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Luque Paz D, Bader MS, Nienhold R, Rai S, Almeida Fonseca T, Stetka J, Hao-Shen H, Mild-Schneider G, Passweg JR, Skoda RC. Impact of Clonal Architecture on Clinical Course and Prognosis in Patients With Myeloproliferative Neoplasms. Hemasphere 2023; 7:e885. [PMID: 37153874 PMCID: PMC10158927 DOI: 10.1097/hs9.0000000000000885] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/31/2023] [Indexed: 05/10/2023] Open
Abstract
Myeloproliferative neoplasms (MPNs) are caused by a somatic gain-of-function mutation in 1 of the 3 disease driver genes JAK2, MPL, or CALR. About half of the MPNs patients also carry additional somatic mutations that modify the clinical course. The order of acquisition of these gene mutations has been proposed to influence the phenotype and evolution of the disease. We studied 50 JAK2-V617F-positive MPN patients who carried at least 1 additional somatic mutation and determined the clonal architecture of their hematopoiesis by sequencing DNA from single-cell-derived colonies. In 22 of these patients, the same blood samples were also studied for comparison by Tapestri single-cell DNA sequencing (scDNAseq). The clonal architectures derived by the 2 methods showed good overall concordance. scDNAseq showed higher sensitivity for mutations with low variant allele fraction, but had more difficulties distinguishing between heterozygous and homozygous mutations. By unsupervised analysis of clonal architecture data from all 50 MPN patients, we defined 4 distinct clusters. Cluster 4, characterized by more complex subclonal structure correlated with reduced overall survival, independent of the MPN subtype, presence of high molecular risk mutations, or the age at diagnosis. Cluster 1 was characterized by additional mutations residing in clones separated from the JAK2-V617F clone. The correlation with overall survival improved when mutation in such separated clones were not counted. Our results show that scDNAseq can reliably decipher the clonal architecture and can be used to refine the molecular prognostic stratification that until now was primarily based on the clinical and laboratory parameters.
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Affiliation(s)
- Damien Luque Paz
- Department of Biomedicine, Experimental Hematology, University Hospital Basel and University of Basel, Switzerland
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, CRCI2NA, Angers, France
| | | | - Ronny Nienhold
- Department of Biomedicine, Experimental Hematology, University Hospital Basel and University of Basel, Switzerland
| | - Shivam Rai
- Department of Biomedicine, Experimental Hematology, University Hospital Basel and University of Basel, Switzerland
| | - Tiago Almeida Fonseca
- Department of Biomedicine, Experimental Hematology, University Hospital Basel and University of Basel, Switzerland
| | - Jan Stetka
- Department of Biomedicine, Experimental Hematology, University Hospital Basel and University of Basel, Switzerland
| | - Hui Hao-Shen
- Department of Biomedicine, Experimental Hematology, University Hospital Basel and University of Basel, Switzerland
| | - Gabriele Mild-Schneider
- Department of Biomedicine, Experimental Hematology, University Hospital Basel and University of Basel, Switzerland
| | | | - Radek C. Skoda
- Department of Biomedicine, Experimental Hematology, University Hospital Basel and University of Basel, Switzerland
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Rontauroli S, Carretta C, Parenti S, Bertesi M, Manfredini R. Novel Molecular Insights into Leukemic Evolution of Myeloproliferative Neoplasms: A Single Cell Perspective. Int J Mol Sci 2022; 23. [PMID: 36499582 DOI: 10.3390/ijms232315256] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/25/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Myeloproliferative neoplasms (MPNs) are clonal disorders originated by the serial acquisition of somatic mutations in hematopoietic stem/progenitor cells. The major clinical entities are represented by polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF), that are caused by driver mutations affecting JAK2, MPL or CALR. Disease progression is related to molecular and clonal evolution. PV and ET can progress to secondary myelofibrosis (sMF) but can also evolve to secondary acute myeloid leukemia (sAML). PMF is associated with the highest frequency of leukemic transformation, which represents the main cause of death. sAML is associated with a dismal prognosis and clinical features that differ from those of de novo AML. The molecular landscape distinguishes sAML from de novo AML, since the most frequent hits involve TP53, epigenetic regulators, spliceosome modulators or signal transduction genes. Single cell genomic studies provide novel and accurate information about clonal architecture and mutation acquisition order, allowing the reconstruction of clonal dynamics and molecular events that accompany leukemic transformation. In this review, we examine our current understanding of the genomic heterogeneity in MPNs and how it affects disease progression and leukemic transformation. We focus on molecular events elicited by somatic mutations acquisition and discuss the emerging findings coming from single cell studies.
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Hautin M, Mornet C, Chauveau A, Bernard DG, Corcos L, Lippert E. Splicing Anomalies in Myeloproliferative Neoplasms: Paving the Way for New Therapeutic Venues. Cancers (Basel) 2020; 12:cancers12082216. [PMID: 32784800 PMCID: PMC7464941 DOI: 10.3390/cancers12082216] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/30/2020] [Accepted: 08/05/2020] [Indexed: 02/06/2023] Open
Abstract
Since the discovery of spliceosome mutations in myeloid malignancies, abnormal pre-mRNA splicing, which has been well studied in various cancers, has attracted novel interest in hematology. However, despite the common occurrence of spliceosome mutations in myelo-proliferative neoplasms (MPN), not much is known regarding the characterization and mechanisms of splicing anomalies in MPN. In this article, we review the current scientific literature regarding “splicing and myeloproliferative neoplasms”. We first analyse the clinical series reporting spliceosome mutations in MPN and their clinical correlates. We then present the current knowledge about molecular mechanisms by which these mutations participate in the pathogenesis of MPN or other myeloid malignancies. Beside spliceosome mutations, splicing anomalies have been described in myeloproliferative neoplasms, as well as in acute myeloid leukemias, a dreadful complication of these chronic diseases. Based on splicing anomalies reported in chronic myelogenous leukemia as well as in acute leukemia, and the mechanisms presiding splicing deregulation, we propose that abnormal splicing plays a major role in the evolution of myeloproliferative neoplasms and may be the target of specific therapeutic strategies.
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Affiliation(s)
- Marie Hautin
- Inserm, Univ Brest, EFS, UMR 1078, GGB, F-29200 Brest, France; (M.H.); (A.C.); (D.G.B.); (L.C.)
| | - Clélia Mornet
- Laboratoire d’Hématologie, CHU de Brest, F-29200 Brest, France;
| | - Aurélie Chauveau
- Inserm, Univ Brest, EFS, UMR 1078, GGB, F-29200 Brest, France; (M.H.); (A.C.); (D.G.B.); (L.C.)
- Laboratoire d’Hématologie, CHU de Brest, F-29200 Brest, France;
| | - Delphine G. Bernard
- Inserm, Univ Brest, EFS, UMR 1078, GGB, F-29200 Brest, France; (M.H.); (A.C.); (D.G.B.); (L.C.)
| | - Laurent Corcos
- Inserm, Univ Brest, EFS, UMR 1078, GGB, F-29200 Brest, France; (M.H.); (A.C.); (D.G.B.); (L.C.)
| | - Eric Lippert
- Inserm, Univ Brest, EFS, UMR 1078, GGB, F-29200 Brest, France; (M.H.); (A.C.); (D.G.B.); (L.C.)
- Laboratoire d’Hématologie, CHU de Brest, F-29200 Brest, France;
- Correspondence:
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6
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Abstract
Activated JAK-STAT signaling is central to the pathogenesis of BCR-ABL-negative myeloproliferative neoplasms (MPNs) and occurs as a result of MPN phenotypic driver mutations in JAK2, CALR, or MPL The spectrum of concomitant somatic mutations in other genes has now largely been defined in MPNs. With the integration of targeted next-generation sequencing (NGS) panels into clinical practice, the clinical significance of concomitant mutations in MPNs has become clearer. In this review, we describe the consequences of concomitant mutations in the most frequently mutated classes of genes in MPNs: (1) DNA methylation pathways, (2) chromatin modification, (3) RNA splicing, (4) signaling pathways, (5) transcription factors, and (6) DNA damage response/stress signaling. The increased use of molecular genetics for early risk stratification of patients brings the possibility of earlier intervention to prevent disease progression in MPNs. However, additional studies are required to decipher underlying molecular mechanisms and effectively target them.
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Affiliation(s)
- Anna E Marneth
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ann Mullally
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute, Cambridge, Massachusetts 02142, USA.,Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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7
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Rao TN, Hansen N, Hilfiker J, Rai S, Majewska JM, Leković D, Gezer D, Andina N, Galli S, Cassel T, Geier F, Delezie J, Nienhold R, Hao-Shen H, Beisel C, Di Palma S, Dimeloe S, Trebicka J, Wolf D, Gassmann M, Fan TWM, Lane AN, Handschin C, Dirnhofer S, Kröger N, Hess C, Radimerski T, Koschmieder S, Čokić VP, Skoda RC. JAK2-mutant hematopoietic cells display metabolic alterations that can be targeted to treat myeloproliferative neoplasms. Blood 2019; 134:1832-1846. [PMID: 31511238 PMCID: PMC6872961 DOI: 10.1182/blood.2019000162] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 08/17/2019] [Indexed: 12/20/2022] Open
Abstract
Increased energy requirement and metabolic reprogramming are hallmarks of cancer cells. We show that metabolic alterations in hematopoietic cells are fundamental to the pathogenesis of mutant JAK2-driven myeloproliferative neoplasms (MPNs). We found that expression of mutant JAK2 augmented and subverted metabolic activity of MPN cells, resulting in systemic metabolic changes in vivo, including hypoglycemia, adipose tissue atrophy, and early mortality. Hypoglycemia in MPN mouse models correlated with hyperactive erythropoiesis and was due to a combination of elevated glycolysis and increased oxidative phosphorylation. Modulating nutrient supply through high-fat diet improved survival, whereas high-glucose diet augmented the MPN phenotype. Transcriptomic and metabolomic analyses identified numerous metabolic nodes in JAK2-mutant hematopoietic stem and progenitor cells that were altered in comparison with wild-type controls. We studied the consequences of elevated levels of Pfkfb3, a key regulatory enzyme of glycolysis, and found that pharmacological inhibition of Pfkfb3 with the small molecule 3PO reversed hypoglycemia and reduced hematopoietic manifestations of MPNs. These effects were additive with the JAK1/2 inhibitor ruxolitinib in vivo and in vitro. Inhibition of glycolysis by 3PO altered the redox homeostasis, leading to accumulation of reactive oxygen species and augmented apoptosis rate. Our findings reveal the contribution of metabolic alterations to the pathogenesis of MPNs and suggest that metabolic dependencies of mutant cells represent vulnerabilities that can be targeted for treating MPNs.
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Affiliation(s)
- Tata Nageswara Rao
- Experimental Hematology, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Nils Hansen
- Experimental Hematology, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Julian Hilfiker
- Experimental Hematology, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Shivam Rai
- Experimental Hematology, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Julia-Magdalena Majewska
- Experimental Hematology, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Danijela Leković
- Clinic of Hematology, Clinical Center of Serbia, Belgrade, Serbia
| | - Deniz Gezer
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Nicola Andina
- Experimental Hematology, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Serena Galli
- Experimental Hematology, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Teresa Cassel
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology and Markey Cancer Center, University of Kentucky, Lexington, KY
| | - Florian Geier
- Experimental Hematology, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | | | - Ronny Nienhold
- Experimental Hematology, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Hui Hao-Shen
- Experimental Hematology, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Serena Di Palma
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Sarah Dimeloe
- Immunobiology, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Jonel Trebicka
- Department of Internal Medicine I, University of Bonn, Bonn, Germany
- European Foundation for the Study of Chronic Liver Failure, Barcelona, Spain
- Department of Gastroenterology, Odense Hospital, University of Southern Denmark, Odense, Denmark
- Institute for Bioengineering of Catalonia, Barcelona, Spain
| | - Dominik Wolf
- Internal Medicine V, Department of Hematology and Oncology, Medical University Innsbruck, Innsbruck, Austria
- Medical Clinic III for Oncology, Hematology, Immunoncology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Max Gassmann
- Institute of Veterinary Physiology, Vetsuisse Faculty and Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Teresa W-M Fan
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology and Markey Cancer Center, University of Kentucky, Lexington, KY
| | - Andrew N Lane
- Center for Environmental and Systems Biochemistry, Department of Toxicology and Cancer Biology and Markey Cancer Center, University of Kentucky, Lexington, KY
| | | | - Stefan Dirnhofer
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Nicolaus Kröger
- Department of Stem Cell Transplantation, University Hospital Eppendorf, Hamburg, Germany
| | - Christoph Hess
- Immunobiology, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Thomas Radimerski
- Disease Area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland; and
| | - Steffen Koschmieder
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Vladan P Čokić
- Institute for Medical Research, University of Belgrade, Belgrade, Serbia
| | - Radek C Skoda
- Experimental Hematology, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
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