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Zhang L, Deeb G, Deeb KK, Vale C, Peker Barclift D, Papadantonakis N. Measurable (Minimal) Residual Disease in Myelodysplastic Neoplasms (MDS): Current State and Perspectives. Cancers (Basel) 2024; 16:1503. [PMID: 38672585 PMCID: PMC11048433 DOI: 10.3390/cancers16081503] [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: 02/17/2024] [Revised: 04/08/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Myelodysplastic Neoplasms (MDS) have been traditionally studied through the assessment of blood counts, cytogenetics, and morphology. In recent years, the introduction of molecular assays has improved our ability to diagnose MDS. The role of Measurable (minimal) Residual Disease (MRD) in MDS is evolving, and molecular and flow cytometry techniques have been used in several studies. In this review, we will highlight the evolving concept of MRD in MDS, outline the various techniques utilized, and provide an overview of the studies reporting MRD and the correlation with outcomes.
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Affiliation(s)
- Linsheng Zhang
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - George Deeb
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kristin K. Deeb
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Colin Vale
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Deniz Peker Barclift
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nikolaos Papadantonakis
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
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2
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Havelange V, Constantinescu SN. Molecular pathogenesis of myeloproliferative neoplasms: Where do we stand in 2023? Am J Hematol 2023; 98:1512-1516. [PMID: 37635451 DOI: 10.1002/ajh.27062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 08/02/2023] [Indexed: 08/29/2023]
Affiliation(s)
- Violaine Havelange
- Université catholique de Louvain and de Duve Institute, Brussels, Belgium
- Department of Hematology, Cliniques universitaires Saint-Luc, Brussels, Belgium
| | - Stefan N Constantinescu
- Université catholique de Louvain and de Duve Institute, Brussels, Belgium
- Department of Hematology, Cliniques universitaires Saint-Luc, Brussels, Belgium
- Ludwig Institute for Cancer Research Brussels, Brussels, Belgium
- WelBio Department, Wel Research Institute, Wavre, Belgium
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, Oxford University, Oxford, UK
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3
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Calabresi L, Carretta C, Romagnoli S, Rotunno G, Parenti S, Bertesi M, Bartalucci N, Rontauroli S, Chiereghin C, Castellano S, Gentili G, Maccari C, Vanderwert F, Mannelli F, Della Porta M, Manfredini R, Vannucchi AM, Guglielmelli P. Clonal dynamics and copy number variants by single-cell analysis in leukemic evolution of myeloproliferative neoplasms. Am J Hematol 2023; 98:1520-1531. [PMID: 37399248 DOI: 10.1002/ajh.27013] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 07/05/2023]
Abstract
Transformation from chronic (CP) to blast phase (BP) in myeloproliferative neoplasm (MPN) remains poorly characterized, and no specific mutation pattern has been highlighted. BP-MPN represents an unmet need, due to its refractoriness to treatment and dismal outcome. Taking advantage of the granularity provided by single-cell sequencing (SCS), we analyzed paired samples of CP and BP in 10 patients to map clonal trajectories and interrogate target copy number variants (CNVs). Already at diagnosis, MPN present as oligoclonal diseases with varying ratio of mutated and wild-type cells, including cases where normal hematopoiesis was entirely surmised by mutated clones. BP originated from increasing clonal complexity, either on top or independent of a driver mutation, through acquisition of novel mutations as well as accumulation of clones harboring multiple mutations, that were detected at CP by SCS but were missed by bulk sequencing. There were progressive copy-number imbalances from CP to BP, that configured distinct clonal profiles and identified recurrences in genes including NF1, TET2, and BCOR, suggesting an additional level of complexity and contribution to leukemic transformation. EZH2 emerged as the gene most frequently affected by single nucleotide and CNVs, that might result in EZH2/PRC2-mediated transcriptional deregulation, as supported by combined scATAC-seq and snRNA-seq analysis of the leukemic clone in a representative case. Overall, findings provided insights into the pathogenesis of MPN-BP, identified CNVs as a hitherto poorly characterized mechanism and point to EZH2 dysregulation as target. Serial assessment of clonal dynamics might potentially allow early detection of impending disease transformation, with therapeutic implications.
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Affiliation(s)
- Laura Calabresi
- Center Research and Innovation of Myeloproliferative Neoplasms (CRIMM), Azienda Ospedaliera-Universitaria Careggi, Florence, Italy
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Chiara Carretta
- Centre for Regenerative Medicine "S. Ferrari", University of Modena and Reggio Emilia, Modena, Italy
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Simone Romagnoli
- Center Research and Innovation of Myeloproliferative Neoplasms (CRIMM), Azienda Ospedaliera-Universitaria Careggi, Florence, Italy
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Giada Rotunno
- Center Research and Innovation of Myeloproliferative Neoplasms (CRIMM), Azienda Ospedaliera-Universitaria Careggi, Florence, Italy
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Sandra Parenti
- Centre for Regenerative Medicine "S. Ferrari", University of Modena and Reggio Emilia, Modena, Italy
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Matteo Bertesi
- Centre for Regenerative Medicine "S. Ferrari", University of Modena and Reggio Emilia, Modena, Italy
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Niccolò Bartalucci
- Center Research and Innovation of Myeloproliferative Neoplasms (CRIMM), Azienda Ospedaliera-Universitaria Careggi, Florence, Italy
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Sebastiano Rontauroli
- Centre for Regenerative Medicine "S. Ferrari", University of Modena and Reggio Emilia, Modena, Italy
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Sara Castellano
- Centre for Regenerative Medicine "S. Ferrari", University of Modena and Reggio Emilia, Modena, Italy
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Giulia Gentili
- Center Research and Innovation of Myeloproliferative Neoplasms (CRIMM), Azienda Ospedaliera-Universitaria Careggi, Florence, Italy
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Chiara Maccari
- Center Research and Innovation of Myeloproliferative Neoplasms (CRIMM), Azienda Ospedaliera-Universitaria Careggi, Florence, Italy
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Fiorenza Vanderwert
- Center Research and Innovation of Myeloproliferative Neoplasms (CRIMM), Azienda Ospedaliera-Universitaria Careggi, Florence, Italy
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Francesco Mannelli
- Center Research and Innovation of Myeloproliferative Neoplasms (CRIMM), Azienda Ospedaliera-Universitaria Careggi, Florence, Italy
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | | | - Rossella Manfredini
- Centre for Regenerative Medicine "S. Ferrari", University of Modena and Reggio Emilia, Modena, Italy
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Alessandro Maria Vannucchi
- Center Research and Innovation of Myeloproliferative Neoplasms (CRIMM), Azienda Ospedaliera-Universitaria Careggi, Florence, Italy
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Paola Guglielmelli
- Center Research and Innovation of Myeloproliferative Neoplasms (CRIMM), Azienda Ospedaliera-Universitaria Careggi, Florence, Italy
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
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Stuckey R, Bilbao-Sieyro C, Segura-Díaz A, Gómez-Casares MT. Molecular Studies for the Early Detection of Philadelphia-Negative Myeloproliferative Neoplasms. Int J Mol Sci 2023; 24:12700. [PMID: 37628880 PMCID: PMC10454334 DOI: 10.3390/ijms241612700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
JAK2 V617F is the predominant driver mutation in patients with Philadelphia-negative myeloproliferative neoplasms (MPN). JAK2 mutations are also frequent in clonal hematopoiesis of indeterminate potential (CHIP) in otherwise "healthy" individuals. However, the period between mutation acquisition and MPN diagnosis (known as latency) varies widely between individuals, with JAK2 mutations detectable several decades before diagnosis and even from birth in some individuals. Here, we will review the current evidence on the biological factors, such as additional mutations and chronic inflammation, which influence clonal expansion and may determine why some JAK2-mutated individuals will progress to an overt neoplasm during their lifetime while others will not. We will also introduce several germline variants that predispose individuals to CHIP (as well as MPN) identified from genome-wide association studies. Finally, we will explore possible mutation screening or interventions that could help to minimize MPN-associated cardiovascular complications or even delay malignant progression.
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Affiliation(s)
- Ruth Stuckey
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrín, 35019 Las Palmas de Gran Canaria, Spain; (R.S.); (C.B.-S.); (A.S.-D.)
| | - Cristina Bilbao-Sieyro
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrín, 35019 Las Palmas de Gran Canaria, Spain; (R.S.); (C.B.-S.); (A.S.-D.)
- Morphology Department, Universidad de Las Palmas de Gran Canaria, 35016 Las Palmas de Gran Canaria, Spain
| | - Adrián Segura-Díaz
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrín, 35019 Las Palmas de Gran Canaria, Spain; (R.S.); (C.B.-S.); (A.S.-D.)
| | - María Teresa Gómez-Casares
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrín, 35019 Las Palmas de Gran Canaria, Spain; (R.S.); (C.B.-S.); (A.S.-D.)
- Department of Medical Sciences, Universidad de Las Palmas de Gran Canaria, 35016 Las Palmas de Gran Canaria, Spain
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5
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Presence of mutant p53 increases stem-cell frequency and is associated with reduced binding to classical TP53 binding sites in cell lines and primary AMLs. Exp Hematol 2022; 110:39-46. [DOI: 10.1016/j.exphem.2022.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 03/06/2022] [Accepted: 03/09/2022] [Indexed: 11/21/2022]
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6
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From Metcalf to myeloproliferative neoplasms - a personal journey. Exp Hematol 2021; 105:2-9. [PMID: 34706253 DOI: 10.1016/j.exphem.2021.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 11/20/2022]
Abstract
The human myeloproliferative neoplasms constitute a biologically fascinating group of chronic myeloid malignancies. This perspective outlines how a postdoctoral fellowship working in Don Metcalf's unit proved a formative and immensely enjoyable experience for my family and me. It laid the foundation for a subsequent body of work over three decades that revealed the genetic basis of these diseases, defined how these genetic alterations subvert normal hematopoiesis, altered clinical practice, and provided insights of broad biological relevance for cancer and cytokine signaling.
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7
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Mughal TI, Psaila B, DeAngelo DJ, Saglio G, Van Etten RA, Radich JP. Interrogating the molecular genetics of chronic myeloproliferative malignancies for personalized management in 2021. Haematologica 2021; 106:1787-1793. [PMID: 33657787 PMCID: PMC8252942 DOI: 10.3324/haematol.2020.267252] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 01/13/2021] [Indexed: 12/15/2022] Open
Affiliation(s)
- Tariq I Mughal
- Tufts University Medical Center, Boston, MA, USA; University of Buckingham Medical School, Buckingham.
| | - Bethan Psaila
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford
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8
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Royston D, Mead AJ, Psaila B. Application of Single-Cell Approaches to Study Myeloproliferative Neoplasm Biology. Hematol Oncol Clin North Am 2021; 35:279-293. [PMID: 33641869 PMCID: PMC7935666 DOI: 10.1016/j.hoc.2021.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Philadelphia-negative myeloproliferative neoplasms (MPNs) are an excellent tractable disease model of a number of aspects of human cancer biology, including genetic evolution, tissue-associated fibrosis, and cancer stem cells. In this review, we discuss recent insights into MPN biology gained from the application of a number of new single-cell technologies to study human disease, with a specific focus on single-cell genomics, single-cell transcriptomics, and digital pathology.
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Affiliation(s)
- Daniel Royston
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine and NIHR Biomedical Research Centre, University of Oxford, Headley Way, Oxford OX39DS, UK
| | - Adam J Mead
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Biomedical Research Centre, University of Oxford, Headley Way, Oxford OX3 9DS, UK.
| | - Bethan Psaila
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Biomedical Research Centre, University of Oxford, Headley Way, Oxford OX3 9DS, UK
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9
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Zhang Y, Xie A, Quan F, Hou X, Liao J, Zhu S, Pang L, Liang X, Zhu X, Cheng P, Li X, Xiao Y. Identifying bifurcated paths with differential function impact in glioblastomas evolution. Int J Cancer 2020; 147:3139-3151. [PMID: 32875565 DOI: 10.1002/ijc.33276] [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: 12/17/2019] [Revised: 08/19/2020] [Accepted: 08/19/2020] [Indexed: 11/10/2022]
Abstract
The evolutionary dynamics of human cancers has been investigated popularly and several bifurcated paths in cancer evolutionary trajectories are revealed to be with differential outcomes and phenotypes. However, whether such bifurcated paths exist in glioblastoma (GBM) remains unclear. In 385 GBM samples, through determining the clonal status of cancer driver events and inferring their temporal order, we constructed a temporal map of evolutionary trajectories at the patient population level. By investigating the differential impact on clinical outcome, we identified four key bifurcated paths, namely, "chromosome 10 copy number loss (ie, 10 loss) → chromosome 19 copy number gain (ie, 19 gain): 10 loss → 13q loss"; "10 loss → 19 gain: 10 loss → 15q loss"; "10 loss → 19 gain: 10 loss → 6q loss" and "10 loss → 19 gain: 10 loss → 16q loss". They formed a core multibranches path, with 10 loss being regarded as the common earliest event followed by 19 gain and four other departure events (13q loss, 15q loss, 6q loss and 16q loss), which may account for their difference in genome instability and patient survival time. Compared to "10 loss → 19 gain", the patients with "10 loss → 13q loss" had higher telomerase activity. Notably, there were obvious discrepancies in immune activity and immune cell infiltration level between patients with "10 loss → 13q/16q loss" and "10 loss → 19 gain", highlighting the bifurcated paths' effect on tumor immune microenvironment. In summary, our study identifies four key bifurcated paths in GBM for the first time, suggesting the feasibility of patient stratification and prognosis prediction based on key bifurcated paths.
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Affiliation(s)
- Yong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Aimin Xie
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Fei Quan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Xiaobo Hou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Jianlong Liao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Shiwei Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Lin Pang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Xin Liang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Xiaojing Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Peng Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China.,Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, Harbin, Heilongjiang, China
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China.,Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, Harbin, Heilongjiang, China
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Kjær L. Clonal Hematopoiesis and Mutations of Myeloproliferative Neoplasms. Cancers (Basel) 2020; 12:cancers12082100. [PMID: 32731609 PMCID: PMC7464548 DOI: 10.3390/cancers12082100] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/17/2020] [Accepted: 07/27/2020] [Indexed: 12/18/2022] Open
Abstract
Myeloproliferative neoplasms (MPNs) are associated with the fewest number of mutations among known cancers. The mutations propelling these malignancies are phenotypic drivers providing an important implement for diagnosis, treatment response monitoring, and gaining insight into the disease biology. The phenotypic drivers of Philadelphia chromosome negative MPN include mutations in JAK2, CALR, and MPL. The most prevalent driver mutation JAK2V617F can cause disease entities such as essential thrombocythemia (ET) and polycythemia vera (PV). The divergent development is considered to be influenced by the acquisition order of the phenotypic driver mutation relative to other MPN-related mutations such as TET2 and DNMT3A. Advances in molecular biology revealed emergence of clonal hematopoiesis (CH) to be inevitable with aging and associated with risk factors beyond the development of blood cancers. In addition to its well-established role in thrombosis, the JAK2V617F mutation is particularly connected to the risk of developing cardiovascular disease (CVD), a pertinent issue, as deep molecular screening has revealed the prevalence of the mutation to be much higher in the background population than previously anticipated. Recent findings suggest a profound under-diagnosis of MPNs, and considering the impact of CVD on society, this calls for early detection of phenotypic driver mutations and clinical intervention.
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Affiliation(s)
- Lasse Kjær
- Department of Hematology, Zealand University Hospital, Vestermarksvej 7-9, DK-4000 Roskilde, Denmark
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11
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Menssen AJ, Walter MJ. Genetics of progression from MDS to secondary leukemia. Blood 2020; 136:50-60. [PMID: 32430504 PMCID: PMC7332895 DOI: 10.1182/blood.2019000942] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 11/27/2019] [Indexed: 12/14/2022] Open
Abstract
Our understanding of the genetics of acute myeloid leukemia (AML) development from myelodysplastic syndrome (MDS) has advanced significantly as a result of next-generation sequencing technology. Although differences in cell biology and maturation exist between MDS and AML secondary to MDS, these 2 diseases are genetically related. MDS and secondary AML cells harbor mutations in many of the same genes and functional categories, including chromatin modification, DNA methylation, RNA splicing, cohesin complex, transcription factors, cell signaling, and DNA damage, confirming that they are a disease continuum. Differences in the frequency of mutated genes in MDS and secondary AML indicate that the order of mutation acquisition is not random during progression. In almost every case, disease progression is associated with clonal evolution, typically defined by the expansion or emergence of a subclone with a unique set of mutations. Monitoring tumor burden and clonal evolution using sequencing provides advantages over using the blast count, which underestimates tumor burden, and could allow for early detection of disease progression prior to clinical deterioration. In this review, we outline advances in the study of MDS to secondary AML progression, with a focus on the genetics of progression, and discuss the advantages of incorporating molecular genetic data in the diagnosis, classification, and monitoring of MDS to secondary AML progression. Because sequencing is becoming routine in the clinic, ongoing research is needed to define the optimal assay to use in different clinical situations and how the data can be used to improve outcomes for patients with MDS and secondary AML.
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Affiliation(s)
- Andrew J Menssen
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO; and
| | - Matthew J Walter
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO; and
- Siteman Cancer Center, Washington University, St. Louis, MO
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12
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Absence of damaging effects of stem cell donation in unrelated donors assessed by FISH and gene variance screening. Bone Marrow Transplant 2020; 55:1290-1296. [PMID: 32440014 DOI: 10.1038/s41409-020-0945-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/06/2020] [Accepted: 05/04/2020] [Indexed: 11/08/2022]
Abstract
ASTRACT Granulocyte-Colony-Stimulating factor (G-CSF) is currently the standard mobilising agent for peripheral blood stem cell (PBSC) donation. Concerns that it may trigger chromosome aberrations similar to those observed in leukaemia patients were refuted but long-term effects of G-CSF mobilisation on genome integrity remains unclear. In the setting of a multi-centre clinical trial we screened blood samples from 50 PBSC donors at cellular and gene level for aberrations common in haematological malignancies using fluorescence in situ hybridisation (FISH) and next generation sequencing (NGS) assays. Analysis of samples collected before, on the day of donation, 90 and 180 days after G-CSF admission confirmed the absence of short-term effects in PBSC donors on both quiescent and dividing cells. This data did not differ from the results of 50 individuals tested 3-5 years after bone marrow donation and 50 healthy persons. NGS using a panel targeting 54 genes recurrently affected in myeloid disorders (TruSight Myeloid panel, Illumina) showed that the gene profiles of samples from 48 PBSC donors remained stable throughout the study period. These data strongly indicate absence of detrimental effects on the genome integrity caused by PBSC donation.
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13
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Teets EM, Gregory C, Shaffer J, Blachly JS, Blaser BW. Quantifying Hematopoietic Stem Cell Clonal Diversity by Selecting Informative Amplicon Barcodes. Sci Rep 2020; 10:2153. [PMID: 32034234 PMCID: PMC7005852 DOI: 10.1038/s41598-020-59119-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 01/24/2020] [Indexed: 11/09/2022] Open
Abstract
Hematopoietic stem cells (HSCs) are functionally and genetically diverse and this diversity decreases with age and disease. Numerous systems have been developed to quantify HSC diversity by genetic barcoding, but no framework has been established to empirically validate barcode sequences. Here we have developed an analytical framework, Selection of informative Amplicon Barcodes from Experimental Replicates (SABER), that identifies barcodes that are unique among a large set of experimental replicates. Amplicon barcodes were sequenced from the blood of 56 adult zebrafish divided into training and validation sets. Informative barcodes were identified and samples with a high fraction of informative barcodes were chosen by bootstrapping. There were 4.2 ± 1.8 barcoded HSC clones per sample in the training set and 3.5 ± 2.1 in the validation set (p = 0.3). SABER reproducibly quantifies functional HSCs and can accommodate a wide range of experimental group sizes. Future large-scale studies aiming to understand the mechanisms of HSC clonal evolution will benefit from this new approach to identifying informative amplicon barcodes.
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Affiliation(s)
- Emily M Teets
- The Ohio State University College of Medicine, Department of Medicine, Division of Hematology, The Ohio State University Comprehensive Cancer Center, Ohio, USA
| | - Charles Gregory
- The Ohio State University College of Medicine, Department of Medicine, Division of Hematology, The Ohio State University Comprehensive Cancer Center, Ohio, USA
| | - Jami Shaffer
- The Ohio State University College of Medicine, Department of Medicine, Division of Hematology, The Ohio State University Comprehensive Cancer Center, Ohio, USA
| | - James S Blachly
- The Ohio State University College of Medicine, Department of Medicine, Division of Hematology, The Ohio State University Comprehensive Cancer Center, Ohio, USA
- The Ohio State University College of Medicine, Department of Biomedical Informatics, Ohio, USA
| | - Bradley W Blaser
- The Ohio State University College of Medicine, Department of Medicine, Division of Hematology, The Ohio State University Comprehensive Cancer Center, Ohio, USA.
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14
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Clonal competition within complex evolutionary hierarchies shapes AML over time. Nat Commun 2020; 11:579. [PMID: 32024830 PMCID: PMC7002407 DOI: 10.1038/s41467-019-14106-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 12/17/2019] [Indexed: 12/21/2022] Open
Abstract
Clonal heterogeneity and evolution has major implications for disease progression and relapse in acute myeloid leukemia (AML). To model clonal dynamics in vivo, we serially transplanted 23 AML cases to immunodeficient mice and followed clonal composition for up to 15 months by whole-exome sequencing of 84 xenografts across two generations. We demonstrate vast changes in clonality that both progress and reverse over time, and define five patterns of clonal dynamics: Monoclonal, Stable, Loss, Expansion and Burst. We also show that subclonal expansion in vivo correlates with a more adverse prognosis. Furthermore, clonal expansion enabled detection of very rare clones with AML driver mutations that were undetectable by sequencing at diagnosis, demonstrating that the vast majority of AML cases harbor multiple clones already at diagnosis. Finally, the rise and fall of related clones enabled deconstruction of the complex evolutionary hierarchies of the clones that compete to shape AML over time. Clonal evolution and heterogeneity has strong implications for treatment response in acute myeloid leukemia. Here, the authors use patient derived in vivo modelling to highlight the complex clonal and evolutionary dynamics underpinning acute myeloid leukemia progression.
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