using liquid biopsy and next-generation sequencing (NGS). AML prognosis is based on various factors, including genetic alterations. NGS has revealed the molecular complexity of AML and helped refine risk stratification and personalized therapies. The long-term survival rates for AML patients are low, and MRD assessment is crucial in predicting prognosis. Currently, the most common methods for MRD detection are flow cytometry and quantitative PCR, but NGS is being incorporated into clinical practice due to its ability to detect genomic aberrations in the majority of AML patients. Typically, bone marrow samples are used for MRD assessment, but using peripheral blood samples or liquid biopsies would be less invasive. Leukemia originates in the bone marrow, along with the cfDNA obtained from peripheral blood. This study aimed to assess the utility of cell-free DNA (cfDNA) from peripheral blood samples for MRD detection in AML patients. A cohort of 20 AML patients was analyzed using NGS, and a correlation between MRD assessment by cfDNA and circulating tumor cells (CTCs) in paired samples was observed. Furthermore, a higher tumor signal was detected in cfDNA compared to CTCs, indicating greater sensitivity. Challenges for the application of liquid biopsy in MRD assessment were discussed, including the selection of appropriate markers and the sensitivity of certain markers. This study emphasizes the potential of liquid biopsy using cfDNA for MRD detection in AML patients and highlights the need for further research in this area.
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Affiliation(s)
- Noemí Álvarez
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, Madrid, Spain
- Hematological Malignancies Clinical Research Unit, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - Alejandro Martín
- Hematological Malignancies Clinical Research Unit, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
- Altum Sequencing Co., Madrid, Spain
| | - Sara Dorado
- Altum Sequencing Co., Madrid, Spain
- Computational Science Department, Carlos III University, Madrid, Spain
| | - Rafael Colmenares
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, Madrid, Spain
| | - Laura Rufián
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, Madrid, Spain
- Altum Sequencing Co., Madrid, Spain
| | - Margarita Rodríguez
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, Madrid, Spain
- Altum Sequencing Co., Madrid, Spain
| | - Alicia Giménez
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, Madrid, Spain
| | - Laura Carneros
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, Madrid, Spain
| | - Ricardo Sanchez
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, Madrid, Spain
| | - Gonzalo Carreño
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, Madrid, Spain
| | - Inmaculada Rapado
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, Madrid, Spain
| | | | - Joaquín Martínez-López
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, Madrid, Spain
- Hematological Malignancies Clinical Research Unit, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
- Department of Medicine, Complutense University of Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, Madrid, Spain
| | - Santiago Barrio
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, Madrid, Spain
- Hematological Malignancies Clinical Research Unit, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
- Altum Sequencing Co., Madrid, Spain
| | - Rosa Ayala
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, Madrid, Spain
- Hematological Malignancies Clinical Research Unit, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
- Department of Medicine, Complutense University of Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, Madrid, Spain
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2
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Figaredo G, Martín-Muñoz A, Barrio S, Parrilla L, Campos-Martín Y, Poza M, Rufián L, Algara P, De La Torre M, Jiménez Ubieto A, Martínez-López J, Casado LF, Mollejo M. Genetic Profiling of Cell-Free DNA in Liquid Biopsies: A Complementary Tool for the Diagnosis of B-Cell Lymphomas and the Surveillance of Measurable Residual Disease. Cancers (Basel) 2023; 15:4022. [PMID: 37627050 PMCID: PMC10452485 DOI: 10.3390/cancers15164022] [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: 07/07/2023] [Revised: 07/26/2023] [Accepted: 08/06/2023] [Indexed: 08/27/2023] Open
Abstract
PURPOSE To assess the potential value of LiqBio as a complementary tool for diagnosis and surveillance of BCL. METHODS This prospective multi-center study included 78 patients (25 follicular lymphomas (FL) and 53 large B-cell lymphomas (LBCL)). We performed next-generation sequencing (NGS) of cfDNA LiqBio and paired gDNA tissue biopsies at diagnosis and compared the mutational statuses. Also, through NGS of LiqBio, we identified MRD biomarkers and compared this novel LiqBio-MRD method with PET/CT in detecting MRD at follow-up. RESULTS We identified mutations in 71% of LiqBio and 95% of tissue biopsies, and found a correlation between variant allele frequency of somatic mutations. Additionally, we identified mutations in 73% of LiqBio from patients with no available tissue samples or no mutations in them. Regarding the utility of LiqBio-MRD as a dynamic monitoring tool, when compared with the PET/CT method, a lower sensitivity was observed for LiqBio-MRD at 92.3% (vs. 100% for PET/CT), but a higher specificity of 91.3% (vs. 86.9% for PET/CT). CONCLUSION Genetic profiling of tumor cfDNA in plasma LiqBio is a complementary tool for BCL diagnosis and MRD surveillance.
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Affiliation(s)
- Gloria Figaredo
- Department of Haematology, Hospital Universitario de Toledo, Av. del Río Guadiana, 45007 Toledo, Spain; (L.P.); (M.D.L.T.); (L.-F.C.)
| | - Alejandro Martín-Muñoz
- Altum Sequencing SL, Av. Gregorio Peces Barba, 1, 28919 Madrid, Spain; (A.M.-M.); (S.B.); (L.R.)
| | - Santiago Barrio
- Altum Sequencing SL, Av. Gregorio Peces Barba, 1, 28919 Madrid, Spain; (A.M.-M.); (S.B.); (L.R.)
- Computational Science Department, Carlos III University, Ronda de Toledo, 1, 28005 Madrid, Spain
| | - Laura Parrilla
- Department of Haematology, Hospital Universitario de Toledo, Av. del Río Guadiana, 45007 Toledo, Spain; (L.P.); (M.D.L.T.); (L.-F.C.)
| | - Yolanda Campos-Martín
- Biobank Department, Hospital Universitario de Toledo, Av. del Río Guadiana, 45007 Toledo, Spain;
| | - María Poza
- Haematology Department, Hospital Universitario 12 de Octubre, Avda. de Córdoba, s/n, 28041 Madrid, Spain; (M.P.); (A.J.U.); (J.M.-L.)
| | - Laura Rufián
- Altum Sequencing SL, Av. Gregorio Peces Barba, 1, 28919 Madrid, Spain; (A.M.-M.); (S.B.); (L.R.)
- Haematology Department, Hospital Universitario 12 de Octubre, Avda. de Córdoba, s/n, 28041 Madrid, Spain; (M.P.); (A.J.U.); (J.M.-L.)
| | - Patrocinio Algara
- Genetics Department, Hospital Universitario de Toledo, Av. del Río Guadiana, 45007 Toledo, Spain;
| | - Marina De La Torre
- Department of Haematology, Hospital Universitario de Toledo, Av. del Río Guadiana, 45007 Toledo, Spain; (L.P.); (M.D.L.T.); (L.-F.C.)
| | - Ana Jiménez Ubieto
- Haematology Department, Hospital Universitario 12 de Octubre, Avda. de Córdoba, s/n, 28041 Madrid, Spain; (M.P.); (A.J.U.); (J.M.-L.)
| | - Joaquín Martínez-López
- Haematology Department, Hospital Universitario 12 de Octubre, Avda. de Córdoba, s/n, 28041 Madrid, Spain; (M.P.); (A.J.U.); (J.M.-L.)
| | - Luis-Felipe Casado
- Department of Haematology, Hospital Universitario de Toledo, Av. del Río Guadiana, 45007 Toledo, Spain; (L.P.); (M.D.L.T.); (L.-F.C.)
| | - Manuela Mollejo
- Anatomopathology Department, Hospital Universitario de Toledo, Av. del Río Guadiana, 45007 Toledo, Spain;
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3
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Morales ML, García-Vicente R, Rodríguez-García A, Reyes-Palomares A, Vincelle-Nieto Á, Álvarez N, Ortiz-Ruiz A, Garrido-García V, Giménez A, Carreño-Tarragona G, Sánchez R, Ayala R, Martínez-López J, Linares M. Posttranslational splicing modifications as a key mechanism in cytarabine resistance in acute myeloid leukemia. Leukemia 2023; 37:1649-1659. [PMID: 37422594 PMCID: PMC10400425 DOI: 10.1038/s41375-023-01963-4] [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: 02/07/2023] [Revised: 06/14/2023] [Accepted: 06/29/2023] [Indexed: 07/10/2023]
Abstract
Despite the approval of several drugs for AML, cytarabine is still widely used as a therapeutic approach. However, 85% of patients show resistance and only 10% overcome the disease. Using RNA-seq and phosphoproteomics, we show that RNA splicing and serine-arginine-rich (SR) proteins phosphorylation were altered during cytarabine resistance. Moreover, phosphorylation of SR proteins at diagnosis were significantly lower in responder than non-responder patients, pointing to their utility to predict response. These changes correlated with altered transcriptomic profiles of SR protein target genes. Notably, splicing inhibitors were therapeutically effective in treating sensitive and resistant AML cells as monotherapy or combination with other approved drugs. H3B-8800 and venetoclax combination showed the best efficacy in vitro, demonstrating synergistic effects in patient samples and no toxicity in healthy hematopoietic progenitors. Our results establish that RNA splicing inhibition, alone or combined with venetoclax, could be useful for the treatment of newly diagnosed or relapsed/refractory AML.
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Affiliation(s)
- María Luz Morales
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain.
| | - Roberto García-Vicente
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain
| | - Alba Rodríguez-García
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain
| | - Armando Reyes-Palomares
- Department of Biochemistry and Molecular Biology, Veterinary School, Universidad Complutense de Madrid, ES 28040, Madrid, Spain
| | - África Vincelle-Nieto
- Department of Biochemistry and Molecular Biology, Veterinary School, Universidad Complutense de Madrid, ES 28040, Madrid, Spain
| | - Noemí Álvarez
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain
| | - Alejandra Ortiz-Ruiz
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain
| | - Vanesa Garrido-García
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain
| | - Alicia Giménez
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain
| | - Gonzalo Carreño-Tarragona
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain
| | - Ricardo Sánchez
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain
| | - Rosa Ayala
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain
- Department of Medicine, Medicine School, Universidad Complutense de Madrid, ES 28040, Madrid, Spain
| | - Joaquín Martínez-López
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain
- Department of Medicine, Medicine School, Universidad Complutense de Madrid, ES 28040, Madrid, Spain
| | - María Linares
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain.
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, ES 28040, Madrid, Spain.
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4
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Jiménez-Ubieto A, Martín-Muñoz A, Poza M, Dorado S, García-Ortiz A, Revilla E, Sarandeses P, Ruiz-Heredia Y, Baumann T, Rodríguez A, Calbacho M, Sánchez PM, Pina JMS, García-Sancho AM, Figaredo G, Gil-Alós D, Rufián L, Rodríguez M, Carneros L, Martínez-Laperche C, Bastos-Oreiro M, Wang C, Cedena MT, Rapado I, de Toledo P, Gallardo M, Valeri A, Ayala R, Martínez-López J, Barrio S. Personalized monitoring of circulating tumor DNA with a specific signature of trackable mutations after chimeric antigen receptor T-cell therapy in follicular lymphoma patients. Front Immunol 2023; 14:1188818. [PMID: 37342332 PMCID: PMC10277746 DOI: 10.3389/fimmu.2023.1188818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 04/26/2023] [Indexed: 06/22/2023] Open
Abstract
Background CART therapy has produced a paradigm shift in the treatment of relapsing FL patients. Strategies to optimize disease surveillance after these therapies are increasingly necessary. This study explores the potential value of ctDNA monitoring with an innovative signature of personalized trackable mutations. Method Eleven FL patients treated with anti-CD19 CAR T-cell therapy were included. One did not respond and was excluded. Genomic profiling was performed before starting lymphodepleting chemotherapy to identify somatic mutations suitable for LiqBio-MRD monitoring. The dynamics of the baseline mutations (4.5 per patient) were further analyzed on 59 cfDNA follow-up samples. PET/CT examinations were performed on days +90, +180, +365, and every six months until disease progression or death. Results After a median follow-up of 36 months, all patients achieved a CR as the best response. Two patients progressed. The most frequently mutated genes were CREBBP, KMT2D and EP300. Simultaneous analysis of ctDNA and PET/CT was available for 18 time-points. When PET/CT was positive, two out of four ctDNA samples were LiqBio-MRD negative. These two negative samples corresponded to women with a unique mesenteric mass in two evaluations and never relapsed. Meanwhile, 14 PET/CT negative images were mutation-free based on our LiqBio-MRD analysis (100%). None of the patients had a negative LiqBio-MRD test by day +7. Interestingly, all durably responding patients had undetectable ctDNA at or around three months after infusion. Two patients presented discordant results by PET/CT and ctDNA levels. No progression was confirmed in these cases. All the progressing patients were LiqBio-MRD positive before progression. Conclusion This is a proof-of-principle for using ctDNA to monitor response to CAR T-cell therapy in FL. Our results confirm that a non-invasive liquid biopsy MRD analysis may correlate with response and could be used to monitor response. Harmonized definitions of ctDNA molecular response and pinpointing the optimal timing for assessing ctDNA responses are necessary for this setting. If using ctDNA analysis, we suggest restricting follow-up PET/CT in CR patients to a clinical suspicion of relapse, to avoid false-positive results.
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Affiliation(s)
- Ana Jiménez-Ubieto
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain
| | - Alejandro Martín-Muñoz
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain
- Altum sequencing Co., Madrid, Spain
| | - María Poza
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain
| | - Sara Dorado
- Altum sequencing Co., Madrid, Spain
- Computational Science Department, Carlos III University, Madrid, Spain
| | - Almudena García-Ortiz
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain
| | - Enrique Revilla
- Departamento de Anatomía Patológica, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Pilar Sarandeses
- Departamento de Medicina Nuclear, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Yanira Ruiz-Heredia
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain
- Altum sequencing Co., Madrid, Spain
| | - Tycho Baumann
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain
| | - Antonia Rodríguez
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain
| | - María Calbacho
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain
| | - Pilar Martínez Sánchez
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain
| | - José María Sánchez Pina
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain
| | | | - Gloria Figaredo
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain
| | - Daniel Gil-Alós
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain
| | - Laura Rufián
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain
- Altum sequencing Co., Madrid, Spain
| | - Margarita Rodríguez
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain
- Altum sequencing Co., Madrid, Spain
| | - Laura Carneros
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain
| | | | | | - Chongwu Wang
- Hosea Precision Medical Technology Co., Ltd., Weihai, Shangdong, China
| | - María-Teresa Cedena
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain
| | - Inmaculada Rapado
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain
| | - Paula de Toledo
- Computational Science Department, Carlos III University, Madrid, Spain
| | - Miguel Gallardo
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain
| | - Antonio Valeri
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain
| | - Rosa Ayala
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain
| | - Joaquín Martínez-López
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain
| | - Santiago Barrio
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain
- Altum sequencing Co., Madrid, Spain
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5
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Jiménez-Ubieto A, Poza M, Martin-Muñoz A, Ruiz-Heredia Y, Dorado S, Figaredo G, Rosa-Rosa JM, Rodriguez A, Barcena C, Navamuel LP, Carrillo J, Sanchez R, Rufian L, Juárez A, Rodriguez M, Wang C, de Toledo P, Grande C, Mollejo M, Casado LF, Calbacho M, Baumann T, Rapado I, Gallardo M, Sarandeses P, Ayala R, Martínez-López J, Barrio S. Real-life disease monitoring in follicular lymphoma patients using liquid biopsy ultra-deep sequencing and PET/CT. Leukemia 2023; 37:659-669. [PMID: 36596983 DOI: 10.1038/s41375-022-01803-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 12/09/2022] [Accepted: 12/19/2022] [Indexed: 01/05/2023]
Abstract
In the present study, we screened 84 Follicular Lymphoma patients for somatic mutations suitable as liquid biopsy MRD biomarkers using a targeted next-generation sequencing (NGS) panel. We found trackable mutations in 95% of the lymph node samples and 80% of the liquid biopsy baseline samples. Then, we used an ultra-deep sequencing approach with 2 · 10-4 sensitivity (LiqBio-MRD) to track those mutations on 151 follow-up liquid biopsy samples from 54 treated patients. Positive LiqBio-MRD at first-line therapy correlated with a higher risk of progression both at the interim evaluation (HRINT 11.0, 95% CI 2.10-57.7, p = 0.005) and at the end of treatment (HREOT, HR 19.1, 95% CI 4.10-89.4, p < 0.001). Similar results were observed by PET/CT Deauville score, with a median PFS of 19 months vs. NR (p < 0.001) at the interim and 13 months vs. NR (p < 0.001) at EOT. LiqBio-MRD and PET/CT combined identified the patients that progressed in less than two years with 88% sensitivity and 100% specificity. Our results demonstrate that LiqBio-MRD is a robust and non-invasive approach, complementary to metabolic imaging, for identifying FL patients at high risk of failure during the treatment and should be considered in future response-adapted clinical trials.
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Affiliation(s)
- Ana Jiménez-Ubieto
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain.
| | - María Poza
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain
| | | | - Yanira Ruiz-Heredia
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain.,Altum sequencing Co., Madrid, Spain
| | - Sara Dorado
- Altum sequencing Co., Madrid, Spain.,Computational Science Department, Carlos III University, Madrid, Spain
| | | | - Juan Manuel Rosa-Rosa
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain
| | - Antonia Rodriguez
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain
| | - Carmen Barcena
- Hospital Universitario 12 de Octubre, Departamento de Anatomía Patológica, Madrid, Spain
| | | | | | - Ricardo Sanchez
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain.,Altum sequencing Co., Madrid, Spain
| | - Laura Rufian
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain.,Altum sequencing Co., Madrid, Spain
| | - Alexandra Juárez
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain.,Altum sequencing Co., Madrid, Spain
| | - Margarita Rodriguez
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain.,Altum sequencing Co., Madrid, Spain
| | - Chongwu Wang
- Hosea Precision Medical Technology Co., Ltd., Weihai, Shangdong, China
| | - Paula de Toledo
- Computational Science Department, Carlos III University, Madrid, Spain
| | | | | | | | - María Calbacho
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain
| | - Tycho Baumann
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain
| | - Inmaculada Rapado
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain
| | - Miguel Gallardo
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain.,H12O-CNIO Haematological Malignancies Clinical Research Unit, CNIO, Madrid, Spain
| | - Pilar Sarandeses
- Hospital Universitario 12 de Octubre, Departamento de Medicina Nuclear, Madrid, Spain
| | - Rosa Ayala
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain
| | - Joaquín Martínez-López
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain
| | - Santiago Barrio
- Department of Hematology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), CNIO, CIBERONC, Madrid, Spain. .,Altum sequencing Co., Madrid, Spain.
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6
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Measurable Residual Disease and Clonal Evolution in Acute Myeloid Leukemia from Diagnosis to Post-Transplant Follow-Up: The Role of Next-Generation Sequencing. Biomedicines 2023; 11:biomedicines11020359. [PMID: 36830896 PMCID: PMC9953407 DOI: 10.3390/biomedicines11020359] [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: 01/09/2023] [Revised: 01/24/2023] [Accepted: 01/24/2023] [Indexed: 01/28/2023] Open
Abstract
It has now been ascertained that acute myeloid leukemias-as in most type of cancers-are mixtures of various subclones, evolving by acquiring additional somatic mutations over the course of the disease. The complexity of leukemia clone architecture and the phenotypic and/or genotypic drifts that can occur during treatment explain why more than 50% of patients-in hematological remission-could relapse. Moreover, the complexity and heterogeneity of clone architecture represent a hindrance for monitoring measurable residual disease, as not all minimal residual disease monitoring methods are able to detect genetic mutations arising during treatment. Unlike with chemotherapy, which imparts a relatively short duration of selective pressure on acute myeloid leukemia clonal architecture, the immunological effect related to allogeneic hematopoietic stem cell transplant is prolonged over time and must be overcome for relapse to occur. This means that not all molecular abnormalities detected after transplant always imply inevitable relapse. Therefore, transplant represents a critical setting where a measurable residual disease-based strategy, performed during post-transplant follow-up by highly sensitive methods such as next-generation sequencing, could optimize and improve treatment outcome. The purpose of our review is to provide an overview of the role of next-generation sequencing in monitoring both measurable residual disease and clonal evolution in acute myeloid leukemia patients during the entire course of the disease, with special focus on the transplant phase.
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7
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Allam S, Nasr K, Khalid F, Shah Z, Khan Suheb MZ, Mulla S, Vikash S, Bou Zerdan M, Anwer F, Chaulagain CP. Liquid biopsies and minimal residual disease in myeloid malignancies. Front Oncol 2023; 13:1164017. [PMID: 37213280 PMCID: PMC10196237 DOI: 10.3389/fonc.2023.1164017] [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: 02/11/2023] [Accepted: 04/25/2023] [Indexed: 05/23/2023] Open
Abstract
Minimal residual disease (MRD) assessment through blood component sampling by liquid biopsies (LBs) is increasingly being investigated in myeloid malignancies. Blood components then undergo molecular analysis by flow cytometry or sequencing techniques and can be used as a powerful tool for prognostic and predictive purposes in myeloid malignancies. There is evidence and more is evolving about the quantification and identification of cell-based and gene-based biomarkers in myeloid malignancies to monitor treatment response. MRD based acute myeloid leukemia protocol and clinical trials are currently incorporating LB testing and preliminary results are encouraging for potential widespread use in clinic in the near future. MRD monitoring using LBs are not standard in myelodysplastic syndrome (MDS) but this is an area of active investigation. In the future, LBs can replace more invasive techniques such as bone marrow biopsies. However, the routine clinical application of these markers continues to be an issue due to lack of standardization and limited number of studies investigating their specificities. Integrating artificial intelligence (AI) could help simplify the complex interpretation of molecular testing and reduce errors related to operator dependency. Though the field is rapidly evolving, the applicability of MRD testing using LB is mostly limited to research setting at this time due to the need for validation, regulatory approval, payer coverage, and cost issues. This review focuses on the types of biomarkers, most recent research exploring MRD and LB in myeloid malignancies, ongoing clinical trials, and the future of LB in the setting of AI.
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Affiliation(s)
- Sabine Allam
- Department of Medicine and Medical Sciences, University of Balamand, Dekwaneh, Lebanon
| | - Kristina Nasr
- Department of Medicine and Medical Sciences, University of Balamand, Dekwaneh, Lebanon
| | - Farhan Khalid
- Department of Internal Medicine, Monmouth Medical Center, Long Branch, NJ, United States
| | - Zunairah Shah
- Department of Internal Medicine, Weiss Memorial Hospital, Chicago, IL, United States
| | | | - Sana Mulla
- Department of Internal Medicine, St Mary’s Medical Center, Apple Valley, CA, United States
| | - Sindhu Vikash
- Department of Medicine, Jacobi Medical center/AECOM Bronx, Bronx, NY, United States
| | - Maroun Bou Zerdan
- Department of Internal Medicine, SUNY Upstate Medical University, New York, NY, United States
| | - Faiz Anwer
- Department of Hematology and Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH, United States
| | - Chakra P. Chaulagain
- Department of Hematology and Oncology, Maroone Cancer Center, Cleveland Clinic Florida, Weston, FL, United States
- *Correspondence: Chakra P. Chaulagain,
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8
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Short NJ, Fu C, Berry DA, Walter RB, Freeman SD, Hourigan CS, Huang X, Gonzalez GN, Hwang H, Qi X, Kantarjian H, Zhou S, Ravandi F. Association of hematologic response and assay sensitivity on the prognostic impact of measurable residual disease in acute myeloid leukemia: a systematic review and meta-analysis. Leukemia 2022; 36:2817-2826. [PMID: 36261575 DOI: 10.1038/s41375-022-01692-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 12/25/2022]
Abstract
Measurable residual disease (MRD) is associated with relapse and survival in acute myeloid leukemia (AML). We aimed to quantify the impact of MRD on outcomes across clinical contexts, including its association with hematologic response and MRD assay sensitivity. We performed systematic literature review and meta-analysis of 48 studies that reported the association between MRD and overall survival (OS) or disease-free survival (DFS) in AML and provided information on the MRD threshold used and the hematologic response of the study population. Among studies limited to patients in complete remission (CR), the estimated 5-year OS for the MRD-negative and MRD-positive groups was 67% (95% Bayesian credible interval [CrI], 53-77%) and 31% (95% CrI, 18-44%), respectively. Achievement of an MRD-negative response was associated with superior DFS and OS, regardless of MRD threshold or analytic sensitivity. Among patients in CR, the benefit of MRD negativity was highest in studies using an MRD cutoff less than 0.1%. The beneficial impact of MRD negativity was observed across MRD assays and timing of MRD assessment. In patients with AML in morphological remission, achievement of MRD negativity is associated with superior DFS and OS, irrespective of hematologic response or the MRD threshold used.
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Affiliation(s)
- Nicholas J Short
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chenqi Fu
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Donald A Berry
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Roland B Walter
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Sylvie D Freeman
- Institute of Infection and Immunity, University of Birmingham, Birmingham, UK
| | - Christopher S Hourigan
- Laboratory of Myeloid Malignancies, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xuelin Huang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Hyunsoo Hwang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xinyue Qi
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hagop Kantarjian
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shouhao Zhou
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA.
| | - Farhad Ravandi
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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9
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Sánchez R, Dorado S, Ruíz-Heredia Y, Martín-Muñoz A, Rosa-Rosa JM, Ribera J, García O, Jimenez-Ubieto A, Carreño-Tarragona G, Linares M, Rufián L, Juárez A, Carrillo J, Espino MJ, Cáceres M, Expósito S, Cuevas B, Vanegas R, Casado LF, Torrent A, Zamora L, Mercadal S, Coll R, Cervera M, Morgades M, Hernández-Rivas JÁ, Bravo P, Serí C, Anguita E, Barragán E, Sargas C, Ferrer-Marín F, Sánchez-Calero J, Sevilla J, Ruíz E, Villalón L, Del Mar Herráez M, Riaza R, Magro E, Steegman JL, Wang C, de Toledo P, García-Gutiérrez V, Ayala R, Ribera JM, Barrio S, Martínez-López J. Detection of kinase domain mutations in BCR::ABL1 leukemia by ultra-deep sequencing of genomic DNA. Sci Rep 2022; 12:13057. [PMID: 35906470 PMCID: PMC9338264 DOI: 10.1038/s41598-022-17271-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 07/22/2022] [Indexed: 11/09/2022] Open
Abstract
The screening of the BCR::ABL1 kinase domain (KD) mutation has become a routine analysis in case of warning/failure for chronic myeloid leukemia (CML) and B-cell precursor acute lymphoblastic leukemia (ALL) Philadelphia (Ph)-positive patients. In this study, we present a novel DNA-based next-generation sequencing (NGS) methodology for KD ABL1 mutation detection and monitoring with a 1.0E-4 sensitivity. This approach was validated with a well-stablished RNA-based nested NGS method. The correlation of both techniques for the quantification of ABL1 mutations was high (Pearson r = 0.858, p < 0.001), offering DNA-DeepNGS a sensitivity of 92% and specificity of 82%. The clinical impact was studied in a cohort of 129 patients (n = 67 for CML and n = 62 for B-ALL patients). A total of 162 samples (n = 86 CML and n = 76 B-ALL) were studied. Of them, 27 out of 86 harbored mutations (6 in warning and 21 in failure) for CML, and 13 out of 76 (2 diagnostic and 11 relapse samples) did in B-ALL patients. In addition, in four cases were detected mutation despite BCR::ABL1 < 1%. In conclusion, we were able to detect KD ABL1 mutations with a 1.0E-4 sensitivity by NGS using DNA as starting material even in patients with low levels of disease.
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Affiliation(s)
- Ricardo Sánchez
- Hematology Department, Hospital UniversitarioHospital Universitario 12 Octubre, Madrid, Spain.
- Instituto de Investigación Hospital 12 de Octubre (i+12), Madrid, Spain.
- Hematological Malignancies Clinical Research Unit, CNIO, Madrid, Spain.
- Altum Sequencing Co., Madrid, Spain.
| | - Sara Dorado
- Altum Sequencing Co., Madrid, Spain
- Computer Science and Engineering Department, Carlos III University, Madrid, Spain
| | | | | | - Juan Manuel Rosa-Rosa
- Instituto de Investigación Hospital 12 de Octubre (i+12), Madrid, Spain
- Hematological Malignancies Clinical Research Unit, CNIO, Madrid, Spain
| | - Jordi Ribera
- Hematology Department, ICO-Hospital Germans Trias i Pujol. Josep Carreras Leukemia Research Institute, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Olga García
- Hematology Department, ICO-Hospital Germans Trias i Pujol. Josep Carreras Leukemia Research Institute, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Ana Jimenez-Ubieto
- Hematology Department, Hospital UniversitarioHospital Universitario 12 Octubre, Madrid, Spain
- Hematological Malignancies Clinical Research Unit, CNIO, Madrid, Spain
| | - Gonzalo Carreño-Tarragona
- Hematology Department, Hospital UniversitarioHospital Universitario 12 Octubre, Madrid, Spain
- Hematological Malignancies Clinical Research Unit, CNIO, Madrid, Spain
| | - María Linares
- Hematological Malignancies Clinical Research Unit, CNIO, Madrid, Spain
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, Madrid, Spain
| | - Laura Rufián
- Instituto de Investigación Hospital 12 de Octubre (i+12), Madrid, Spain
- Altum Sequencing Co., Madrid, Spain
| | - Alexandra Juárez
- Hematology Department, Hospital UniversitarioHospital Universitario 12 Octubre, Madrid, Spain
- Altum Sequencing Co., Madrid, Spain
| | | | - María José Espino
- Hematology Department, Hospital UniversitarioHospital Universitario 12 Octubre, Madrid, Spain
| | - Mercedes Cáceres
- Hematology Department, Hospital UniversitarioHospital Universitario 12 Octubre, Madrid, Spain
| | - Sara Expósito
- Laboratory of Neurophysiology and Synaptic Plasticity, Instituto Cajal, CSIC, Madrid, Spain
| | | | - Raúl Vanegas
- Hospital General Universitario de Ciudad Real, Ciudad Real, Spain
| | | | - Anna Torrent
- Hematology Department, ICO-Hospital Germans Trias i Pujol. Josep Carreras Leukemia Research Institute, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Lurdes Zamora
- Hematology Department, ICO-Hospital Germans Trias i Pujol. Josep Carreras Leukemia Research Institute, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Santiago Mercadal
- Hematology Department, ICO-Hospital Duran i Reynals (Bellvitge), Barcelona, Spain
| | - Rosa Coll
- Hematology Department, ICO-Hospital Dr. Josep Trueta, Girona, Spain
| | - Marta Cervera
- Hematology Department, ICO-Hospital Universitari Joan XXIII, Tarragona, Spain
| | - Mireia Morgades
- Hematology Department, ICO-Hospital Germans Trias i Pujol. Josep Carreras Leukemia Research Institute, Universitat Autònoma de Barcelona, Badalona, Spain
| | | | - Pilar Bravo
- Hospital Universitario de Fuenlabrada, Fuenlabrada (Madrid), Spain
| | - Cristina Serí
- Hospital Central de la Defensa Gómez Ulla, Madrid, Spain
| | - Eduardo Anguita
- Hospital Clínico San Carlos, Department of Medicine, UCM, Madrid, Spain
| | - Eva Barragán
- Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Claudia Sargas
- Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | | | | | | | - Elena Ruíz
- Hospital del Tajo, Aranjuez (Madrid), Spain
| | - Lucía Villalón
- Hospital Universitario Fundación Alcorcón, Alcorcón (Madrid), Spain
| | | | - Rosalía Riaza
- Hospital Universitario Severo Ochoa, Leganés, Madrid, Spain
| | - Elena Magro
- Hospital Universitario Príncipe de Asturias, Alcalá de Henares, Madrid, Spain
| | | | - Chongwu Wang
- Hosea Precision Medical Technology Co., Ltd., Weihai, Shangdong, China
| | - Paula de Toledo
- Computer Science and Engineering Department, Carlos III University, Madrid, Spain
| | | | - Rosa Ayala
- Hematology Department, Hospital UniversitarioHospital Universitario 12 Octubre, Madrid, Spain
- Instituto de Investigación Hospital 12 de Octubre (i+12), Madrid, Spain
- Hematological Malignancies Clinical Research Unit, CNIO, Madrid, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
| | - Josep-Maria Ribera
- Hematology Department, ICO-Hospital Germans Trias i Pujol. Josep Carreras Leukemia Research Institute, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Santiago Barrio
- Hematology Department, Hospital UniversitarioHospital Universitario 12 Octubre, Madrid, Spain
- Instituto de Investigación Hospital 12 de Octubre (i+12), Madrid, Spain
- Hematological Malignancies Clinical Research Unit, CNIO, Madrid, Spain
- Altum Sequencing Co., Madrid, Spain
| | - Joaquín Martínez-López
- Hematology Department, Hospital UniversitarioHospital Universitario 12 Octubre, Madrid, Spain.
- Instituto de Investigación Hospital 12 de Octubre (i+12), Madrid, Spain.
- Hematological Malignancies Clinical Research Unit, CNIO, Madrid, Spain.
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain.
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10
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Azenkot T, Jonas BA. Clinical Impact of Measurable Residual Disease in Acute Myeloid Leukemia. Cancers (Basel) 2022; 14:cancers14153634. [PMID: 35892893 PMCID: PMC9330895 DOI: 10.3390/cancers14153634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 07/21/2022] [Indexed: 11/24/2022] Open
Abstract
Simple Summary Advances in immunophenotyping and molecular techniques have allowed for the development of more sensitive diagnostic tests in acute leukemia. These techniques can identify low levels of leukemic cells (quantified as 10−4 to 10−6 ratio to white blood cells) in patient samples. The presence of such low levels of leukemic cells, termed “measurable/minimal residual disease” (MRD), has been shown to be a marker of disease burden and patient outcomes. In acute lymphoblastic leukemia, new agents are highly effective at eliminating MRD for patients whose leukemia progressed despite first line therapies. By comparison, the role of MRD in acute myeloid leukemia is less clear. This commentary reviews select data and remaining questions about the clinical application of MRD to the treatment of patients with acute myeloid leukemia. Abstract Measurable residual disease (MRD) has emerged as a primary marker of risk severity and prognosis in acute myeloid leukemia (AML). There is, however, ongoing debate about MRD-based surveillance and treatment. A literature review was performed using the PubMed database with the keywords MRD or residual disease in recently published journals. Identified articles describe the prognostic value of pre-transplant MRD and suggest optimal timing and techniques to quantify MRD. Several studies address the implications of MRD on treatment selection and hematopoietic stem cell transplant, including patient candidacy, conditioning regimen, and transplant type. More prospective, randomized studies are needed to guide the application of MRD in the treatment of AML, particularly in transplant.
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Affiliation(s)
- Tali Azenkot
- Department of Internal Medicine, University of California Davis School of Medicine, Sacramento, CA 95817, USA;
| | - Brian A. Jonas
- Division of Cellular Therapy, Bone Marrow Transplant, and Malignant Hematology, Department of Internal Medicine, University of California Davis School of Medicine, Sacramento, CA 95817, USA
- Correspondence: ; Tel.: +1-916-734-3772
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11
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Colmenares R, Álvarez N, Barrio S, Martínez-López J, Ayala R. The Minimal Residual Disease Using Liquid Biopsies in Hematological Malignancies. Cancers (Basel) 2022; 14:1310. [PMID: 35267616 PMCID: PMC8909350 DOI: 10.3390/cancers14051310] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/23/2022] [Accepted: 02/27/2022] [Indexed: 12/02/2022] Open
Abstract
The study of cell-free DNA (cfDNA) and other peripheral blood components (known as "liquid biopsies") is promising, and has been investigated especially in solid tumors. Nevertheless, it is increasingly showing a greater utility in the diagnosis, prognosis, and response to treatment of hematological malignancies; in the future, it could prevent invasive techniques, such as bone marrow (BM) biopsies. Most of the studies about this topic have focused on B-cell lymphoid malignancies; some of them have shown that cfDNA can be used as a novel way for the diagnosis and minimal residual monitoring of B-cell lymphomas, using techniques such as next-generation sequencing (NGS). In myelodysplastic syndromes, multiple myeloma, or chronic lymphocytic leukemia, liquid biopsies may allow for an interesting genomic representation of the tumor clones affecting different lesions (spatial heterogeneity). In acute leukemias, it can be helpful in the monitoring of the early treatment response and the prediction of treatment failure. In chronic lymphocytic leukemia, the evaluation of cfDNA permits the definition of clonal evolution and drug resistance in real time. However, there are limitations, such as the difficulty in obtaining sufficient circulating tumor DNA for achieving a high sensitivity to assess the minimal residual disease, or the lack of standardization of the method, and clinical studies, to confirm its prognostic impact. This review focuses on the clinical applications of cfDNA on the minimal residual disease in hematological malignancies.
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Affiliation(s)
- Rafael Colmenares
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, 28041 Madrid, Spain; (R.C.); (N.Á.); (S.B.); (J.M.-L.)
| | - Noemí Álvarez
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, 28041 Madrid, Spain; (R.C.); (N.Á.); (S.B.); (J.M.-L.)
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain
| | - Santiago Barrio
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, 28041 Madrid, Spain; (R.C.); (N.Á.); (S.B.); (J.M.-L.)
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain
| | - Joaquín Martínez-López
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, 28041 Madrid, Spain; (R.C.); (N.Á.); (S.B.); (J.M.-L.)
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain
- Department of Medicine, Complutense University of Madrid, 28040 Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, 28029 Madrid, Spain
| | - Rosa Ayala
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, 28041 Madrid, Spain; (R.C.); (N.Á.); (S.B.); (J.M.-L.)
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain
- Department of Medicine, Complutense University of Madrid, 28040 Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, 28029 Madrid, Spain
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12
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El Achi H, Kanagal-Shamanna R. Biomarkers in Acute Myeloid Leukemia: Leveraging Next Generation Sequencing Data for Optimal Therapeutic Strategies. Front Oncol 2021; 11:748250. [PMID: 34660311 PMCID: PMC8514876 DOI: 10.3389/fonc.2021.748250] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/14/2021] [Indexed: 12/19/2022] Open
Abstract
Next generation sequencing (NGS) is routinely used for mutation profiling of acute myeloid leukemia. The extensive application of NGS in hematologic malignancies, and its significant association with the outcomes in multiple large cohorts constituted a proof of concept that AML phenotype is driven by underlying mutational signature and is amenable for targeted therapies. These findings urged incorporation of molecular results into the latest World Health Organization (WHO) sub-classification and integration into risk-stratification and treatment guidelines by the European Leukemia Net. NGS mutation profiling provides a large amount of information that guides diagnosis and management, dependent on the type and number of gene mutations, variant allele frequency and amenability to targeted therapeutics. Hence, molecular mutational profiling is an integral component for work-up of AML and multiple leukemic entities. In addition, there is a vast amount of informative data that can be obtained from routine clinical NGS sequencing beyond diagnosis, prognostication and therapeutic targeting. These include identification of evidence regarding the ontogeny of the disease, underlying germline predisposition and clonal hematopoiesis, serial monitoring to assess the effectiveness of therapy and resistance mutations, which have broader implications for management. In this review, using a few prototypic genes in AML, we will summarize the clinical applications of NGS generated data for optimal AML management, with emphasis on the recently described entities and Food and Drug Administration approved target therapies.
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Affiliation(s)
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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13
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Onecha E, Rapado I, Luz Morales M, Carreño-Tarragona G, Martinez-Sanchez P, Gutierrez X, Sáchez Pina JM, Linares M, Gallardo M, Martinez-López J, Ayala R. Monitoring of clonal evolution of acute myeloid leukemia identifies the leukemia subtype, clinical outcome and potential new drug targets for post-remission strategies or relapse. Haematologica 2021; 106:2325-2333. [PMID: 32732356 PMCID: PMC8409047 DOI: 10.3324/haematol.2020.254623] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Indexed: 12/16/2022] Open
Abstract
In cases of treatment failure in acute myeloid leukemia (AML), the utility of mutational profiling in primary refractoriness and relapse is not established. We undertook a perspective study using next-generation sequencing (NGS) of clinical follow-up samples (n=91) from 23 patients with AML with therapeutic failure to cytarabine plus idarubicin or fludarabine. Cases of primary refractoriness to treatment were associated with a lower number of DNA variants at diagnosis than cases of relapse (median 1.67 and 3.21, respectively, P=0.029). The most frequently affected pathways in patients with primary refractoriness were signaling, transcription and tumor suppression, whereas methylation and splicing pathways were mainly implicated in relapsed patients. New therapeutic targets, either by an approved drug or within clinical trials, were not identified in any of the cases of refractoriness (zero of ten); however, eight potential new targets were found in five relapsed patients (five of 13, P=0.027): one IDH2, three SF3B1, two KRAS, one KIT and one JAK2. Sixty-five percent of all variants detected at diagnosis were not detected at complete response. Specifically, 100% of variants in EZH2, RUNX1, VHL, FLT3, ETV6, U2AF1, PHF6 and SF3B1 disappeared at complete response, indicating their potential use as markers to evaluate minimal residual disease for follow-up of AML. Molecular follow-up using a custom NGS myeloid panel of 32 genes in the post-treatment evaluation of AML can help in the stratification of prognostic risk, the selection of minimal residual disease markers to monitor the response to treatment and guide post-remission strategies targeting AML, and the selection of new drugs for leukemia relapse.
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Affiliation(s)
- Esther Onecha
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid
| | | | | | | | | | - Xabier Gutierrez
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid
| | | | - María Linares
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid
| | - Miguel Gallardo
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid
| | | | - Rosa Ayala
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid
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14
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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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15
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Pettersson L, Johansson Alm S, Almstedt A, Chen Y, Orrsjö G, Shah-Barkhordar G, Zhou L, Kotarsky H, Vidovic K, Asp J, Lazarevic V, Saal LH, Fogelstrand L, Ehinger M. Comparison of RNA- and DNA-based methods for measurable residual disease analysis in NPM1-mutated acute myeloid leukemia. Int J Lab Hematol 2021; 43:664-674. [PMID: 34053184 DOI: 10.1111/ijlh.13608] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 05/02/2021] [Accepted: 05/06/2021] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Reverse transcriptase quantitative PCR (RT-qPCR) is considered the method of choice for measurable residual disease (MRD) assessment in NPM1-mutated acute myeloid leukemia (AML). MRD can also be determined with DNA-based methods offering certain advantages. We here compared the DNA-based methods quantitative PCR (qPCR), droplet digital PCR (ddPCR), and targeted deep sequencing (deep seq) with RT-qPCR. METHODS Of 110 follow-up samples from 30 patients with NPM1-mutated AML were analyzed by qPCR, ddPCR, deep seq, and RT-qPCR. To select DNA MRD cutoffs for bone marrow, we performed receiver operating characteristic analyses for each DNA method using prognostically relevant RT-qPCR cutoffs. RESULTS The DNA-based methods showed strong intermethod correlation, but were less sensitive than RT-qPCR. A bone marrow cutoff at 0.1% leukemic DNA for qPCR or 0.05% variant allele frequency for ddPCR and deep seq offered optimal sensitivity and specificity with respect to 3 log10 reduction of NPM1 transcripts and/or 2% mutant NPM1/ABL. With these cutoffs, MRD results agreed in 95% (191/201) of the analyses. Although more sensitive, RT-qPCR failed to detect leukemic signals in 10% of samples with detectable leukemic DNA. CONCLUSION DNA-based MRD techniques may complement RT-qPCR for assessment of residual leukemia. DNA-based methods offer high positive and negative predictive values with respect to residual leukemic NPM1 transcripts at levels of importance for response to treatment. However, moving to DNA-based MRD methods will miss a proportion of patients with residual leukemic RNA, but on the other hand some MRD samples with detectable leukemic DNA can be devoid of measurable leukemic RNA.
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Affiliation(s)
- Louise Pettersson
- Department of Clinical Sciences, Division of Pathology, Lund University, Skane University Hospital, Lund, Sweden.,Department of Pathology, Halland Hospital Halmstad, Region Halland, Halmstad, Sweden
| | - Sofie Johansson Alm
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Alvar Almstedt
- SciLife Clinical Genomics Gothenburg, Gothenburg, Sweden
| | - Yilun Chen
- Department of Clinical Sciences, Division of Oncology, Faculty of Medicine, Lund University, Lund, Sweden
| | - Gustav Orrsjö
- Section for Hematology and Coagulation, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Giti Shah-Barkhordar
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Li Zhou
- Klinisk Patologi, Region Laboratories, Region Skåne, Lund, Sweden
| | - Heike Kotarsky
- Klinisk Patologi, Region Laboratories, Region Skåne, Lund, Sweden
| | - Karina Vidovic
- Department of Clinical Sciences, Division of Pathology, Lund University, Skane University Hospital, Lund, Sweden
| | - Julia Asp
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Vladimir Lazarevic
- Department of Hematology, Oncology and Radiation Physics, Lund University, Skane University Hospital, Lund, Sweden
| | - Lao H Saal
- Department of Clinical Sciences, Division of Oncology, Faculty of Medicine, Lund University, Lund, Sweden.,Lund University Cancer Center, Medicon Village, Lund, Sweden
| | - Linda Fogelstrand
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Mats Ehinger
- Department of Clinical Sciences, Division of Pathology, Lund University, Skane University Hospital, Lund, Sweden.,Klinisk Patologi, Region Laboratories, Region Skåne, Lund, Sweden
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16
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How I diagnose and treat NPM1-mutated AML. Blood 2021; 137:589-599. [PMID: 33171486 DOI: 10.1182/blood.2020008211] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/30/2020] [Indexed: 12/13/2022] Open
Abstract
Mutations of the nucleophosmin (NPM1) gene, encoding for a nucleolar multifunctional protein, occur in approximately one-third of adult acute myeloid leukemia (AML). NPM1-mutated AML exhibits unique molecular, pathological, and clinical features, which led to its recognition as distinct entity in the 2017 World Health Organization (WHO) classification of myeloid neoplasms. Although WHO criteria for the diagnosis of NPM1-mutated AML are well established, its distinction from other AML entities may be difficult. Moreover, the percentage of blasts required to diagnose NPM1-mutated AML remains controversial. According to the European LeukemiaNet (ELN), determining the mutational status of NPM1 (together with FLT3) is mandatory for accurate relapse-risk assessment. NPM1 mutations are ideal targets for measurable residual disease (MRD) monitoring, since they are AML specific, frequent, very stable at relapse, and do not drive clonal hematopoiesis of undetermined significance. MRD monitoring by quantitative polymerase chain reaction of NPM1-mutant transcripts, possibly combined with ELN genetic-based risk stratification, can guide therapeutic decisions after remission. Furthermore, immunohistochemistry can be very useful in selected situations, such as diagnosis of NPM1-mutated myeloid sarcoma. Herein, we present 4 illustrative cases of NPM1-mutated AML that address important issues surrounding the biology, diagnosis, and therapy of this common form of leukemia.
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17
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Ayala R, Rapado I, Onecha E, Martínez-Cuadrón D, Carreño-Tarragona G, Bergua JM, Vives S, Algarra JL, Tormo M, Martinez P, Serrano J, Herrera P, Ramos F, Salamero O, Lavilla E, Gil C, López Lorenzo JL, Vidriales MB, Labrador J, Falantes JF, Sayas MJ, Paiva B, Barragán E, Prosper F, Sanz MÁ, Martínez-López J, Montesinos P. The Mutational Landscape of Acute Myeloid Leukaemia Predicts Responses and Outcomes in Elderly Patients from the PETHEMA-FLUGAZA Phase 3 Clinical Trial. Cancers (Basel) 2021; 13:cancers13102458. [PMID: 34070172 PMCID: PMC8158477 DOI: 10.3390/cancers13102458] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/06/2021] [Accepted: 05/12/2021] [Indexed: 12/30/2022] Open
Abstract
We sought to predict treatment responses and outcomes in older patients with newly diagnosed acute myeloid leukemia (AML) from our FLUGAZA phase III clinical trial (PETHEMA group) based on mutational status, comparing azacytidine (AZA) with fludarabine plus low-dose cytarabine (FLUGA). Mutational profiling using a custom 43-gene next-generation sequencing panel revealed differences in profiles between older and younger patients, and several prognostic markers that were useful in young patients were ineffective in older patients. We examined the associations between variables and overall responses at the end of the third cycle. Patients with mutated DNMT3A or EZH2 were shown to benefit from azacytidine in the treatment-adjusted subgroup analysis. An analysis of the associations with tumor burden using variant allele frequency (VAF) quantification showed that a higher overall response was associated with an increase in TET2 VAF (odds ratio (OR), 1.014; p = 0.030) and lower TP53 VAF (OR, 0.981; p = 0.003). In the treatment-adjusted multivariate survival analyses, only the NRAS (hazard ratio (HR), 1.9, p = 0.005) and TP53 (HR, 2.6, p = 9.8 × 10-7) variants were associated with shorter overall survival (OS), whereas only mutated BCOR (HR, 3.6, p = 0.0003) was associated with a shorter relapse-free survival (RFS). Subgroup analyses of OS according to biological and genomic characteristics showed that patients with low-intermediate cytogenetic risk (HR, 1.51, p = 0.045) and mutated NRAS (HR, 3.66, p = 0.047) benefited from azacytidine therapy. In the subgroup analyses, patients with mutated TP53 (HR, 4.71, p = 0.009) showed a better RFS in the azacytidine arm. In conclusion, differential mutational profiling might anticipate the outcomes of first-line treatment choices (AZA or FLUGA) in older patients with AML. The study is registered at ClinicalTrials.gov as NCT02319135.
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Affiliation(s)
- Rosa Ayala
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, 28041 Madrid, Spain; (I.R.); (E.O.); (G.C.-T.)
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain
- Departament of Medicine, Complutense University, 28040 Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, 28029 Madrid, Spain; (B.P.); (E.B.); (F.P.); (M.Á.S.); (P.M.)
- Correspondence: (R.A.); (J.M.-L.)
| | - Inmaculada Rapado
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, 28041 Madrid, Spain; (I.R.); (E.O.); (G.C.-T.)
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, 28029 Madrid, Spain; (B.P.); (E.B.); (F.P.); (M.Á.S.); (P.M.)
| | - Esther Onecha
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, 28041 Madrid, Spain; (I.R.); (E.O.); (G.C.-T.)
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain
| | - David Martínez-Cuadrón
- Hematology Department, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain;
| | - Gonzalo Carreño-Tarragona
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, 28041 Madrid, Spain; (I.R.); (E.O.); (G.C.-T.)
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain
| | - Juan Miguel Bergua
- Hematology Department, Hospital San Pedro Acantara, 10003 Cáceres, Spain;
| | - Susana Vives
- Department of Hematology, ICO Badalona-Hospital Germans Trias i Pujol. Josep Carreras Leukemia Research Institute. Universitat Autònoma de Barcelona, 08916 Badalona, Spain;
| | | | - Mar Tormo
- Hematology Department, Hospital Clínico Universitario de Valencia, 46010 Valencia, Spain;
| | - Pilar Martinez
- Hematology Department, Hospital 12 de Octubre, 28041 Madrid, Spain;
| | - Josefina Serrano
- Hematology Department, Hospital Universitario Reina Sofía, 14004 Cordoba, Spain;
| | - Pilar Herrera
- Hematology Department, Hospital Ramon y Cajal, 28034 Madrid, Spain;
| | - Fernando Ramos
- Hematology Department, Hospital Universitario de León, 24008 León, Spain;
| | - Olga Salamero
- Hematology Department, Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain;
| | - Esperanza Lavilla
- Hematology Department, Hospital Universitario Xeral de Lugo, 27003 Lugo, Spain;
| | - Cristina Gil
- Hematology Department, Hospital General de Alicante, 03010 Alicante, Spain;
| | | | - María Belén Vidriales
- Hematology Department, Hospital Universitario de Salamanca, IBSAL, 37007 Salamanca, Spain;
| | - Jorge Labrador
- Hematology Department, Hospital Universitario de Burgos, 09001 Burgos, Spain;
| | - José Francisco Falantes
- Hematology Department, Hospital Universitario Vírgen del Rocío, Instituto de BioMedicina de Sevilla, 41013 Sevilla, Spain;
| | - María José Sayas
- Hematology Department, Hospital Doctor Peset, 46017 Valencia, Spain;
| | - Bruno Paiva
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, 28029 Madrid, Spain; (B.P.); (E.B.); (F.P.); (M.Á.S.); (P.M.)
- Hematology Department, Clínica Universitaria de Navarra, 31008 Navarra, Spain
| | - Eva Barragán
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, 28029 Madrid, Spain; (B.P.); (E.B.); (F.P.); (M.Á.S.); (P.M.)
- Hematology Department, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain;
| | - Felipe Prosper
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, 28029 Madrid, Spain; (B.P.); (E.B.); (F.P.); (M.Á.S.); (P.M.)
- Hematology Department, Clínica Universitaria de Navarra, 31008 Navarra, Spain
| | - Miguel Ángel Sanz
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, 28029 Madrid, Spain; (B.P.); (E.B.); (F.P.); (M.Á.S.); (P.M.)
- Hematology Department, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain;
| | - Joaquín Martínez-López
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, 28041 Madrid, Spain; (I.R.); (E.O.); (G.C.-T.)
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain
- Departament of Medicine, Complutense University, 28040 Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, 28029 Madrid, Spain; (B.P.); (E.B.); (F.P.); (M.Á.S.); (P.M.)
- Correspondence: (R.A.); (J.M.-L.)
| | - Pau Montesinos
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, 28029 Madrid, Spain; (B.P.); (E.B.); (F.P.); (M.Á.S.); (P.M.)
- Hematology Department, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain;
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18
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Álvarez N, Rodríguez-García A, Morales ML, Gutiérrez M, Montero M, Poza M, López N, Carreño G, Sánchez R, Cedena T, Rapado I, Martínez-López J, Ayala R. Clonal hematopoiesis-defining mutations have no impact on the development of thrombosis in a cohort of patients with myeloid pathology. Leuk Res 2021; 108:106613. [PMID: 34087683 DOI: 10.1016/j.leukres.2021.106613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 05/06/2021] [Indexed: 11/28/2022]
Affiliation(s)
- Noemí Álvarez
- Hematology Department, Hospital 12 de Octubre, Madrid, Spain.
| | | | | | | | - Marta Montero
- Hematology Department, Hospital 12 de Octubre, Madrid, Spain.
| | - María Poza
- Hematology Department, Hospital 12 de Octubre, Madrid, Spain.
| | - Nieves López
- Hematology Department, Hospital 12 de Octubre, Madrid, Spain.
| | - Gonzalo Carreño
- Hematology Department, Hospital 12 de Octubre, Madrid, Spain.
| | - Ricardo Sánchez
- Hematology Department, Hospital 12 de Octubre, Madrid, Spain.
| | - Teresa Cedena
- Hematology Department, Hospital 12 de Octubre, Complutense University, H12O-CNIO Clinical Research Unit, CIBERONC, Madrid, Spain.
| | | | - Joaquín Martínez-López
- Hematology Department, Hospital 12 de Octubre, Complutense University, H12O-CNIO Clinical Research Unit, CIBERONC, Madrid, Spain.
| | - Rosa Ayala
- Hematology Department, Hospital 12 de Octubre, Complutense University, H12O-CNIO Clinical Research Unit, CIBERONC, Madrid, Spain.
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19
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Hughes CFM, Gallipoli P, Agarwal R. Design, implementation and clinical utility of next generation sequencing in myeloid malignancies: acute myeloid leukaemia and myelodysplastic syndrome. Pathology 2021; 53:328-338. [PMID: 33676768 DOI: 10.1016/j.pathol.2021.01.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/26/2021] [Accepted: 01/26/2021] [Indexed: 12/25/2022]
Abstract
Next generation sequencing (NGS) based technology has contributed enormously to our understanding of the biology of myeloid malignancies including acute myeloid leukaemia (AML) and myelodysplastic syndrome (MDS). Assessment of clinically important mutations by NGS is a powerful tool to define diagnosis, determine prognostic risk, monitor measurable residual disease and uncover predictive mutational markers/therapeutic targets, and is now a routine component in the workup and monitoring of haematological disorders. There are many technical challenges in the design, implementation, analysis and reporting of NGS based results, and expert interpretation is essential. It is vital to distinguish relevant somatic disease associated mutations from those that are known polymorphisms, rare germline variants and clonal haematopoiesis of indeterminate potential (CHIP) associated variants. This review highlights and addresses the technical and biological challenges that should be considered before the implementation of NGS based testing in diagnostic laboratories and seeks to outline the essential and expanding role NGS plays in myeloid malignancies. Broad aspects of NGS panel design and reporting including inherent technological, biological and economic considerations are covered, following which the utility of NGS based testing in AML and MDS are discussed. In current practice, patient care is now strongly shaped by the results of NGS assessment and is considered a vital piece of the puzzle for clinicians as they manage these complex haematological disorders.
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Affiliation(s)
| | - Paolo Gallipoli
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
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20
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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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21
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Diagnostic and therapeutic pitfalls in NPM1-mutated AML: notes from the field. Leukemia 2021; 35:3113-3126. [PMID: 33879827 PMCID: PMC8056374 DOI: 10.1038/s41375-021-01222-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/21/2021] [Accepted: 03/09/2021] [Indexed: 02/02/2023]
Abstract
Mutations of Nucleophosmin (NPM1) are the most common genetic abnormalities in adult acute myeloid leukaemia (AML), accounting for about 30% of cases. NPM1-mutated AML has been recognized as distinct entity in the 2017 World Health Organization (WHO) classification of lympho-haematopoietic neoplasms. WHO criteria allow recognition of this leukaemia entity and its distinction from AML with myelodysplasia-related changes, AML with BCR-ABL1 rearrangement and AML with RUNX1 mutations. Nevertheless, controversial issues include the percentage of blasts required for the diagnosis of NPM1-mutated AML and whether cases of NPM1-mutated myelodysplasia and chronic myelomonocytic leukaemia do exist. Evaluation of NPM1 and FLT3 status represents a major pillar of the European LeukemiaNet (ELN) genetic-based risk stratification model. Moreover, NPM1 mutations are particularly suitable for assessing measurable residual disease (MRD) since they are frequent, stable at relapse and do not drive clonal haematopoiesis. Ideally, combining monitoring of MRD with the ELN prognostication model can help to guide therapeutic decisions. Here, we provide examples of instructive cases of NPM1-mutated AML, in order to provide criteria for the appropriate diagnosis and therapy of this frequent leukaemia entity.
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22
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Short NJ, Zhou S, Fu C, Berry DA, Walter RB, Freeman SD, Hourigan CS, Huang X, Nogueras Gonzalez G, Hwang H, Qi X, Kantarjian H, Ravandi F. Association of Measurable Residual Disease With Survival Outcomes in Patients With Acute Myeloid Leukemia: A Systematic Review and Meta-analysis. JAMA Oncol 2020; 6:1890-1899. [PMID: 33030517 PMCID: PMC7545346 DOI: 10.1001/jamaoncol.2020.4600] [Citation(s) in RCA: 190] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 07/20/2020] [Indexed: 12/21/2022]
Abstract
IMPORTANCE Measurable residual disease (MRD) refers to neoplastic cells that cannot be detected by standard cytomorphologic analysis. In patients with acute myeloid leukemia (AML), determining the association of MRD with survival may improve prognostication and inform selection of efficient clinical trial end points. OBJECTIVE To examine the association between MRD status and disease-free survival (DFS) and overall survival (OS) in patients with AML using scientific literature. DATA SOURCES Clinical studies on AML published between January 1, 2000, and October 1, 2018, were identified via searches of PubMed, Embase, and MEDLINE. STUDY SELECTION Literature search and study screening were performed according to the Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines. Studies that assessed DFS or OS by MRD status in patients with AML were included. Reviews, non-English-language articles, and studies reporting only outcomes after hematopoietic cell transplantation or those with insufficient description of MRD information were excluded. DATA EXTRACTION AND SYNTHESIS Study sample size, median patient age, median follow-up time, MRD detection method, MRD assessment time points, AML subtype, specimen source, and survival outcomes were extracted. Meta-analyses were performed separately for DFS and OS using bayesian hierarchical modeling. MAIN OUTCOMES AND MEASURES Meta-analyses of survival probabilities and hazard ratios (HRs) were conducted for OS and DFS according to MRD status. RESULTS Eighty-one publications reporting on 11 151 patients were included. The average HR for achieving MRD negativity was 0.36 (95% bayesian credible interval [CrI], 0.33-0.39) for OS and 0.37 (95% CrI, 0.34-0.40) for DFS. The estimated 5-year DFS was 64% for patients without MRD and 25% for those with MRD, and the estimated OS was 68% for patients without MRD and 34% for those with MRD. The association of MRD negativity with DFS and OS was significant for all subgroups, with the exception of MRD assessed by cytogenetics or fluorescent in situ hybridization. CONCLUSIONS AND RELEVANCE The findings of this meta-analysis suggest that achievement of MRD negativity is associated with superior DFS and OS in patients with AML. The value of MRD negativity appears to be consistent across age groups, AML subtypes, time of MRD assessment, specimen source, and MRD detection methods. These results support MRD status as an end point that may allow for accelerated evaluation of novel therapies in AML.
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Affiliation(s)
- Nicholas J. Short
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston
| | - Shouhao Zhou
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, Pennsylvania
| | - Chenqi Fu
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, Pennsylvania
| | - Donald A. Berry
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston
| | - Roland B. Walter
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Sylvie D. Freeman
- Institute of Infection and Immunity, University of Birmingham, Birmingham, United Kingdom
| | - Christopher S. Hourigan
- Laboratory of Myeloid Malignancies, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Xuelin Huang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston
| | | | - Hyunsoo Hwang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston
| | - Xinyue Qi
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston
| | - Hagop Kantarjian
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston
| | - Farhad Ravandi
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston
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23
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Daga S, Rosenberger A, Kashofer K, Heitzer E, Quehenberger F, Halbwedl I, Graf R, Krisper N, Prietl B, Höfler G, Reinisch A, Zebisch A, Sill H, Wölfler A. Sensitive and broadly applicable residual disease detection in acute myeloid leukemia using flow cytometry-based leukemic cell enrichment followed by mutational profiling. Am J Hematol 2020; 95:1148-1157. [PMID: 32602117 PMCID: PMC7540028 DOI: 10.1002/ajh.25918] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/18/2020] [Accepted: 06/23/2020] [Indexed: 12/19/2022]
Abstract
Persistent measurable residual disease (MRD) is an increasingly important prognostic marker in acute myeloid leukemia (AML). Currently, MRD is determined by multi-parameter flow cytometry (MFC) or PCR-based methods detecting leukemia-specific fusion transcripts and mutations. However, while MFC is highly operator-dependent and difficult to standardize, PCR-based methods are only available for a minority of AML patients. Here we describe a novel, highly sensitive and broadly applicable method for MRD detection by combining MFC-based leukemic cell enrichment using an optimized combinatorial antibody panel targeting CLL-1, TIM-3, CD123 and CD117, followed by mutational analysis of recurrently mutated genes in AML. In dilution experiments this method showed a sensitivity of 10-4 to 10-5 for residual disease detection. In prospectively collected remission samples this marker combination allowed for a median 67-fold cell enrichment with sufficient DNA quality for mutational analysis using next generation sequencing (NGS) or digital PCR in 39 out of 41 patients. Twenty-one samples (53.8%) tested MRD positive, whereas 18 (46.2%) were negative. With a median follow-up of 559 days, 71.4% of MRD positive (15/21) and 27.8% (5/18) of MRD negative patients relapsed (P = .007). The cumulative incidence of relapse (CIR) was higher for MRD positive patients (5-year CIR: 90.5% vs 28%, P < .001). In multivariate analysis, MRD positivity was a prominent factor for CIR. Thus, MFC-based leukemic cell enrichment using antibodies against CLL-1, TIM-3, CD123 and CD117 followed by mutational analysis allows high sensitive MRD detection and is informative on relapse risk in the majority of AML patients.
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Affiliation(s)
- Shruti Daga
- Division of HematologyMedical University of GrazGrazAustria
- CBmed Center of Biomarker Research in MedicineGrazAustria
| | | | - Karl Kashofer
- Division of PathologyMedical University of GrazGrazAustria
| | - Ellen Heitzer
- Institute of Human GeneticsMedical University of GrazGrazAustria
| | - Franz Quehenberger
- Institute of Medical InformaticsStatistics and Documentation, Medical University of GrazGrazAustria
| | - Iris Halbwedl
- Division of PathologyMedical University of GrazGrazAustria
| | - Ricarda Graf
- Institute of Human GeneticsMedical University of GrazGrazAustria
| | - Nina Krisper
- CBmed Center of Biomarker Research in MedicineGrazAustria
| | - Barbara Prietl
- CBmed Center of Biomarker Research in MedicineGrazAustria
| | - Gerald Höfler
- Division of PathologyMedical University of GrazGrazAustria
| | | | - Armin Zebisch
- Division of HematologyMedical University of GrazGrazAustria
- Otto Loewi Research Center for Vascular Biology, Immunology and Inflammation, Division of PharmacologyMedical University of GrazGrazAustria
| | - Heinz Sill
- Division of HematologyMedical University of GrazGrazAustria
| | - Albert Wölfler
- Division of HematologyMedical University of GrazGrazAustria
- CBmed Center of Biomarker Research in MedicineGrazAustria
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24
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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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25
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Sánchez Prieto I, López Rubio M, Arranz E, Ayala R, Callejas Charavía M, Martín Guerrero Y, Gil Fernández JJ, Valenciano Martínez S, Castilla García L, Argüello Marina M, Aspa Cilleruelo JM, Martínez Vázquez C, García Suárez J. Jumping Translocation in a Patient with Acute Leukemia and Fatal Evolution. Case Rep Oncol 2020; 13:1026-1030. [PMID: 33082743 PMCID: PMC7548953 DOI: 10.1159/000508999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 05/27/2020] [Indexed: 11/19/2022] Open
Abstract
Jumping translocations are uncommon cytogenetic abnormalities in which a segment of a donor chromosome, often 1q, is transferred to two or more receptor chromosomes. We describe the case of a 64-year-old man with a history of acute myeloid leukemia associated with myelodysplastic syndrome, who presented with a relapse of the leukemia and, concomitantly, with the appearance of a jumping translocation involving chromosome 1q. The patient had a poor clinical course without the possibility of performing targeted treatment, and he died 5 months after relapse. Jumping translocations are a reflection of chromosomal instability, and they could be related to epigenetic alterations such as pericentromeric chromatin hypomethylation, telomere shortening, or pathogenic variants of the TP53 gene. The existing data suggests a poor clinical outcome, a high risk of disease progression, and an unfavorable prognosis. More molecular studies are required to gain an in-depth understanding of the genetic mechanism underlying these alterations and their clinical significance and to be able to apply an optimal treatment to patients.
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Affiliation(s)
- Irene Sánchez Prieto
- Department of Hematology, Hospital Universitario Príncipe de Asturias, Alcalá de Henares, Spain
- *Irene Sánchez Prieto, Department of Hematology, Hospital Universitario Príncipe de Asturias, Carretera de Alcalá Meco, s/n, ES–28805 Alcalá de Henares (Spain),
| | - Montserrat López Rubio
- Department of Hematology, Hospital Universitario Príncipe de Asturias, Alcalá de Henares, Spain
| | - Eva Arranz
- Cytogenetic Unit, Department of Hematology, Hospital Universitario de La Princesa, Madrid, Spain
| | - Rosa Ayala
- Department of Hematology, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Marta Callejas Charavía
- Department of Hematology, Hospital Universitario Príncipe de Asturias, Alcalá de Henares, Spain
| | - Yolanda Martín Guerrero
- Department of Hematology, Hospital Universitario Príncipe de Asturias, Alcalá de Henares, Spain
| | - Juan José Gil Fernández
- Department of Hematology, Hospital Universitario Príncipe de Asturias, Alcalá de Henares, Spain
| | | | - Lucía Castilla García
- Department of Hematology, Hospital Universitario Príncipe de Asturias, Alcalá de Henares, Spain
| | - María Argüello Marina
- Department of Hematology, Hospital Universitario Príncipe de Asturias, Alcalá de Henares, Spain
| | | | - Celia Martínez Vázquez
- Department of Hematology, Hospital Universitario Príncipe de Asturias, Alcalá de Henares, Spain
| | - Julio García Suárez
- Department of Hematology, Hospital Universitario Príncipe de Asturias, Alcalá de Henares, Spain
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26
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Next-Generation Sequencing in High-Sensitive Detection of Mutations in Tumors: Challenges, Advances, and Applications. J Mol Diagn 2020; 22:994-1007. [PMID: 32480002 DOI: 10.1016/j.jmoldx.2020.04.213] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/17/2020] [Accepted: 04/23/2020] [Indexed: 02/06/2023] Open
Abstract
Next-generation sequencing (NGS) technologies have come of age as preferred technologies for screening of genomic variants of pathologic and therapeutic potential. Because of their capability for high-throughput and massively parallel sequencing, they can screen for a variety of genomic changes in multiple samples simultaneously. This has made them platforms of choice for clinical testing of solid tumors and hematological malignancies. Consequently, they are increasingly replacing conventional technologies, such as Sanger sequencing and pyrosequencing, expression arrays, real-time PCR, and fluorescence in situ hybridization methods, for routine molecular testing of tumors. However, one limitation of routinely used NGS technologies is the inability to detect low-level genomic variants with high accuracy. This can be attributed to the frequent occurrence of low-level sequencing errors and artifacts in NGS workflow that need specialized approaches to be identified and eliminated. This review focuses on the origins and nature of these artifacts and recent improvements in the NGS technologies to overcome them to facilitate accurate high-sensitive detection of low-level mutations. Potential applications of high-sensitive NGS in oncology and comparisons with non-NGS technologies of similar capabilities are also summarized.
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27
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Flach J, Shumilov E, Wiedemann G, Porret N, Shakhanova I, Bürki S, Legros M, Joncourt R, Pabst T, Bacher U. Clinical potential of introducing next-generation sequencing in patients at relapse of acute myeloid leukemia. Hematol Oncol 2020; 38:425-431. [PMID: 32306411 DOI: 10.1002/hon.2739] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/02/2020] [Accepted: 04/14/2020] [Indexed: 12/19/2022]
Abstract
Relapse of acute myeloid leukemia (AML) remains a major determinant of outcome. A number of molecularly directed treatment options have recently emerged making comprehensive diagnostics an important pillar of clinical decision making at relapse. Acknowledging the high degree of individual genetic variability at AML relapse, next-generation sequencing (NGS) has opened the opportunity for assessing the unique clonal hierarchy of individual AML patients. Knowledge on the genetic makeup of AML is reflected in patient customized treatment strategies thereby providing improved outcomes. For example, the emergence of druggable mutations at relapse enable the use of novel targeted therapies, including FLT3 inhibitors or the recently approved IDH1/2 inhibitors ivosidenib and enasidenib, respectively. Consequently, some patients may undergo novel bridging approaches for reinduction before allogeneic stem cell transplantation, or the identification of an adverse prognostic marker may initiate early donor search. In this review, we summarize the current knowledge of NGS in identifying clonal stability, clonal evolution, and clonal devolution in the context of AML relapse. In light of recent improvements in AML treatment options, NGS-based molecular diagnostics emerges as the basis for molecularly directed treatment decisions in patients at relapse.
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Affiliation(s)
- Johanna Flach
- Department of Hematology and Oncology, Medical Faculty Mannheim of the Heidelberg University, Mannheim, Germany
| | - Evgenii Shumilov
- Department of Hematology and Medical Oncology, University Medicine Göttingen (UMG), Göttingen, Germany
| | - Gertrud Wiedemann
- University Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, Bern, Switzerland.,Center of Laboratory Medicine (ZLM)/University Institute of Clinical Chemistry, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Naomi Porret
- University Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, Bern, Switzerland.,Center of Laboratory Medicine (ZLM)/University Institute of Clinical Chemistry, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Inna Shakhanova
- Department of Nephrology and Rheumatology, University Medicine Göttingen (UMG), Göttingen, Germany
| | - Susanne Bürki
- Department of Medical Oncology, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Myriam Legros
- Center of Laboratory Medicine (ZLM)/University Institute of Clinical Chemistry, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Raphael Joncourt
- University Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, Bern, Switzerland.,Center of Laboratory Medicine (ZLM)/University Institute of Clinical Chemistry, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Thomas Pabst
- Department of Medical Oncology, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Ulrike Bacher
- University Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, Bern, Switzerland.,Center of Laboratory Medicine (ZLM)/University Institute of Clinical Chemistry, Inselspital, Bern University Hospital, Bern, Switzerland
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28
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Onecha E, Ruiz-Heredia Y, Martínez-Cuadrón D, Barragán E, Martinez-Sanchez P, Linares M, Rapado I, Perez-Oteyza J, Magro E, Herrera P, Rojas JL, Gorrochategui J, Villoria J, Boluda B, Sargas C, Ballesteros J, Montesinos P, Martínez-López J, Ayala R. Improving the prediction of acute myeloid leukaemia outcomes by complementing mutational profiling with ex vivo chemosensitivity. Br J Haematol 2020; 189:672-683. [PMID: 32068246 DOI: 10.1111/bjh.16432] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/31/2019] [Accepted: 11/01/2019] [Indexed: 02/06/2023]
Abstract
Refractoriness to induction therapy and relapse after complete remission are the leading causes of death in patients with acute myeloid leukaemia (AML). This study focussed on the prediction of response to standard induction therapy and outcome of patients with AML using a combined strategy of mutational profiling by next-generation sequencing (NGS, n = 190) and ex vivo PharmaFlow testing (n = 74) for the 10 most widely used drugs for AML induction therapy, in a cohort of adult patients uniformly treated according to Spanish PETHEMA guidelines. We identified an adverse mutational profile (EZH2, KMT2A, U2AF1 and/or TP53 mutations) that carries a greater risk of death [hazard ratio (HR): 3·29, P < 0·0001]. A high correlation was found between the ex vivo PharmaFlow results and clinical induction response (69%). Clinical correlation analysis showed that the pattern of multiresistance revealed by ex vivo PharmaFlow identified patients with a high risk of death (HR: 2·58). Patients with mutation status also ran a high risk (HR 4·19), and the risk was increased further in patients with both adverse profiles (HR 4·82). We have developed a new score based on NGS and ex vivo drug testing for AML patients that improves upon current prognostic risk stratification and allows clinicians to tailor treatments to minimise drug resistance.
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Affiliation(s)
- Esther Onecha
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid, Spain.,Hematological Malignancies Clinical Research Unit, CNIO, Madrid, Spain
| | - Yanira Ruiz-Heredia
- Hematological Malignancies Clinical Research Unit, CNIO, Madrid, Spain.,Vivia Biotech, Tres Cantos, Madrid, Spain
| | - David Martínez-Cuadrón
- Department of Hematology, Hospital Universitari i Politècnic La Fe, Valencia, Madrid, Spain
| | - Eva Barragán
- Department of Hematology, Hospital Universitari i Politècnic La Fe, Valencia, Madrid, Spain
| | - Pilar Martinez-Sanchez
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid, Spain.,Hematological Malignancies Clinical Research Unit, CNIO, Madrid, Spain.,Complutense University, Madrid, Spain
| | - María Linares
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid, Spain.,Hematological Malignancies Clinical Research Unit, CNIO, Madrid, Spain.,Complutense University, Madrid, Spain
| | - Inmaculada Rapado
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid, Spain.,Hematological Malignancies Clinical Research Unit, CNIO, Madrid, Spain.,CIBERONC, Instituto Carlos III, Madrid, Spain
| | - Jaime Perez-Oteyza
- Hematology Department, Hospital Universitario Sanchinarro, Madrid, Spain
| | - Elena Magro
- Hematology Department, Hospital Universitario Principe de Asturias, Madrid, Spain
| | - Pilar Herrera
- Hematology Department, Hospital Universitario Ramon y Cajal, Madrid, Spain
| | | | | | | | - Blanca Boluda
- Department of Hematology, Hospital Universitari i Politècnic La Fe, Valencia, Madrid, Spain
| | - Claudia Sargas
- Department of Hematology, Hospital Universitari i Politècnic La Fe, Valencia, Madrid, Spain
| | | | - Pau Montesinos
- Department of Hematology, Hospital Universitari i Politècnic La Fe, Valencia, Madrid, Spain
| | - Joaquín Martínez-López
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid, Spain.,Hematological Malignancies Clinical Research Unit, CNIO, Madrid, Spain.,Complutense University, Madrid, Spain.,CIBERONC, Instituto Carlos III, Madrid, Spain
| | - Rosa Ayala
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid, Spain.,Hematological Malignancies Clinical Research Unit, CNIO, Madrid, Spain.,Complutense University, Madrid, Spain.,CIBERONC, Instituto Carlos III, Madrid, Spain
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29
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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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30
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FERMI: A Novel Method for Sensitive Detection of Rare Mutations in Somatic Tissue. G3-GENES GENOMES GENETICS 2019; 9:2977-2987. [PMID: 31352405 PMCID: PMC6723130 DOI: 10.1534/g3.119.400438] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
With growing interest in monitoring mutational processes in normal tissues, tumor heterogeneity, and cancer evolution under therapy, the ability to accurately and economically detect ultra-rare mutations is becoming increasingly important. However, this capability has often been compromised by significant sequencing, PCR and DNA preparation error rates. Here, we describe FERMI (Fast Extremely Rare Mutation Identification) - a novel method designed to eliminate the majority of these sequencing and library-preparation errors in order to significantly improve rare somatic mutation detection. This method leverages barcoded targeting probes to capture and sequence DNA of interest with single copy resolution. The variant calls from the barcoded sequencing data are then further filtered in a position-dependent fashion against an adaptive, context-aware null model in order to distinguish true variants. As a proof of principle, we employ FERMI to probe bone marrow biopsies from leukemia patients, and show that rare mutations and clonal evolution can be tracked throughout cancer treatment, including during historically intractable periods like minimum residual disease. Importantly, FERMI is able to accurately detect nascent clonal expansions within leukemias in a manner that may facilitate the early detection and characterization of cancer relapse.
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31
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Sánchez R, Ayala R, Martínez-López J. Minimal Residual Disease Monitoring with Next-Generation Sequencing Methodologies in Hematological Malignancies. Int J Mol Sci 2019; 20:ijms20112832. [PMID: 31185671 PMCID: PMC6600313 DOI: 10.3390/ijms20112832] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/05/2019] [Accepted: 06/07/2019] [Indexed: 12/15/2022] Open
Abstract
Ultra-deep next-generation sequencing has emerged in recent years as an important diagnostic tool for the detection and follow-up of tumor burden in most of the known hematopoietic malignancies. Meticulous and high-throughput methods for the lowest possible quantified disease are needed to address the deficiencies of more classical techniques. Precision-based approaches will allow us to correctly stratify each patient based on the minimal residual disease (MRD) after a treatment cycle. In this review, we consider the most prominent ways to approach next-generation sequencing methodologies to follow-up MRD in hematological neoplasms.
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Affiliation(s)
- Ricardo Sánchez
- Servicio de Hematología y Hemoterapia. Hospital Universitario 12 de Octubre, 28041 Madrid, Spain.
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain.
| | - Rosa Ayala
- Servicio de Hematología y Hemoterapia. Hospital Universitario 12 de Octubre, 28041 Madrid, Spain.
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain.
- Universidad Complutense de Madrid (UCM), 28040 Madrid, Spain.
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain.
| | - Joaquín Martínez-López
- Servicio de Hematología y Hemoterapia. Hospital Universitario 12 de Octubre, 28041 Madrid, Spain.
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain.
- Universidad Complutense de Madrid (UCM), 28040 Madrid, Spain.
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain.
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32
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Levine RL, Valk PJM. Next-generation sequencing in the diagnosis and minimal residual disease assessment of acute myeloid leukemia. Haematologica 2019; 104:868-871. [PMID: 30923100 PMCID: PMC6518900 DOI: 10.3324/haematol.2018.205955] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 02/14/2019] [Indexed: 12/19/2022] Open
Affiliation(s)
- Ross L Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA .,Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Peter J M Valk
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA .,Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
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33
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Minimal/Measurable Residual Disease Monitoring in NPM1-Mutated Acute Myeloid Leukemia: A Clinical Viewpoint and Perspectives. Int J Mol Sci 2018; 19:ijms19113492. [PMID: 30404199 PMCID: PMC6274702 DOI: 10.3390/ijms19113492] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 11/02/2018] [Accepted: 11/03/2018] [Indexed: 02/06/2023] Open
Abstract
Acute myeloid leukemia (AML) with NPM1 gene mutations is currently recognized as a distinct entity, due to its unique biological and clinical features. We summarize here the results of published studies investigating the clinical application of minimal/measurable residual disease (MRD) in patients with NPM1-mutated AML, receiving either intensive chemotherapy or hematopoietic stem cell transplantation. Several clinical trials have so far demonstrated a significant independent prognostic impact of molecular MRD monitoring in NPM1-mutated AML and, accordingly, the Consensus Document from the European Leukemia Net MRD Working Party has recently recommended that NPM1-mutated AML patients have MRD assessment at informative clinical timepoints during treatment and follow-up. However, several controversies remain, mainly with regard to the most clinically significant timepoints and the MRD thresholds to be considered, but also with respect to the optimal source to be analyzed, namely bone marrow or peripheral blood samples, and the correlation of MRD with other known prognostic indicators. Moreover, we discuss potential advantages, as well as drawbacks, of newer molecular technologies such as digital droplet PCR and next-generation sequencing in comparison to conventional RQ-PCR to quantify NPM1-mutated MRD. In conclusion, further prospective clinical trials are warranted to standardize MRD monitoring strategies and to optimize MRD-guided therapeutic interventions in NPM1-mutated AML patients.
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