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Lim J, Chin V, Fairfax K, Moutinho C, Suan D, Ji H, Powell JE. Transitioning single-cell genomics into the clinic. Nat Rev Genet 2023:10.1038/s41576-023-00613-w. [PMID: 37258725 DOI: 10.1038/s41576-023-00613-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2023] [Indexed: 06/02/2023]
Abstract
The use of genomics is firmly established in clinical practice, resulting in innovations across a wide range of disciplines such as genetic screening, rare disease diagnosis and molecularly guided therapy choice. This new field of genomic medicine has led to improvements in patient outcomes. However, most clinical applications of genomics rely on information generated from bulk approaches, which do not directly capture the genomic variation that underlies cellular heterogeneity. With the advent of single-cell technologies, research is rapidly uncovering how genomic data at cellular resolution can be used to understand disease pathology and mechanisms. Both DNA-based and RNA-based single-cell technologies have the potential to improve existing clinical applications and open new application spaces for genomics in clinical practice, with oncology, immunology and haematology poised for initial adoption. However, challenges in translating cellular genomics from research to a clinical setting must first be overcome.
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Affiliation(s)
- Jennifer Lim
- Cellular Science, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Department of Oncology, St George Hospital, Sydney, NSW, Australia
- The Kinghorn Cancer Centre, St Vincent's Hospital, Sydney, NSW, Australia
- Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Venessa Chin
- Cellular Science, Garvan Institute of Medical Research, Sydney, NSW, Australia
- The Kinghorn Cancer Centre, St Vincent's Hospital, Sydney, NSW, Australia
- Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Kirsten Fairfax
- School of Medicine, University of Tasmania, Hobart, Australia
| | - Catia Moutinho
- Cellular Science, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Dan Suan
- Cellular Science, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Westmead Clinical School, University of Sydney, Sydney, NSW, Australia
| | - Hanlee Ji
- School of Medicine, Stanford University, Palo Alto, CA, USA
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
| | - Joseph E Powell
- Cellular Science, Garvan Institute of Medical Research, Sydney, NSW, Australia.
- Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.
- UNSW Cellular Genomics Futures Institute, University of New South Wales, Sydney, NSW, Australia.
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2
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Zhao SY, Xu ZF, Qin TJ, Qu SQ, Li CW, Jia YJ, Pan LJ, Li B, Gao QY, Jiao M, Huang HJ, Xiao ZJ. [Risk factors for leukemia transformation in patients with myelodysplastic syndromes]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2022; 43:818-825. [PMID: 36709195 PMCID: PMC9669629 DOI: 10.3760/cma.j.issn.0253-2727.2022.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Indexed: 01/30/2023]
Abstract
Objective: To explore the risk factors in leukemia transformation (LT) in those with myelodysplastic syndromes (MDS) . Methods: From January 2012 to December 2020,data on 320 patients with newly diagnosed primary MDS were gathered from the MDS center. The clinical features and molecular characteristics are explored. Additionally, a retrospective analysis of risk factors for the development of acute leukemia from MDS was done. Results: The median follow-up was13.6 (0.4-107.3) months. 23.4% (75/320) of the MDS patients had LT group. Significant differences between the LT group and non-LT group can be seen in age (P<0.001) , bone marrow blast percentage (P<0.001) , bone marrow fibrosis (P=0.046) , WHO classification (P<0.001) , IPSS-R (P<0.001) and IPSS-R karyotype group (P=0.001) . The median number of mutation of LT group was 1 (1, 3) , that in non-LT group was 1 (0, 2) ,which had a statistical difference (P=0.003) .At the time of the initial diagnosis of MDS, the LT group had higher rates of the TP53 mutation (P=0.034) , DNMT3A mutation (P=0.026) , NRAS mutation (P=0.027) and NPM1 mutation (P=0.017) . Compared with the mutations at first diagnosis and LT of six patients, the number of mutations increased and the variant allele frequencies (VAF) increased significantly in LT patients. Higher bone marrow blast percentage (Refer to <5% , 5% -10% : HR=4.587, 95% CI 2.214 to 9.504, P<0.001, >10% : HR=9.352, 95% CI 4.049 to 21.600, P<0.001) , IPSS-R cytogenetic risk groups (HR=2.603, 95% CI 1.229-5.511, P=0.012) , DNMT3A mutation (HR=4.507, 95% CI 1.889-10.753, P=0.001) , and NPM1 mutation (HR=3.341, 95% CI 1.164-9.591, P=0.025) were all independently associated with LT in MDS patients, according to results of multivariate Cox regression. Conclusion: Bone marrow blast percentage, IPSS-R cytogenetic risk groups, DNMT3A mutation, and NPM1 mutation are independent risk factors in LT for MDS patients.
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Affiliation(s)
- S Y Zhao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020,China
| | - Z F Xu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020,China
| | - T J Qin
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020,China
| | - S Q Qu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020,China
| | - C W Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020,China
| | - Y J Jia
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020,China
| | - L J Pan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020,China
| | - B Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020,China
| | - Q Y Gao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020,China
| | - M Jiao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020,China
| | - H J Huang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020,China
| | - Z J Xiao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020,China
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3
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Comparative analysis of Decitabine intensified BUCY2 and BUCY2 conditioning regimen for high-risk MDS patients undergoing allogeneic hematopoietic stem cell transplantation. Bone Marrow Transplant 2022; 57:1063-1071. [PMID: 35459877 DOI: 10.1038/s41409-022-01645-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 03/01/2022] [Accepted: 03/15/2022] [Indexed: 11/08/2022]
Abstract
The optimal conditioning regimen for high-risk myelodysplastic syndrome (MDS) patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT) remains elusive. This study aimed to explore the anti-leukemic efficacy and toxicity of Decitabine (Dec, 20 mg/m2/day, day -11 to -7) intensified BUCY2 vs. traditional regimen in high-risk MDS population. We retrospectively evaluated 93 consecutive high-risk MDS patients undergoing allo-HSCT in our institution, comparing discrepancies in clinical characteristics and outcomes between cases using Dec-intensified BUCY2 (n = 52) and traditional BUCY2 regimen (n = 41). Three-year cumulative incidence of relapse after Dec-intensified BUCY2 conditioning was remarkably lower than that of patients using BUCY2 regimen (20.2% vs. 39.0%, p = 0.034). Overall survival and disease-free survival at 3 years for Dec-intensified BUCY2 group were 70.2% and 64.9%, respectively, which were significantly improved when compared with BUCY2 group (51.1% and 43.9%, p = 0.031 and p = 0.027). Furthermore, overall survival and disease-free survival for MDS cases receiving cytoreduction therapy were dramatically better than patients in non-cytoreduction group (p = 0.041, p = 0.047). In summary, the Dec-intensified conditioning regimen could be effective and feasible, providing prominent recurrence control with moderate toxicity for high-risk MDS patients. These patients might also benefit from pre-transplant cytoreductive therapeutic schedules. Larger randomized controlled trials are still needed to further confirm these conclusions.
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4
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Dermawan JK, Wensel C, Visconte V, Maciejewski JP, Cook JR, Bosler DS. Clinically Significant CUX1 Mutations Are Frequently Subclonal and Common in Myeloid Disorders With a High Number of Co-mutated Genes and Dysplastic Features. Am J Clin Pathol 2022; 157:586-594. [PMID: 34661647 DOI: 10.1093/ajcp/aqab157] [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: 06/14/2021] [Accepted: 08/11/2021] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES CUX1 mutations have been reported in myeloid neoplasms. We aimed to characterize the mutational landscape, clonal architecture, and clinical characteristics of myeloid disorders with CUX1 variants. METHODS We reviewed data from a targeted 62-gene panel with CUX1 variants. Variants were classified as of strong or potential clinical significance (tier I/tier II) or of unknown significance (VUS). RESULTS CUX1 variants were identified in 169 cases. The 49 tier I/tier II variants were found in older patients (mean age, 71 vs 60 years old) and predominantly inactivating alterations, while the 120 VUS cases were missense mutations. Monosomy 7/deletion 7q was more common in tier I/tier II cases. Co-mutations were detected in 96% of tier I/tier II cases (average, 3.7/case) but in only 61% of VUS cases (average, 1.5/case). Tier I/tier II CUX1 variants tend to be subclonal to co-mutations (ASXL1, SF3B1, SRSF2, TET2). Among myeloid disorders, tier I/tier II cases were more frequently diagnosed with myelodysplastic syndromes and had a higher number of bone marrow dysplastic lineages. CONCLUSIONS CUX1 mutations are seen with adverse prognostic features and could be a late clonal evolutional event of myeloid disorders. The differences between CUX1 tier I/tier II and VUS underscore the importance of accurate variant classification in reporting of multigene panels.
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Affiliation(s)
- Josephine K Dermawan
- Robert J. Tomsich Pathology & Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Christine Wensel
- Robert J. Tomsich Pathology & Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Valeria Visconte
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - James R Cook
- Robert J. Tomsich Pathology & Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - David S Bosler
- Robert J. Tomsich Pathology & Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
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5
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New insights into Human Hematopoietic Stem and Progenitor Cells via Single-Cell Omics. Stem Cell Rev Rep 2022; 18:1322-1336. [PMID: 35318612 PMCID: PMC8939482 DOI: 10.1007/s12015-022-10330-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2022] [Indexed: 10/25/2022]
Abstract
Residing at the apex of the hematopoietic hierarchy, hematopoietic stem and progenitor cells (HSPCs) give rise to all mature blood cells. In the last decade, significant progress has been made in single-cell RNA sequencing as well as multi-omics technologies that have facilitated elucidation of the heterogeneity of previously defined human HSPCs. From the embryonic stage through the adult stage to aging, single-cell studies have enabled us to trace the origins of hematopoietic stem cells (HSCs), demonstrating different hematopoietic differentiation during development, as well as identifying novel cell populations. In both hematological benign diseases and malignancies, single-cell omics technologies have begun to reveal tissue heterogeneity and have permitted mapping of microenvironmental ecosystems and tracking of cell subclones, thereby greatly broadening our understanding of disease development. Furthermore, advances have also been made in elucidating the molecular mechanisms for relapse and identifying therapeutic targets of hematological disorders and other non-hematological diseases. Extensive exploration of hematopoiesis at the single-cell level may thus have great potential for broad clinical applications of HSPCs, as well as disease prognosis.
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6
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Martín-Izquierdo M, Abáigar M, Hernández-Sánchez JM, Tamborero D, López-Cadenas F, Ramos F, Lumbreras E, Madinaveitia-Ochoa A, Megido M, Labrador J, Sánchez-Real J, Olivier C, Dávila J, Aguilar C, Rodríguez JN, Martín-Nuñez G, Santos-Mínguez S, Miguel-García C, Benito R, Díez-Campelo M, Hernández-Rivas JM. Co-occurrence of cohesin complex and Ras signaling mutations during progression from myelodysplastic syndromes to secondary acute myeloid leukemia. Haematologica 2021; 106:2215-2223. [PMID: 32675227 PMCID: PMC8327724 DOI: 10.3324/haematol.2020.248807] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 07/14/2020] [Indexed: 01/01/2023] Open
Abstract
Myelodysplastic syndromes (MDS) are hematological disorders at high risk of progression to secondary acute myeloid leukemia (sAML). However, the mutational dynamics and clonal evolution underlying disease progression are poorly understood at present. To elucidate the mutational dynamics of pathways and genes occurring during the evolution to sAML, next generation sequencing was performed on 84 serially paired samples of MDS patients who developed sAML (discovery cohort) and 14 paired samples from MDS patients who did not progress to sAML during follow-up (control cohort). Results were validated in an independent series of 388 MDS patients (validation cohort). We used an integrative analysis to identify how mutations, alone or in combination, contribute to leukemic transformation. The study showed that MDS progression to sAML is characterized by greater genomic instability and the presence of several types of mutational dynamics, highlighting increasing (STAG2) and newly-acquired (NRAS and FLT3) mutations. Moreover, we observed cooperation between genes involved in the cohesin and Ras pathways in 15-20% of MDS patients who evolved to sAML, as well as a high proportion of newly acquired or increasing mutations in the chromatin-modifier genes in MDS patients receiving a disease-modifying therapy before their progression to sAML.
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Affiliation(s)
- Marta Martín-Izquierdo
- Institute of Biomedical Research of Salamanca, Cancer Research Center-University of Salamanca, Spain
| | - María Abáigar
- Institute of Biomedical Research of Salamanca, Cancer Research Center-University of Salamanca, Spain
| | - Jesús M Hernández-Sánchez
- Institute of Biomedical Research of Salamanca, Cancer Research Center-University of Salamanca, Spain
| | - David Tamborero
- Hospital del Mar Medical Research Institute (IMIM), Barcelona and Karolinska Institutet, Stockholm
| | - Félix López-Cadenas
- University of Salamanca, IBSAL, Hematology, Hospital Clinico Universitario, Salamanca, Spain
| | - Fernando Ramos
- Hematology, Hospital Universitario de León, Institute of Biomedicine (IBIOMED), Spain
| | - Eva Lumbreras
- Institute of Biomedical Research of Salamanca, Cancer Research Center-University of Salamanca, Spain
| | | | - Marta Megido
- Hematology, Hospital del Bierzo, Ponferrada, León, Spain
| | - Jorge Labrador
- Hematology, Hospital Universitario de Burgos, Burgos, Spain
| | - Javier Sánchez-Real
- Hematology, Hospital Universitario de León, Institute of Biomedicine (IBIOMED), Spain
| | | | - Julio Dávila
- Hematology, Hospital Nuestra Señora de Sónsoles, Ávila, Spain
| | | | | | | | - Sandra Santos-Mínguez
- Institute of Biomedical Research of Salamanca, Cancer Research Center-University of Salamanca, Spain
| | - Cristina Miguel-García
- Institute of Biomedical Research of Salamanca, Cancer Research Center-University of Salamanca, Spain
| | - Rocío Benito
- Institute of Biomedical Research of Salamanca, Cancer Research Center-University of Salamanca, Spain
| | - María Díez-Campelo
- University of Salamanca, IBSAL, Hematology, Hospital Clínico Universitario, Salamanca, Spain
| | - Jesús M Hernández-Rivas
- Institute of Biomedical Research of Salamanca, Cancer Research Center-University of Salamanca, Spain
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7
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Stauber J, Greally JM, Steidl U. Preleukemic and leukemic evolution at the stem cell level. Blood 2021; 137:1013-1018. [PMID: 33275656 PMCID: PMC7907728 DOI: 10.1182/blood.2019004397] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 12/01/2020] [Indexed: 02/07/2023] Open
Abstract
Hematological malignancies are an aggregate of diverse populations of cells that arise following a complex process of clonal evolution and selection. Recent approaches have facilitated the study of clonal populations and their evolution over time across multiple phenotypic cell populations. In this review, we present current concepts on the role of clonal evolution in leukemic initiation, disease progression, and relapse. We highlight recent advances and unanswered questions about the contribution of the hematopoietic stem cell population to these processes.
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Affiliation(s)
- Jacob Stauber
- Albert Einstein College of Medicine-Montefiore Health System, The Bronx, NY
| | - John M Greally
- Albert Einstein College of Medicine-Montefiore Health System, The Bronx, NY
| | - Ulrich Steidl
- Albert Einstein College of Medicine-Montefiore Health System, The Bronx, NY
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8
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Bisulfite-free epigenomics and genomics of single cells through methylation-sensitive restriction. Commun Biol 2021; 4:153. [PMID: 33526904 PMCID: PMC7851132 DOI: 10.1038/s42003-021-01661-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 01/06/2021] [Indexed: 12/15/2022] Open
Abstract
Single-cell multi-omics are powerful means to study cell-to-cell heterogeneity. Here, we present a single-tube, bisulfite-free method for the simultaneous, genome-wide analysis of DNA methylation and genetic variants in single cells: epigenomics and genomics of single cells analyzed by restriction (epi-gSCAR). By applying this method, we obtained DNA methylation measurements of up to 506,063 CpGs and up to 1,244,188 single-nucleotide variants from single acute myeloid leukemia-derived cells. We demonstrate that epi-gSCAR generates accurate and reproducible measurements of DNA methylation and allows to differentiate between cell lines based on the DNA methylation and genetic profiles.
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9
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Hebeda K, Boudova L, Beham-Schmid C, Orazi A, Kvasnicka HM, Gianelli U, Tzankov A. Progression, transformation, and unusual manifestations of myelodysplastic syndromes and myelodysplastic-myeloproliferative neoplasms: lessons learned from the XIV European Bone Marrow Working Group Course 2019. Ann Hematol 2020; 100:117-133. [PMID: 33128619 DOI: 10.1007/s00277-020-04307-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 10/15/2020] [Indexed: 11/30/2022]
Abstract
Disease progression in myelodysplastic syndromes (MDS) and myelodysplastic-myeloproliferative neoplasms (MDS/MPN) is a major source of mortality. The European Bone Marrow Working Group organized a dedicated workshop to address MDS and MDS/MPN progression, and myeloid neoplasms with histiocytic and lymphoblastic outgrowths in 2019 in Frankfurt, Germany. In this report, we summarize clinical, histopathological, and molecular features of 28 cases. Most cases illustrate that prognostic mutational profiles change during follow-up due to accumulation of high-risk mutations in the trunk clone, and that results from repeated molecular testing can often explain the clinical progression, suggesting that regular genetic testing may predict transformation by early detection of aggressive clones. Importantly, identical mutations can be linked to different clinical behaviors or risks of fibrotic progression and/or transformation in a context-dependent manner, i.e., MDS or MDS/MPN. Moreover, the order of mutational acquisition and the involved cell lineages matter. Several cases exemplify that histiocytic outgrowths in myeloid neoplasms are usually accompanied by a more aggressive clinical course and may be considered harbinger of disease progression. Exceptionally, lymphoblastic transformations can be seen. As best estimable, the histiocytic and lymphoblastic compounds in all occasions were clonally related to the myeloid compound and-where studied-displayed genomic alterations of, e.g., transcription factor genes or genes involved in MAPK signaling that might be mechanistically linked to the respective type of non-myeloid outgrowth.
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Affiliation(s)
- Konnie Hebeda
- Department of Pathology, University Medical Center Utrecht, Utrecht, Netherlands
| | | | | | - Attilio Orazi
- Department of Pathology, Texas Tech Health Sciences Center El Paso, El Paso, TX, USA
| | | | - Umberto Gianelli
- Pathology Unit, Department of Pathophysiology and Transplantation, University of Milan and Fondazione IRCCS, Ca' Granda-Maggiore Policlinico, Milan, Italy
| | - Alexandar Tzankov
- Institute of Medical Genetics and Pathology, University Hospital of Basel, Schoenbeinstrasse 40, CH-4031, Basel, Switzerland.
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10
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Shoumariyeh K, Hussung S, Niemöller C, Bleul S, Veratti P, Follo M, Riba J, Philipp U, Palmer JM, Pfeifer D, Pantic M, Meggendorfer M, Hackanson B, Finke J, Haferlach T, Duyster J, Miething C, Becker H, von Bubnoff N. Blastic transformation of BCR-ABL1 positive chronic myeloid leukaemia through acquisition of CBFB-MYH11 and mutant KIT. Br J Haematol 2020; 190:e339-e343. [PMID: 32579287 DOI: 10.1111/bjh.16904] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Khalid Shoumariyeh
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), Freiburg, Germany
| | - Saskia Hussung
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Christoph Niemöller
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sabine Bleul
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Pia Veratti
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marie Follo
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Julian Riba
- Department of Microsystems Engineering - IMTEK, University of Freiburg, Freiburg, Germany
| | - Ulrike Philipp
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Juliane M Palmer
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dietmar Pfeifer
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Milena Pantic
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | - Björn Hackanson
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Department of Hematology/Oncology, University Medical Center Augsburg, Augsburg, Germany
| | - Jürgen Finke
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | - Justus Duyster
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), Freiburg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Cornelius Miething
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), Freiburg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Heiko Becker
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Nikolas von Bubnoff
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Department of Hematology and Oncology, Medical Center, University of Schleswig-Holstein, Lubeck, Germany
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11
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Simonsen AT, Bill M, Rosenberg CA, Hansen MH, Møller PL, Kjeldsen E, Johansen KD, Ommen HB, Nederby L, Aggerholm A, Hokland P, Ludvigsen M. Unraveling clonal heterogeneity at the stem cell level in myelodysplastic syndrome: In pursuit of cell subsets driving disease progression. Leuk Res 2020; 92:106350. [PMID: 32334198 DOI: 10.1016/j.leukres.2020.106350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/13/2020] [Accepted: 03/16/2020] [Indexed: 02/02/2023]
Affiliation(s)
| | - Marie Bill
- Department of Hematology, Aarhus University Hospital, Aarhus, Denmark
| | | | - Marcus Høy Hansen
- Department of Hematology, Aarhus University Hospital, Aarhus, Denmark
| | - Peter Loof Møller
- Department of Hematology, Aarhus University Hospital, Aarhus, Denmark
| | - Eigil Kjeldsen
- Department of Hematology, Aarhus University Hospital, Aarhus, Denmark
| | | | - Hans Beier Ommen
- Department of Hematology, Aarhus University Hospital, Aarhus, Denmark
| | - Line Nederby
- Department of Clinical Immunology and Biochemistry, Lillebaelt Hospital, Vejle, Denmark
| | - Anni Aggerholm
- Department of Hematology, Aarhus University Hospital, Aarhus, Denmark
| | - Peter Hokland
- Department of Hematology, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Maja Ludvigsen
- Department of Hematology, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
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12
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Calleja A, Yun S, Moreilhon C, Karsenti JM, Gastaud L, Mannone L, Komrokji R, Al Ali N, Dadone-Montaudie B, Robert G, Auberger P, Raynaud S, Sallman DA, Cluzeau T. Clonal selection in therapy-related myelodysplastic syndromes and acute myeloid leukemia under azacitidine treatment. Eur J Haematol 2020; 104:488-498. [PMID: 31990086 DOI: 10.1111/ejh.13390] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/14/2020] [Accepted: 01/16/2020] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Therapy-related myelodysplastic syndrome and acute myeloid leukemia (t-MDS/AML) are defined as complications of previous cytotoxic therapy. Azacitidine (AZA), a hypomethylating agent, has showed activity in t-MDS/AML. OBJECTIVES We evaluated the clonal dynamics of AZA-treated t-MDS/AML. METHODS We collected bone marrow samples, at diagnosis and during treatment, from AZA-treated t-MDS/AML patients. NGS on 19 myeloid genes was performed, and candidate mutations with a variant allele frequency >5% were selected. RESULTS Seven t-AML and 12 t-MDS were included with median age of 71 (56-82) years old, median number of AZA cycles of 6 (1-15), and median overall survival (OS) of 14 (3-29) months. We observed correlation between AZA response and clonal selection. Decrease of TP53-mutated clone was correlated with response to AZA, confirming AZA efficacy in this subgroup. In some patients, emergence of mutations was correlated with progression or relapse without impact on OS. Clones with mutations in genes for DNA methylation regulation frequently occurred with other mutations and remained stable during AZA treatment, independent of AZA response. CONCLUSION We confirmed that the molecular complexity of t-MNs and that the follow-up of clonal selection during AZA treatment could be useful to define treatment combination.
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Affiliation(s)
- Anne Calleja
- Hematology Department, Cote D'Azur University, Nice Sophia Antipolis University, CHU of Nice, Nice, France.,Cote d'Azur University, INSERM U1065, Mediterranean Center of Molecular Medecine, Nice, France
| | - Seongseok Yun
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Chimène Moreilhon
- Cote D'Azur University, Nice Sophia Antipolis University, CHU of Nice, Onco-hematology Laboratory, Nice, France
| | - Jean Michel Karsenti
- Hematology Department, Cote D'Azur University, Nice Sophia Antipolis University, CHU of Nice, Nice, France
| | - Lauris Gastaud
- Oncology Department, Antoine Lacassagne Center, Nice, France
| | - Lionel Mannone
- Hematology Department, Cote D'Azur University, Nice Sophia Antipolis University, CHU of Nice, Nice, France
| | - Rami Komrokji
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Najla Al Ali
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Bérangère Dadone-Montaudie
- Anatomopathology Department, Cote d'Azur University, Nice Sophia Antipolis University, CHU of Nice, Nice, France
| | - Guillaume Robert
- Cote d'Azur University, INSERM U1065, Mediterranean Center of Molecular Medecine, Nice, France
| | - Patrick Auberger
- Cote d'Azur University, INSERM U1065, Mediterranean Center of Molecular Medecine, Nice, France
| | - Sophie Raynaud
- Cote D'Azur University, Nice Sophia Antipolis University, CHU of Nice, Onco-hematology Laboratory, Nice, France
| | - David A Sallman
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Thomas Cluzeau
- Hematology Department, Cote D'Azur University, Nice Sophia Antipolis University, CHU of Nice, Nice, France.,Cote d'Azur University, INSERM U1065, Mediterranean Center of Molecular Medecine, Nice, France
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13
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Borchiellini M, Ummarino S, Di Ruscio A. The Bright and Dark Side of DNA Methylation: A Matter of Balance. Cells 2019; 8:cells8101243. [PMID: 31614870 PMCID: PMC6830319 DOI: 10.3390/cells8101243] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/06/2019] [Accepted: 10/10/2019] [Indexed: 12/11/2022] Open
Abstract
DNA methylation controls several cellular processes, from early development to old age, including biological responses to endogenous or exogenous stimuli contributing to disease transition. As a result, minimal DNA methylation changes during developmental stages drive severe phenotypes, as observed in germ-line imprinting disorders, while genome-wide alterations occurring in somatic cells are linked to cancer onset and progression. By summarizing the molecular events governing DNA methylation, we focus on the methods that have facilitated mapping and understanding of this epigenetic mark in healthy conditions and diseases. Overall, we review the bright (health-related) and dark (disease-related) side of DNA methylation changes, outlining how bulk and single-cell genomic analyses are moving toward the identification of new molecular targets and driving the development of more specific and less toxic demethylating agents.
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Affiliation(s)
- Marta Borchiellini
- Department of Health Sciences, University of Eastern Piedmont, 28100 Novara, Italy.
- Department of Translational Medicine, University of Eastern Piedmont, 28100 Novara, Italy.
| | - Simone Ummarino
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA.
| | - Annalisa Di Ruscio
- Department of Translational Medicine, University of Eastern Piedmont, 28100 Novara, Italy.
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA.
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14
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Becker H, Greve G, Kataoka K, Mallm JP, Duque-Afonso J, Ma T, Niemöller C, Pantic M, Duyster J, Cleary ML, Schüler J, Rippe K, Ogawa S, Lübbert M. Identification of enhancer of mRNA decapping 4 as a novel fusion partner of MLL in acute myeloid leukemia. Blood Adv 2019; 3:761-765. [PMID: 30833276 PMCID: PMC6418506 DOI: 10.1182/bloodadvances.2018023879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 01/23/2019] [Indexed: 01/15/2023] Open
Abstract
mRNA decapping gene EDC4 is a novel fusion partner of MLL in AML. Genes functioning in mRNA decapping may compose a distinct group of MLL fusion partners that links MLL function with mRNA decapping in AML.
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Affiliation(s)
- Heiko Becker
- Department of Medicine I, Medical Center, and
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium partner site, Freiburg, Germany
| | - Gabriele Greve
- Department of Medicine I, Medical Center, and
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Keisuke Kataoka
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Jan-Philipp Mallm
- Division of Chromatin Networks and
- Single-cell Open Laboratory, German Cancer Research Center, Heidelberg, Germany
| | - Jesús Duque-Afonso
- Department of Medicine I, Medical Center, and
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of Pathology, Stanford University, Stanford, CA; and
| | - Tobias Ma
- Department of Medicine I, Medical Center, and
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Christoph Niemöller
- Department of Medicine I, Medical Center, and
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | - Justus Duyster
- Department of Medicine I, Medical Center, and
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium partner site, Freiburg, Germany
| | | | - Julia Schüler
- Charles River Discovery Research Services Germany GmbH, Freiburg, Germany
| | - Karsten Rippe
- Division of Chromatin Networks and
- Single-cell Open Laboratory, German Cancer Research Center, Heidelberg, Germany
| | - Seishi Ogawa
- German Cancer Consortium partner site, Freiburg, Germany
| | - Michael Lübbert
- Department of Medicine I, Medical Center, and
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium partner site, Freiburg, Germany
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15
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Castelli G, Pelosi E, Testa U. Emerging Therapies for Acute Myelogenus Leukemia Patients Targeting Apoptosis and Mitochondrial Metabolism. Cancers (Basel) 2019; 11:E260. [PMID: 30813354 PMCID: PMC6406361 DOI: 10.3390/cancers11020260] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 02/14/2019] [Indexed: 02/06/2023] Open
Abstract
Acute Myelogenous Leukemia (AML) is a malignant disease of the hematopoietic cells, characterized by impaired differentiation and uncontrolled clonal expansion of myeloid progenitors/precursors, resulting in bone marrow failure and impaired normal hematopoiesis. AML comprises a heterogeneous group of malignancies, characterized by a combination of different somatic genetic abnormalities, some of which act as events driving leukemic development. Studies carried out in the last years have shown that AML cells invariably have abnormalities in one or more apoptotic pathways and have identified some components of the apoptotic pathway that can be targeted by specific drugs. Clinical results deriving from studies using B-cell lymphoma 2 (BCL-2) inhibitors in combination with standard AML agents, such as azacytidine, decitabine, low-dose cytarabine, provided promising results and strongly support the use of these agents in the treatment of AML patients, particularly of elderly patients. TNF-related apoptosis-inducing ligand (TRAIL) and its receptors are frequently deregulated in AML patients and their targeting may represent a promising strategy for development of new treatments. Altered mitochondrial metabolism is a common feature of AML cells, as supported through the discovery of mutations in the isocitrate dehydrogenase gene and in mitochondrial electron transport chain and of numerous abnormalities of oxidative metabolism existing in AML subgroups. Overall, these observations strongly support the view that the targeting of mitochondrial apoptotic or metabolic machinery is an appealing new therapeutic perspective in AML.
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Affiliation(s)
- Germana Castelli
- Department of Oncology, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.
| | - Elvira Pelosi
- Department of Oncology, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.
| | - Ugo Testa
- Department of Oncology, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.
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Response of high-risk MDS to azacitidine and lenalidomide is impacted by baseline and acquired mutations in a cluster of three inositide-specific genes. Leukemia 2019; 33:2276-2290. [PMID: 30787430 PMCID: PMC6733710 DOI: 10.1038/s41375-019-0416-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/18/2019] [Accepted: 01/22/2019] [Indexed: 12/26/2022]
Abstract
Specific myeloid-related and inositide-specific gene mutations can be linked to myelodysplastic syndromes (MDS) pathogenesis and therapy. Here, 44 higher-risk MDS patients were treated with azacitidine and lenalidomide and mutations analyses were performed at baseline and during the therapy. Results were then correlated to clinical outcome, overall survival (OS), leukemia-free-survival (LFS) and response to therapy. Collectively, 34/44 patients were considered evaluable for response, with an overall response rate of 76.25% (26/34 cases): 17 patients showed a durable response, 9 patients early lost response and 8 patients never responded. The most frequently mutated genes were ASXL1, TET2, RUNX1, and SRSF2. All patients early losing response, as well as cases never responding, acquired the same 3 point mutations during therapy, affecting respectively PIK3CD (D133E), AKT3 (D280G), and PLCG2 (Q548R) genes, that regulate cell proliferation and differentiation. Moreover, Kaplan–Meier analyses revealed that this mutated cluster was significantly associated with a shorter OS, LFS, and duration of response. All in all, a common mutated cluster affecting 3 inositide-specific genes is significantly associated with loss of response to azacitidine and lenalidomide therapy in higher risk MDS. Further studies are warranted to confirm these data and to further analyze the functional role of this 3-gene cluster.
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