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Li R, Huang D, Zhao Y, Yuan Y, Sun X, Dai Z, Huo D, Liu X, Helin K, Li MJ, Wu X. PR-DUB safeguards Polycomb repression through H2AK119ub1 restriction. Cell Prolif 2023; 56:e13457. [PMID: 36959757 PMCID: PMC10542648 DOI: 10.1111/cpr.13457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 01/06/2023] [Revised: 03/01/2023] [Accepted: 03/11/2023] [Indexed: 03/25/2023] Open
Abstract
Polycomb group (PcG) proteins are critical chromatin regulators for cell fate control. The mono-ubiquitylation on histone H2AK119 (H2AK119ub1) is one of the well-recognized mechanisms for Polycomb repressive complex 1 (PRC1)-mediated transcription repression. Unexpectedly, the specific H2AK119 deubiquitylation complex composed by additional sex comb-like proteins and BAP1 has also been genetically characterized as Polycomb repressive deubiquitnase (PR-DUB) for unclear reasons. However, it remains a mystery whether and how PR-DUB deficiency affects chromatin states and cell fates through impaired PcG silencing. Here through a careful epigenomic analysis, we demonstrate that a bulk of H2AK119ub1 is diffusely distributed away from promoter regions and their enrichment is positively correlated with PRC1 occupancy. Upon deletion of Asxl2 in mouse embryonic stem cells (ESCs), a pervasive gain of H2AK119ub1 is coincident with increased PRC1 sampling at chromatin. Accordingly, PRC1 is significantly lost from a subset of highly occupied promoters, leading to impaired silencing of associated genes before and after lineage differentiation of Asxl2-null ESCs. Therefore, our study highlights the importance of genome-wide H2AK119ub1 restriction by PR-DUB in safeguarding robust PRC1 deposition and its roles in developmental regulation.
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Affiliation(s)
- Rui Li
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Cell Biology, School of Basic Medical SciencesTianjin Medical UniversityTianjin300070China
| | - Dandan Huang
- Wuxi School of MedicineJiangnan UniversityWuxi214000China
| | - Yingying Zhao
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Cell Biology, School of Basic Medical SciencesTianjin Medical UniversityTianjin300070China
| | - Ye Yuan
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Cell Biology, School of Basic Medical SciencesTianjin Medical UniversityTianjin300070China
| | - Xiaoyu Sun
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Cell Biology, School of Basic Medical SciencesTianjin Medical UniversityTianjin300070China
| | - Zhongye Dai
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Cell Biology, School of Basic Medical SciencesTianjin Medical UniversityTianjin300070China
| | - Dawei Huo
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Cell Biology, School of Basic Medical SciencesTianjin Medical UniversityTianjin300070China
| | - Xiaozhi Liu
- Pediatric Center, Tianjin Key Laboratory of Epigenetics for Organ Development of Premature InfantsThe Fifth Central Hospital of TianjinTianjin300450China
| | - Kristian Helin
- Biotech Research and Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Institute of Cancer Research (ICR)LondonUK
| | - Mulin Jun Li
- Department of Bioinformatics, School of Basic Medical SciencesTianjin Medical UniversityTianjin300070China
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and HospitalTianjin Medical UniversityTianjin300070China
| | - Xudong Wu
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Cell Biology, School of Basic Medical SciencesTianjin Medical UniversityTianjin300070China
- Department of OrthopedicsTianjin Medical University General HospitalTianjin300052China
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2
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Imataki O, Ishida T, Kubo H, Uemura M, Nanya Y, Kawakami K, Ogawa S, Kadowaki N. A Case of Tyrosine Kinase Inhibitor-Resistant Chronic Myeloid Leukemia, Chronic Phase with ASXL1 Mutation. Case Rep Oncol 2020; 13:449-455. [PMID: 32399015 PMCID: PMC7204851 DOI: 10.1159/000506452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 02/07/2020] [Accepted: 02/10/2020] [Indexed: 12/11/2022] Open
Abstract
Hematological malignancies, including chronic myeloid leukemia (CML), exhibit ASXL1 mutations; however, the function and molecular mechanism of these mutations remain unclear. ASXL1 was originally identified as tumor suppressor gene, in which loss of function causes myelodysplastic syndrome (MDS). ASXL1 mutations are common and associated with disease progression in myeloid malignancies including MDS, acute myeloid leukemia, and similarly in CML. In MDS, ASXL1 mutations have been associated with poor prognosis; however, the impact of ASXL1 mutations in CML has not been well described. A 31-year-old male was diagnosed as CML-chronic phase (CP). Laboratory findings showed a white blood cell count of 187,200/µL, with asymptomatic splenomegaly. Blast count was 5.0% in peripheral blood and 7.3% in bone marrow. There was no additional chromosomal abnormality except for t(9;22)(q34;q11.2) by chromosomal analysis. At onset, the Sokal score was 1.4, indicating high risk. The patient received tyrosine kinase inhibitor (TKI) therapy, comprising nilotinib ∼600 mg/day, bosutinib ∼600 mg/day, ponatinib ∼45 mg/day, and dasatinib ∼100 mg/day. Nevertheless, after 1.5 years of continuous TKI therapy, the best outcome was a hematological response. Although additional chromosomal aberrations and ABL1 kinase mutations were analyzed repeatedly before and during TKI therapy, known genetic abnormalities were not detected. Thereafter, the patient underwent bone marrow transplantation from an HLA 7/8 matched unrelated donor (HLA-Cw 1 locus mismatch, graft-versus-host direction). The patient achieved neutrophil engraftment, 18 days after transplantation, leading to complete remission with an undetectable level of BCR-ABL1 mRNA. The patient, however, died from graft-versus-host disease and thrombotic microangiopathy after 121 days. Gene sequence analysis of his CML cell before stem cell transplantation revealed ASXL1 mutations. Physiologically, ASXL1 contributes to epigenetic regulation. In the CML-CP patient in this case report, ASXL1 mutation conferred resistance to TKI through obscure resistance mechanisms. Even though a molecular mechanism for TKI resistance in ASXL1 mutation in CML has remained obscure, epigenetic modulation is a plausible mode of CML disease progression. The clinical impact including prognosis of ASXL1 for CML is underscored. And the treatment strategy of CML with ASXL1 mutation has not been established. A discussion of this case was expected to facilitate treatment options.
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Affiliation(s)
- Osamu Imataki
- Division of Hematology, Faculty of Medicine, Kagawa University, Kagawa, Japan
| | - Tomoya Ishida
- Division of Hematology, Faculty of Medicine, Kagawa University, Kagawa, Japan.,Kagawa University Hospital Post Graduate Clinical Education Center, Kagawa, Japan
| | - Hiroyuki Kubo
- Division of Hematology, Faculty of Medicine, Kagawa University, Kagawa, Japan
| | - Makiko Uemura
- Division of Hematology, Faculty of Medicine, Kagawa University, Kagawa, Japan
| | - Yasuhito Nanya
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Kimihiro Kawakami
- Department of Hematology, Kagawa Prefectural Central Hospital, Kagawa, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Norimitsu Kadowaki
- Division of Hematology, Faculty of Medicine, Kagawa University, Kagawa, Japan
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3
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Shokouhian M, Bagheri M, Poopak B, Chegeni R, Davari N, Saki N. Altering chromatin methylation patterns and the transcriptional network involved in regulation of hematopoietic stem cell fate. J Cell Physiol 2020; 235:6404-6423. [PMID: 32052445 DOI: 10.1002/jcp.29642] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 01/31/2020] [Indexed: 12/15/2022]
Abstract
Hematopoietic stem cells (HSCs) are quiescent cells with self-renewal capacity and potential multilineage development. Various molecular regulatory mechanisms such as epigenetic modifications and transcription factor (TF) networks play crucial roles in establishing a balance between self-renewal and differentiation of HSCs. Histone/DNA methylations are important epigenetic modifications involved in transcriptional regulation of specific lineage HSCs via controlling chromatin structure and accessibility of DNA. Also, TFs contribute to either facilitation or inhibition of gene expression through binding to enhancer or promoter regions of DNA. As a result, epigenetic factors and TFs regulate the activation or repression of HSCs genes, playing a central role in normal hematopoiesis. Given the importance of histone/DNA methylation and TFs in gene expression regulation, their aberrations, including changes in HSCs-related methylation of histone/DNA and TFs (e.g., CCAAT-enhancer-binding protein α, phosphatase and tensin homolog deleted on the chromosome 10, Runt-related transcription factor 1, signal transducers and activators of transcription, and RAS family proteins) could disrupt HSCs fate. Herewith, we summarize how dysregulations in the expression of genes related to self-renewal, proliferation, and differentiation of HSCs caused by changes in epigenetic modifications and transcriptional networks lead to clonal expansion and leukemic transformation.
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Affiliation(s)
- Mohammad Shokouhian
- Department of Hematology and Blood Transfusion, School of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Marziye Bagheri
- Thalassemia and Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Behzad Poopak
- Department of Hematology, Faculty of Paramedical Sciences, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Rouzbeh Chegeni
- Michener Institute of Education at University Health Network, Toronto, Canada
| | - Nader Davari
- Thalassemia and Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Najmaldin Saki
- Thalassemia and Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Abstract
Comprehensive cataloguing of the acute myeloid leukaemia (AML) genome has revealed a high frequency of mutations and deletions in epigenetic factors that are frequently linked to treatment resistance and poor patient outcome. In this review, we discuss how the epigenetic mechanisms that underpin normal haematopoiesis are subverted in AML, and in particular how these processes are altered in childhood and adolescent leukaemias. We also provide a brief summary of the burgeoning field of epigenetic-based therapies, and how AML treatment might be improved through provision of better conceptual frameworks for understanding the pleiotropic molecular effects of epigenetic disruption.
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Affiliation(s)
- Luke Jones
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland.,National Children's Research Centre, Dublin, Ireland
| | - Peter McCarthy
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland.,Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Jonathan Bond
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland.,National Children's Research Centre, Dublin, Ireland.,Children's Health Ireland at Crumlin, Dublin, Ireland
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5
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Abstract
Ex vivo differentiation of human hematopoietic stem cells is a widely used model for studying hematopoiesis. The protocol described here is for cytokine induced differentiation of CD34+ hematopoietic stem and progenitor cells to the four myeloid lineage cells. CD34+ cells are isolated from human umbilical cord blood and co-cultured with MS-5 stromal cells in the presence of cytokines. Immunophenotypic characterization of the stem and progenitor cells, and the differentiated myeloid lineage cells are described. Using this protocol, CD34+ cells may be incubated with small molecules or transduced with lentiviruses to express myeloid disease mutations to investigate their impact on myeloid differentiation.
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Affiliation(s)
- Aditi Bapat
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona
| | - Nakia Keita
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona
| | - Shalini Sharma
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona;
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6
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Chase A, Pellagatti A, Singh S, Score J, Tapper WJ, Lin F, Hoade Y, Bryant C, Trim N, Yip BH, Zoi K, Rasi C, Forsberg LA, Dumanski JP, Boultwood J, Cross NCP. PRR14L mutations are associated with chromosome 22 acquired uniparental disomy, age-related clonal hematopoiesis and myeloid neoplasia. Leukemia 2019; 33:1184-94. [PMID: 30573780 DOI: 10.1038/s41375-018-0340-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 10/03/2018] [Indexed: 12/31/2022]
Abstract
Acquired uniparental disomy (aUPD, also known as copy-neutral loss of heterozygosity) is a common feature of cancer cells and characterized by extended tracts of somatically-acquired homozygosity without any concurrent loss or gain of genetic material. The presumed genetic targets of many regions of aUPD remain unknown. Here we describe the association of chromosome 22 aUPD with mutations that delete the C-terminus of PRR14L in patients with chronic myelomonocytic leukemia (CMML), related myeloid neoplasms and age-related clonal hematopoiesis (ARCH). Myeloid panel analysis identified a median of 3 additional mutated genes (range 1-6) in cases with a myeloid neoplasm (n=8), but no additional mutations in cases with ARCH (n=2) suggesting that mutated PRR14L alone may be sufficient to drive clonality. PRR14L has very limited homology to other proteins and its function is unknown. ShRNA knockdown of PRR14L in human CD34+ cells followed by in vitro growth and differentiation assays showed an increase in monocytes and decrease in neutrophils consistent, with a CMML-like phenotype. RNA-Seq and cellular localization studies suggest a role for PRR14L in cell division. PRR14L is thus a novel, biallelically mutated gene and potential founding abnormality in myeloid neoplasms.
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Abstract
BACKGROUND ASXL1 gene mutations include nonsense, missense, and frameshift mutations. Although their clinical significance is still debated, they may play an important role in the pathogenesis of several hematologic malignancies. METHODS Herein, we offer a comprehensive review on ASXL1 mutations, and link them with survival and clinical outcomes in patients with various myeloid neoplasms. Most relevant publications were identified through searching the PubMed/Medline database for articles published from inception to February 2016. FINDINGS In acute myeloid leukemia (AML), ASXL1 mutations tend to correlate with older age and male gender, and affect predominantly patients with secondary AML. De novo AML patients with ASXL1 mutations had significantly lower complete remission rates after standard high-dose chemotherapy and shorter survival. In chronic myelomonocytic leukemia and low- or intermediate-risk myelodysplastic syndromes, frameshift and nonsense mutations correlated with shorter survival and a higher risk of leukemic transformation. Overall survival was also shorter in primary myelofibrosis in the presence of ASXL1 mutations. CONCLUSIONS Further research on the role of ASXL1 mutations and therapeutic implications in neoplastic myeloid disorders is stringently needed. Given the relatively high prevalence of ASXL1 mutations, larger studies involving patients affected by these mutations will be feasible in the near future.
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Affiliation(s)
| | - Constantin A Dasanu
- b Lucy Curci Cancer Center, Eisenhower Medical Center, Hematology Oncology , Rancho Mirage , CA , USA
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Wu ZJ, Zhao X, Banaszak LG, Gutierrez-Rodrigues F, Keyvanfar K, Gao SG, Quinones Raffo D, Kajigaya S, Young NS. CRISPR/Cas9-mediated ASXL1 mutations in U937 cells disrupt myeloid differentiation. Int J Oncol 2018. [PMID: 29532865 PMCID: PMC5843401 DOI: 10.3892/ijo.2018.4290] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [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] [Indexed: 01/06/2023] Open
Abstract
Additional sex combs-like 1 (ASXL1) is a well‑known tumor suppressor gene and epigenetic modifier. ASXL1 mutations are frequent in myeloid malignances; these mutations are risk factors for the development of myelodysplasia and also appear as small clones during normal aging. ASXL1 appears to act as an epigenetic regulator of cell survival and myeloid differentiation; however, the molecular mechanisms underlying the malignant transformation of cells with ASXL1 mutations are not well defined. Using Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein-9 nuclease (Cas9) genome editing, heterozygous and homozygous ASXL1 mutations were introduced into human U937 leukemic cells. Comparable cell growth and cell cycle progression were observed between wild-type (WT) and ASXL1-mutated U937 cells. Drug-induced cytotoxicity, as measured by growth inhibition and apoptosis in the presence of the cell-cycle active agent 5-fluorouracil, was variable among the mutated clones but was not significantly different from WT cells. In addition, ASXL1-mutated cells exhibited defects in monocyte/macrophage differentiation. Transcriptome analysis revealed that ASXL1 mutations altered differentiation of U937 cells by disturbing genes involved in myeloid differentiation, including cytochrome B-245 β chain and C-type lectin domain family 5, member A. Dysregulation of numerous gene sets associated with cell death and survival were also observed in ASXL1-mutated cells. These data provide evidence regarding the underlying molecular mechanisms induced by mutated ASXL1 in leukemogenesis.
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Affiliation(s)
- Zhi-Jie Wu
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892-1202, USA
| | - Xin Zhao
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892-1202, USA
| | - Lauren G Banaszak
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892-1202, USA
| | - Fernanda Gutierrez-Rodrigues
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892-1202, USA
| | - Keyvan Keyvanfar
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892-1202, USA
| | - Shou-Guo Gao
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892-1202, USA
| | - Diego Quinones Raffo
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892-1202, USA
| | - Sachiko Kajigaya
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892-1202, USA
| | - Neal S Young
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892-1202, USA
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Sallman DA, Komrokji R, Cluzeau T, Vaupel C, Al Ali NH, Lancet J, Hall J, List A, Padron E, Song J. ASXL1 frameshift mutations drive inferior outcomes in CMML without negative impact in MDS. Blood Cancer J 2017; 7:633. [PMID: 29176559 DOI: 10.1038/s41408-017-0004-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 08/23/2017] [Indexed: 12/11/2022] Open
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10
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Yip BH, Steeples V, Repapi E, Armstrong RN, Llorian M, Roy S, Shaw J, Dolatshad H, Taylor S, Verma A, Bartenstein M, Vyas P, Cross NC, Malcovati L, Cazzola M, Hellström-Lindberg E, Ogawa S, Smith CW, Pellagatti A, Boultwood J. The U2AF1S34F mutation induces lineage-specific splicing alterations in myelodysplastic syndromes. J Clin Invest 2017; 127:2206-2221. [PMID: 28436936 PMCID: PMC5451246 DOI: 10.1172/jci91363] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [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: 10/21/2016] [Accepted: 02/21/2017] [Indexed: 12/23/2022] Open
Abstract
Mutations of the splicing factor–encoding gene U2AF1 are frequent in the myelodysplastic syndromes (MDS), a myeloid malignancy, and other cancers. Patients with MDS suffer from peripheral blood cytopenias, including anemia, and an increasing percentage of bone marrow myeloblasts. We studied the impact of the common U2AF1S34F mutation on cellular function and mRNA splicing in the main cell lineages affected in MDS. We demonstrated that U2AF1S34F expression in human hematopoietic progenitors impairs erythroid differentiation and skews granulomonocytic differentiation toward granulocytes. RNA sequencing of erythroid and granulomonocytic colonies revealed that U2AF1S34F induced a higher number of cassette exon splicing events in granulomonocytic cells than in erythroid cells. U2AF1S34F altered mRNA splicing of many transcripts that were expressed in both cell types in a lineage-specific manner. In hematopoietic progenitors, the introduction of isoform changes identified in the U2AF1S34F target genes H2AFY, encoding an H2A histone variant, and STRAP, encoding serine/threonine kinase receptor–associated protein, recapitulated phenotypes associated with U2AF1S34F expression in erythroid and granulomonocytic cells, suggesting a causal link. Furthermore, we showed that isoform modulation of H2AFY and STRAP rescues the erythroid differentiation defect in U2AF1S34F MDS cells, suggesting that splicing modulators could be used therapeutically. These data have critical implications for understanding MDS phenotypic heterogeneity and support the development of therapies targeting splicing abnormalities.
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Affiliation(s)
- Bon Ham Yip
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and BRC Blood Theme, National Institute for Health Research (NIHR) Oxford Biomedical Centre, Oxford University Hospital, Oxford, United Kingdom
| | - Violetta Steeples
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and BRC Blood Theme, National Institute for Health Research (NIHR) Oxford Biomedical Centre, Oxford University Hospital, Oxford, United Kingdom
| | - Emmanouela Repapi
- The Computational Biology Research Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Richard N Armstrong
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and BRC Blood Theme, National Institute for Health Research (NIHR) Oxford Biomedical Centre, Oxford University Hospital, Oxford, United Kingdom
| | - Miriam Llorian
- Department of Biochemistry, Downing Site, University of Cambridge, Cambridge, United Kingdom
| | - Swagata Roy
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and BRC Blood Theme, National Institute for Health Research (NIHR) Oxford Biomedical Centre, Oxford University Hospital, Oxford, United Kingdom
| | - Jacqueline Shaw
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and BRC Blood Theme, National Institute for Health Research (NIHR) Oxford Biomedical Centre, Oxford University Hospital, Oxford, United Kingdom
| | - Hamid Dolatshad
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and BRC Blood Theme, National Institute for Health Research (NIHR) Oxford Biomedical Centre, Oxford University Hospital, Oxford, United Kingdom
| | - Stephen Taylor
- The Computational Biology Research Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Amit Verma
- Albert Einstein College of Medicine, Bronx, New York, USA
| | | | - Paresh Vyas
- Medical Research Council, Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, and Department of Hematology, Oxford University Hospital National Health Service Trust, Oxford, United Kingdom
| | - Nicholas Cp Cross
- Faculty of Medicine, University of Southampton, Southampton, and National Genetics Reference Laboratory (Wessex), Salisbury, United Kingdom
| | - Luca Malcovati
- Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Mario Cazzola
- Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Eva Hellström-Lindberg
- Center for Hematology and Regenerative Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Christopher Wj Smith
- Department of Biochemistry, Downing Site, University of Cambridge, Cambridge, United Kingdom
| | - Andrea Pellagatti
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and BRC Blood Theme, National Institute for Health Research (NIHR) Oxford Biomedical Centre, Oxford University Hospital, Oxford, United Kingdom
| | - Jacqueline Boultwood
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and BRC Blood Theme, National Institute for Health Research (NIHR) Oxford Biomedical Centre, Oxford University Hospital, Oxford, United Kingdom
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11
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Ganguly BB, Kadam N. Mutations of myelodysplastic syndromes (MDS): An update. Mutation Research/Reviews in Mutation Research 2016; 769:47-62. [DOI: 10.1016/j.mrrev.2016.04.009] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/11/2016] [Indexed: 01/08/2023]
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12
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Affiliation(s)
- Andrea Pellagatti
- Leukaemia & Lymphoma Research Molecular Haematology Unit; Nuffield Division of Clinical Laboratory Sciences; Radcliffe Department of Medicine; University of Oxford; Oxford UK
| | - Jacqueline Boultwood
- Leukaemia & Lymphoma Research Molecular Haematology Unit; Nuffield Division of Clinical Laboratory Sciences; Radcliffe Department of Medicine; University of Oxford; Oxford UK
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Abstract
Blood is a fluid connective tissue which plays a vital role for normal body function. It consist different type of blood cells which is continuously reproduce inside the bone marrow from hematopoietic system. Xenobiotics could be specifically toxic to the hematopoietic system and they can cause hematological disorders by disturbing the normal functions. In vitro hematopoietic colony-forming cell assays play a crucial role to evaluate potential toxic effects of new xenobiotics and also helpful in bridging the gap between preclinical toxicology studies in animal models and clinical investigations. Use of these assays in conjunction with, high-throughput screening reduces the cost and time associated with these assays. This article provides a critical view over in vitro hematopoietic colony-forming cell assays in assessment of hematotoxicity.
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Affiliation(s)
- Navneet Kumar Yadav
- a Hematological Facility, Division of Toxicology , CSIR-Central Drug Research Institute , Lucknow , Uttar Pradesh , India and
| | - Pooja Shukla
- a Hematological Facility, Division of Toxicology , CSIR-Central Drug Research Institute , Lucknow , Uttar Pradesh , India and.,b Academy of Scientific and Innovative Research , New Delhi , India
| | - Ankur Omer
- a Hematological Facility, Division of Toxicology , CSIR-Central Drug Research Institute , Lucknow , Uttar Pradesh , India and.,b Academy of Scientific and Innovative Research , New Delhi , India
| | - Poonam Singh
- a Hematological Facility, Division of Toxicology , CSIR-Central Drug Research Institute , Lucknow , Uttar Pradesh , India and.,b Academy of Scientific and Innovative Research , New Delhi , India
| | - R K Singh
- a Hematological Facility, Division of Toxicology , CSIR-Central Drug Research Institute , Lucknow , Uttar Pradesh , India and.,b Academy of Scientific and Innovative Research , New Delhi , India
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14
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Gerstung M, Pellagatti A, Malcovati L, Giagounidis A, Porta MG, Jädersten M, Dolatshad H, Verma A, Cross NC, Vyas P, Killick S, Hellström-Lindberg E, Cazzola M, Papaemmanuil E, Campbell PJ, Boultwood J. Combining gene mutation with gene expression data improves outcome prediction in myelodysplastic syndromes. Nat Commun 2015; 6:5901. [PMID: 25574665 DOI: 10.1038/ncomms6901] [Citation(s) in RCA: 158] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 11/18/2014] [Indexed: 12/15/2022] Open
Abstract
Cancer is a genetic disease, but two patients rarely have identical genotypes. Similarly, patients differ in their clinicopathological parameters, but how genotypic and phenotypic heterogeneity are interconnected is not well understood. Here we build statistical models to disentangle the effect of 12 recurrently mutated genes and 4 cytogenetic alterations on gene expression, diagnostic clinical variables and outcome in 124 patients with myelodysplastic syndromes. Overall, one or more genetic lesions correlate with expression levels of ~20% of all genes, explaining 20–65% of observed expression variability. Differential expression patterns vary between mutations and reflect the underlying biology, such as aberrant polycomb repression for ASXL1 and EZH2 mutations or perturbed gene dosage for copy-number changes. In predicting survival, genomic, transcriptomic and diagnostic clinical variables all have utility, with the largest contribution from the transcriptome. Similar observations are made on the TCGA acute myeloid leukaemia cohort, confirming the general trends reported here. The myelodysplastic syndromes (MDS) are a heterogeneous group of chronic blood cancers. Here, the authors analyse genomic and gene expression data from MDS patients to investigate how driver mutations alter gene expression, diagnostic clinical variables and survival.
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Bravo GM, Lee E, Merchan B, Kantarjian HM, García-Manero G. Integrating genetics and epigenetics in myelodysplastic syndromes: advances in pathogenesis and disease evolution. Br J Haematol 2014; 166:646-59. [PMID: 24903747 PMCID: PMC5553700 DOI: 10.1111/bjh.12957] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 04/19/2014] [Indexed: 01/09/2023]
Abstract
The myelodysplastic syndromes (MDS) are a group of clonal diseases characterized by inefficient haematopoiesis, increased apoptosis and risk of evolution to acute myeloid leukaemia. Alterations in epigenetic processes, including DNA methylation, histone modifications, miRNA and splicing machinery, are well known pathogenical events in MDS. Although many advances have been made in determining the mutational frequency, distribution and association affecting these epigenomic regulators, functional integration to better understand pathogenesis of the disease is a challenging and expanding area. Recent studies are shedding light on the molecular basis of myelodysplasia and how mutations and epimutations can induce and promote this neoplastic process through aberrant transcription factor function (RUNX1, ETV6, TP53), kinase signalling (FLT3, NRAS, KIT, CBL) and epigenetic deregulation (TET2, IDH1/2, DNMT3A, EZH2, ASXL1, SF3B1, U2AF1, SRSF2, ZRSR2). In this review we will try to focus on the description of these mutations, their impact on prognosis, the functional connections between the different epigenetic pathways, and the existing and future therapies targeting these processes.
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Abstract
During many years, very limited data had been available on specific gene mutations in MDS in particular due to the fact that balanced chromosomal translocations (which have allowed to discover many "leukemia" genes) are very rare in MDS, while chromosomal deletions are generally very large, making it difficult to identify genes of interest. Recently, the advent of next generation sequencing (NGS) techniques has helped identify somatic gene mutations in 75-80% of MDS, that cluster mainly in four functional groups, i.e. cytokine signaling (RAS genes), DNA methylation, (TET2, IDH1/2, DNMT3a genes) histone modifications (ASXL1 and EZH2 genes), and spliceosome (SF3B1 and SRSF2 genes) along with mutations of RUNX1 and TP 53 genes. Most of those mutations, except SF3B1 and TET2 mutations, are associated with an overall poorer prognosis, while some gene mutations (mainly TET2 mutation), may be associated to better response to hypomethylating agents. The frequent mutations of epigenetic modulators in MDS appear to largely contribute to the importance of epigenetic deregulation (in particular gene hypermethylation and histone deacetylation) in MDS progression, and may account at least partially for the efficacy of hypomethylating agents in the treatment of MDS.
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Affiliation(s)
- Raphael Itzykson
- Hematology Department, Hôpital Saint-Louis, Assistance Publique - Hôpitaux de Paris (AP-HP), France; Université Paris 7, France; INSERM Unit U944, Hôpital St Louis, Paris, France
| | - Olivier Kosmider
- Laboratoire d'hématologie, Hôpital Cochin, Assistance Publique - Hôpitaux de Paris (AP-HP), France; Université Paris 5, France
| | - Pierre Fenaux
- Hematology Department, Hôpital Saint-Louis, Assistance Publique - Hôpitaux de Paris (AP-HP), France; Université Paris 7, France; INSERM UMR-S-940, Hôpital St Louis, Paris, France.
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Itzykson R, Fenaux P. Epigenetics of myelodysplastic syndromes. Leukemia 2013; 28:497-506. [DOI: 10.1038/leu.2013.343] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 10/27/2013] [Accepted: 10/30/2013] [Indexed: 12/23/2022]
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Saliba J, Hamidi S, Lenglet G, Langlois T, Yin J, Cabagnols X, Secardin L, Legrand C, Galy A, Opolon P, Benyahia B, Solary E, Bernard OA, Chen L, Debili N, Raslova H, Norol F, Vainchenker W, Plo I, Di Stefano A. Heterozygous and homozygous JAK2(V617F) states modeled by induced pluripotent stem cells from myeloproliferative neoplasm patients. PLoS One 2013; 8:e74257. [PMID: 24066127 PMCID: PMC3774801 DOI: 10.1371/journal.pone.0074257] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 07/29/2013] [Indexed: 12/30/2022] Open
Abstract
JAK2V617F is the predominant mutation in myeloproliferative neoplasms (MPN). Modeling MPN in a human context might be helpful for the screening of molecules targeting JAK2 and its intracellular signaling. We describe here the derivation of induced pluripotent stem (iPS) cell lines from 2 polycythemia vera patients carrying a heterozygous and a homozygous mutated JAK2V617F, respectively. In the patient with homozygous JAK2V617F, additional ASXL1 mutation and chromosome 20 allowed partial delineation of the clonal architecture and assignation of the cellular origin of the derived iPS cell lines. The marked difference in the response to erythropoietin (EPO) between homozygous and heterozygous cell lines correlated with the constitutive activation level of signaling pathways. Strikingly, heterozygous iPS cells showed thrombopoietin (TPO)-independent formation of megakaryocytic colonies, but not EPO-independent erythroid colony formation. JAK2, PI3K and HSP90 inhibitors were able to block spontaneous and EPO-induced growth of erythroid colonies from GPA+CD41+ cells derived from iPS cells. Altogether, this study brings the proof of concept that iPS can be used for studying MPN pathogenesis, clonal architecture, and drug efficacy.
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Affiliation(s)
- Joseph Saliba
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 1009, Laboratory of Excellence, Globule rouge-Excellence (GR-Ex), Villejuif, France
- University Paris-Sud 11, Le Kremlin-Bicêtre, France
- Institut Gustave Roussy, Villejuif, France
| | - Sofiane Hamidi
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 1009, Laboratory of Excellence, Globule rouge-Excellence (GR-Ex), Villejuif, France
- University Paris-Sud 11, Le Kremlin-Bicêtre, France
- Institut Gustave Roussy, Villejuif, France
| | - Gaëlle Lenglet
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 1009, Laboratory of Excellence, Globule rouge-Excellence (GR-Ex), Villejuif, France
- University Paris-Sud 11, Le Kremlin-Bicêtre, France
- Institut Gustave Roussy, Villejuif, France
| | - Thierry Langlois
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 1009, Laboratory of Excellence, Globule rouge-Excellence (GR-Ex), Villejuif, France
- University Paris-Sud 11, Le Kremlin-Bicêtre, France
- Institut Gustave Roussy, Villejuif, France
| | - Jingkui Yin
- Beijing Genomic Institute (BGI), Shenzhen, Shenzhen, China
| | - Xénia Cabagnols
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 1009, Laboratory of Excellence, Globule rouge-Excellence (GR-Ex), Villejuif, France
- University Paris-Sud 11, Le Kremlin-Bicêtre, France
- Institut Gustave Roussy, Villejuif, France
| | - Lise Secardin
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 1009, Laboratory of Excellence, Globule rouge-Excellence (GR-Ex), Villejuif, France
- University Paris-Sud 11, Le Kremlin-Bicêtre, France
- Institut Gustave Roussy, Villejuif, France
| | - Céline Legrand
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 1009, Laboratory of Excellence, Globule rouge-Excellence (GR-Ex), Villejuif, France
- University Paris-Sud 11, Le Kremlin-Bicêtre, France
- Institut Gustave Roussy, Villejuif, France
| | - Anne Galy
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 951, University of Évry Val d’Essonne, Genethon, Évry, France
| | - Paule Opolon
- Institut Gustave Roussy, Pathology platform, Villejuif, France
| | - Baya Benyahia
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Unité Fonctionnelle de Génétique Chromosomique, Département de Génétique, Paris, France
| | - Eric Solary
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 1009, Laboratory of Excellence, Globule rouge-Excellence (GR-Ex), Villejuif, France
- University Paris-Sud 11, Le Kremlin-Bicêtre, France
- Institut Gustave Roussy, Villejuif, France
| | - Olivier A. Bernard
- University Paris-Sud 11, Le Kremlin-Bicêtre, France
- Institut Gustave Roussy, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 985, Villejuif, France
| | - Longyun Chen
- Beijing Genomic Institute (BGI), Shenzhen, Shenzhen, China
| | - Najet Debili
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 1009, Laboratory of Excellence, Globule rouge-Excellence (GR-Ex), Villejuif, France
- University Paris-Sud 11, Le Kremlin-Bicêtre, France
- Institut Gustave Roussy, Villejuif, France
| | - Hana Raslova
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 1009, Laboratory of Excellence, Globule rouge-Excellence (GR-Ex), Villejuif, France
- University Paris-Sud 11, Le Kremlin-Bicêtre, France
- Institut Gustave Roussy, Villejuif, France
| | - Françoise Norol
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 1009, Laboratory of Excellence, Globule rouge-Excellence (GR-Ex), Villejuif, France
- University Paris-Sud 11, Le Kremlin-Bicêtre, France
- Institut Gustave Roussy, Villejuif, France
| | - William Vainchenker
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 1009, Laboratory of Excellence, Globule rouge-Excellence (GR-Ex), Villejuif, France
- University Paris-Sud 11, Le Kremlin-Bicêtre, France
- Institut Gustave Roussy, Villejuif, France
- * E-mail:
| | - Isabelle Plo
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 1009, Laboratory of Excellence, Globule rouge-Excellence (GR-Ex), Villejuif, France
- University Paris-Sud 11, Le Kremlin-Bicêtre, France
- Institut Gustave Roussy, Villejuif, France
| | - Antonio Di Stefano
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 1009, Laboratory of Excellence, Globule rouge-Excellence (GR-Ex), Villejuif, France
- University Paris-Sud 11, Le Kremlin-Bicêtre, France
- Institut Gustave Roussy, Villejuif, France
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