1
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Zhang JY, Chen CR, Qin JY, Shen DY, Liu LX, Song H, Xia T, Xu WQ, Wang Y, Zhu F, Fang MX, Shen HP, Liao C, Dong A, Cao SB, Tang YM, Xu XJ. Targeted gene sequencing and transcriptome sequencing reveal characteristics of NUP98 rearrangement in pediatric acute myeloid leukemia. Eur J Med Res 2024; 29:448. [PMID: 39223643 PMCID: PMC11370121 DOI: 10.1186/s40001-024-02042-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 08/23/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND NUP98 rearrangements (NUP98-r) are rare but overrepresented mutations in pediatric acute myeloid leukemia (AML) patients. NUP98-r is often associated with chemotherapy resistance and a particularly poor prognosis. Therefore, characterizing pediatric AML with NUP98-r to identify aberrations is critically important. METHODS Here, we retrospectively analyzed the clinicopathological features, genomic and transcriptomic landscapes, treatments, and outcomes of pediatric patients with AML. RESULTS Nine patients with NUP98-r mutations were identified in our cohort of 142 patients. Ten mutated genes were detected in patients with NUP98-r. The frequency of FLT3-ITD mutations differed significantly between the groups harboring NUP98-r and those without NUP98-r (P = 0.035). Unsupervised hierarchical clustering via RNA sequencing data from 21 AML patients revealed that NUP98-r samples clustered together, strongly suggesting a distinct subtype. Compared with that in the non-NUP98-r fusion and no fusion groups, CMAHP expression was significantly upregulated in the NUP98-r samples (P < 0.001 and P = 0.001, respectively). Multivariate Cox regression analyses demonstrated that patients harboring NUP98-r (P < 0.001) and WT1 mutations (P = 0.030) had worse relapse-free survival, and patients harboring NUP98-r (P < 0.008) presented lower overall survival. CONCLUSIONS These investigations contribute to the understanding of the molecular characteristics, risk stratification, and prognostic evaluation of pediatric AML patients.
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Affiliation(s)
- Jing-Ying Zhang
- Division/Center of Hematology-Oncology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310005, China
- The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, Hangzhou, 310005, China
- National Clinical Research Center for Child Health, Hangzhou, 310005, China
| | - Chun-Rong Chen
- Division/Center of Hematology-Oncology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310005, China
- The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, Hangzhou, 310005, China
- National Clinical Research Center for Child Health, Hangzhou, 310005, China
| | - Jia-Yue Qin
- Department of Medical Affairs, Acornmed Biotechnology Co., Ltd., Beijing, 100176, China
| | - Di-Ying Shen
- Division/Center of Hematology-Oncology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310005, China
- The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, Hangzhou, 310005, China
- National Clinical Research Center for Child Health, Hangzhou, 310005, China
| | - Li-Xia Liu
- Department of Medical Affairs, Acornmed Biotechnology Co., Ltd., Beijing, 100176, China
| | - Hua Song
- Division/Center of Hematology-Oncology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310005, China
- The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, Hangzhou, 310005, China
- National Clinical Research Center for Child Health, Hangzhou, 310005, China
| | - Tian Xia
- Division/Center of Hematology-Oncology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310005, China
- The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, Hangzhou, 310005, China
- National Clinical Research Center for Child Health, Hangzhou, 310005, China
| | - Wei-Qun Xu
- Division/Center of Hematology-Oncology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310005, China
- The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, Hangzhou, 310005, China
- National Clinical Research Center for Child Health, Hangzhou, 310005, China
| | - Yan Wang
- Division/Center of Hematology-Oncology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310005, China
- The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, Hangzhou, 310005, China
- National Clinical Research Center for Child Health, Hangzhou, 310005, China
| | - Feng Zhu
- Division/Center of Hematology-Oncology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310005, China
- The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, Hangzhou, 310005, China
- National Clinical Research Center for Child Health, Hangzhou, 310005, China
| | - Mei-Xin Fang
- Division/Center of Hematology-Oncology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310005, China
- The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, Hangzhou, 310005, China
- National Clinical Research Center for Child Health, Hangzhou, 310005, China
| | - He-Ping Shen
- Division/Center of Hematology-Oncology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310005, China
- The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, Hangzhou, 310005, China
- National Clinical Research Center for Child Health, Hangzhou, 310005, China
| | - Chan Liao
- Division/Center of Hematology-Oncology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310005, China
- The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, Hangzhou, 310005, China
- National Clinical Research Center for Child Health, Hangzhou, 310005, China
| | - Ao Dong
- National Clinical Research Center for Child Health, Hangzhou, 310005, China
- Department of Clinical Laboratory, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310005, China
| | - Shan-Bo Cao
- Department of Medical Affairs, Acornmed Biotechnology Co., Ltd., Beijing, 100176, China
| | - Yong-Min Tang
- Division/Center of Hematology-Oncology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310005, China
- The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, Hangzhou, 310005, China
- National Clinical Research Center for Child Health, Hangzhou, 310005, China
| | - Xiao-Jun Xu
- Division/Center of Hematology-Oncology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310005, China.
- The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, Hangzhou, 310005, China.
- National Clinical Research Center for Child Health, Hangzhou, 310005, China.
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2
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Fischer A, Hernández-Rodríguez B, Mulet-Lazaro R, Nuetzel M, Hölzl F, van Herk S, Kavelaars FG, Stanewsky H, Ackermann U, Niang AH, Diaz N, Reuschel E, Strieder N, Hernández-López I, Valk PJM, Vaquerizas JM, Rehli M, Delwel R, Gebhard C. STAG2 mutations reshape the cohesin-structured spatial chromatin architecture to drive gene regulation in acute myeloid leukemia. Cell Rep 2024; 43:114498. [PMID: 39084219 DOI: 10.1016/j.celrep.2024.114498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 05/24/2024] [Accepted: 06/27/2024] [Indexed: 08/02/2024] Open
Abstract
Cohesin shapes the chromatin architecture, including enhancer-promoter interactions. Its components, especially STAG2, but not its paralog STAG1, are frequently mutated in myeloid malignancies. To elucidate the underlying mechanisms of leukemogenesis, we comprehensively characterized genetic, transcriptional, and chromatin conformational changes in acute myeloid leukemia (AML) patient samples. Specific loci displayed altered cohesin occupancy, gene expression, and local chromatin activation, which were not compensated by the remaining STAG1-cohesin. These changes could be linked to disrupted spatial chromatin looping in cohesin-mutated AMLs. Complementary depletion of STAG2 or STAG1 in primary human hematopoietic progenitors (HSPCs) revealed effects resembling STAG2-mutant AML-specific changes following STAG2 knockdown, not invoked by the depletion of STAG1. STAG2-deficient HSPCs displayed impaired differentiation capacity and maintained HSPC-like gene expression. This work establishes STAG2 as a key regulator of chromatin contacts, gene expression, and differentiation in the hematopoietic system and identifies candidate target genes that may be implicated in human leukemogenesis.
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MESH Headings
- Humans
- Cohesins
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/metabolism
- Cell Cycle Proteins/metabolism
- Cell Cycle Proteins/genetics
- Chromatin/metabolism
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosomal Proteins, Non-Histone/genetics
- Mutation/genetics
- Hematopoietic Stem Cells/metabolism
- Cell Differentiation/genetics
- Gene Expression Regulation, Leukemic
- Antigens, Nuclear/metabolism
- Antigens, Nuclear/genetics
- Nuclear Proteins
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Affiliation(s)
- Alexander Fischer
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany; Leibniz Institute for Immunotherapy, Regensburg, Germany
| | | | - Roger Mulet-Lazaro
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Margit Nuetzel
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Fabian Hölzl
- Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Stanley van Herk
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - François G Kavelaars
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Hanna Stanewsky
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Ute Ackermann
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Amadou H Niang
- Regulatory Genomics, Max Plank Institute for Molecular Medicine, Münster, Germany
| | - Noelia Diaz
- Regulatory Genomics, Max Plank Institute for Molecular Medicine, Münster, Germany
| | - Edith Reuschel
- Department of Obstetrics and Gynecology, Hospital St. Hedwig of the Order of St. John, Regensburg, Germany
| | | | | | - Peter J M Valk
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Juan M Vaquerizas
- Regulatory Genomics, Max Plank Institute for Molecular Medicine, Münster, Germany; Department of Developmental Epigenomics, MRC London Institute of Medical Sciences, London, UK; Institute of Clinical Sciences, Imperial College London, London, UK
| | - Michael Rehli
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany; Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Ruud Delwel
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands; Oncode Institute, Utrecht, the Netherlands
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3
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Gutch S, Beasley L, Cooper S, Kaplan MH, Capitano ML, Ropa J. Protocol for enrichment and functional analysis of human hematopoietic cells from umbilical cord blood. STAR Protoc 2024; 5:103024. [PMID: 38662544 PMCID: PMC11061328 DOI: 10.1016/j.xpro.2024.103024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/11/2024] [Accepted: 04/03/2024] [Indexed: 05/04/2024] Open
Abstract
Umbilical cord blood (CB) is a donor source for hematopoietic cell therapies. Understanding what drives hematopoietic stem and progenitor cell function is critical to our understanding of the usage of CB in hematopoietic cell therapies. Here, we describe how to isolate and analyze the function of human hematopoietic cells from umbilical CB. This protocol demonstrates assays that measure phenotypic properties and hematopoietic cell potency. For complete details on the use and execution of this protocol, please refer to Broxmeyer et al.1.
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Affiliation(s)
- Sarah Gutch
- Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Lindsay Beasley
- Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Scott Cooper
- Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Mark H Kaplan
- Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | | | - James Ropa
- Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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4
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Scott MT, Liu W, Mitchell R, Clarke CJ, Kinstrie R, Warren F, Almasoudi H, Stevens T, Dunn K, Pritchard J, Drotar ME, Michie AM, Jørgensen HG, Higgins B, Copland M, Vetrie D. Activating p53 abolishes self-renewal of quiescent leukaemic stem cells in residual CML disease. Nat Commun 2024; 15:651. [PMID: 38246924 PMCID: PMC10800356 DOI: 10.1038/s41467-024-44771-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/04/2024] [Indexed: 01/23/2024] Open
Abstract
Whilst it is recognised that targeting self-renewal is an effective way to functionally impair the quiescent leukaemic stem cells (LSC) that persist as residual disease in chronic myeloid leukaemia (CML), developing therapeutic strategies to achieve this have proved challenging. We demonstrate that the regulatory programmes of quiescent LSC in chronic phase CML are similar to that of embryonic stem cells, pointing to a role for wild type p53 in LSC self-renewal. In support of this, increasing p53 activity in primitive CML cells using an MDM2 inhibitor in combination with a tyrosine kinase inhibitor resulted in reduced CFC outputs and engraftment potential, followed by loss of multilineage priming potential and LSC exhaustion when combination treatment was discontinued. Our work provides evidence that targeting LSC self-renewal is exploitable in the clinic to irreversibly impair quiescent LSC function in CML residual disease - with the potential to enable more CML patients to discontinue therapy and remain in therapy-free remission.
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Affiliation(s)
- Mary T Scott
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Wei Liu
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Rebecca Mitchell
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Cassie J Clarke
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Ross Kinstrie
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Felix Warren
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Hassan Almasoudi
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Thomas Stevens
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Karen Dunn
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - John Pritchard
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Mark E Drotar
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Alison M Michie
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Heather G Jørgensen
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | | | - Mhairi Copland
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - David Vetrie
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK.
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5
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Yang T, Mahmood N, Goldberg B, Cevallos J, Hsu P, Kolitz J, Cohen N, Zhang X. Myeloid/lymphoid neoplasm with a novel cryptic RBPMS::FGFR1 rearrangement presenting as de novo acute leukemias. Leuk Lymphoma 2023; 64:2338-2342. [PMID: 37791611 DOI: 10.1080/10428194.2023.2262640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/19/2023] [Indexed: 10/05/2023]
Affiliation(s)
- Tianyu Yang
- Northwell Health, Greenvale, NY, USA
- Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Greenvale, NY, USA
| | - Nayyara Mahmood
- Northwell Health, Greenvale, NY, USA
- Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Greenvale, NY, USA
| | - Bradley Goldberg
- Northwell Health, Greenvale, NY, USA
- Zuckerberg Cancer Center, Department of Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Greenvale, NY, USA
| | - Johnny Cevallos
- Northwell Health, Greenvale, NY, USA
- Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Greenvale, NY, USA
| | - Peihong Hsu
- Northwell Health, Greenvale, NY, USA
- Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Greenvale, NY, USA
| | - Jonathan Kolitz
- Northwell Health, Greenvale, NY, USA
- Zuckerberg Cancer Center, Department of Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Greenvale, NY, USA
| | - Ninette Cohen
- Northwell Health, Greenvale, NY, USA
- Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Greenvale, NY, USA
| | - Xinmin Zhang
- Northwell Health, Greenvale, NY, USA
- Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Greenvale, NY, USA
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6
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Galera P, Dilip D, Derkach A, Chan A, Zhang Y, Persuad S, Mishera T, Liu Y, Famulare C, Gao Q, Mata DA, Arcila M, Geyer MB, Stein E, Dogan A, Levine RL, Roshal M, Glass J, Xiao W. Acute myeloid leukemia with mixed phenotype is characterized by stemness transcriptomic signatures and limited lineage plasticity. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.01.23297696. [PMID: 37961275 PMCID: PMC10635245 DOI: 10.1101/2023.11.01.23297696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Mixed phenotype (MP) in acute leukemias poses unique classification and management dilemmas and can be seen in entities other than de novo mixed phenotype acute leukemia (MPAL). Although WHO classification empirically recommends excluding AML with myelodysplasia related changes (AML-MRC) and therapy related AML (t-AML) with mixed phenotype (AML-MP) from MPAL, there is lack of studies investigating the clinical, genetic, and biologic features of AML-MP. We report the first cohort of AML-MRC and t-AML with MP integrating their clinical, immunophenotypic, genomic and transcriptomic features with comparison to MPAL and AML-MRC/t-AML without MP. Both AML cohorts with and without MP shared similar clinical features including adverse outcomes but were different from MPAL. The genomic landscape of AML-MP overlaps with AML without MP but differs from MPAL. AML-MP harbors more frequent RUNX1 mutations than AML without MP and MPAL. RUNX1 mutations did not impact the survival of patients with MPAL. Unsupervised hierarchal clustering based on immunophenotype identified biologically distinct clusters with phenotype/genotype correlation and outcome differences. Furthermore, transcriptomic analysis showed an enrichment for stemness signature in AML-MP and AML without MP as compared to MPAL. Lastly, MPAL but not AML-MP often switched to lymphoid only immunophenotype after treatment. Expression of transcription factors critical for lymphoid differentiation were upregulated only in MPAL, but not in AML-MP. Our study for the first time demonstrates that AML-MP clinically and biologically resembles its AML counterpart without MP and differs from MPAL, supporting the recommendation to exclude these patients from the diagnosis of MPAL. Future studies are needed to elucidate the molecular mechanism of mixed phenotype in AML. Key points AML-MP clinically and biologically resembles AML but differs from MPAL. AML-MP shows RUNX1 mutations, stemness signatures and limited lymphoid lineage plasticity.
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7
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Nakajima S, Okuma K. Mouse Models for HTLV-1 Infection and Adult T Cell Leukemia. Int J Mol Sci 2023; 24:11737. [PMID: 37511495 PMCID: PMC10380921 DOI: 10.3390/ijms241411737] [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: 06/22/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Adult T cell leukemia (ATL) is an aggressive hematologic disease caused by human T cell leukemia virus type 1 (HTLV-1) infection. Various animal models of HTLV-1 infection/ATL have been established to elucidate the pathogenesis of ATL and develop appropriate treatments. For analyses employing murine models, transgenic and immunodeficient mice are used because of the low infectivity of HTLV-1 in mice. Each mouse model has different characteristics that must be considered before use for different HTLV-1 research purposes. HTLV-1 Tax and HBZ transgenic mice spontaneously develop tumors, and the roles of both Tax and HBZ in cell transformation and tumor growth have been established. Severely immunodeficient mice were able to be engrafted with ATL cell lines and have been used in preclinical studies of candidate molecules for the treatment of ATL. HTLV-1-infected humanized mice with an established human immune system are a suitable model to characterize cells in the early stages of HTLV-1 infection. This review outlines the characteristics of mouse models of HTLV-1 infection/ATL and describes progress made in elucidating the pathogenesis of ATL and developing related therapies using these mice.
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Affiliation(s)
- Shinsuke Nakajima
- Department of Microbiology, Faculty of Medicine, Kansai Medical University, Hirakata 573-1010, Osaka, Japan
| | - Kazu Okuma
- Department of Microbiology, Faculty of Medicine, Kansai Medical University, Hirakata 573-1010, Osaka, Japan
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8
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Boyd AL, Lu J, Hollands CG, Alsostovar L, Murali S, Reid JC, Ye W, Vandersluis S, Johnson P, ElRafie A, Porras DP, Xenocostas D, Leber A, Leber B, Foley R, Trus M, Berg T, Kawata E, Xenocostas A, Bhatia M. Leukemic progenitor compartment serves as a prognostic measure of cancer stemness in patients with acute myeloid leukemia. Cell Rep Med 2023:101108. [PMID: 37433297 PMCID: PMC10394166 DOI: 10.1016/j.xcrm.2023.101108] [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: 08/12/2022] [Revised: 01/29/2023] [Accepted: 06/16/2023] [Indexed: 07/13/2023]
Abstract
We systematically investigate functional and molecular measures of stemness in patients with acute myeloid leukemia (AML) using a cohort of 121 individuals. We confirm that the presence of leukemic stem cells (LSCs) detected through in vivo xenograft transplantation is associated with poor survival. However, the measurement of leukemic progenitor cells (LPCs) through in vitro colony-forming assays provides an even stronger predictor of overall and event-free survival. LPCs not only capture patient-specific mutations but also retain serial re-plating ability, demonstrating their biological relevance. Notably, LPC content represents an independent prognostic factor in multivariate analyses including clinical guidelines of risk stratification. Our findings suggest that LPCs provide a robust functional measure of AML, enabling quantitative and rapid assessment of a wide range of patients. This highlights the potential of LPCs as a valuable prognostic factor in AML management.
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Affiliation(s)
- Allison L Boyd
- Michael G. DeGroote School of Medicine, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Justin Lu
- Michael G. DeGroote School of Medicine, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Cameron G Hollands
- Michael G. DeGroote School of Medicine, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Lili Alsostovar
- Michael G. DeGroote School of Medicine, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Shiva Murali
- Michael G. DeGroote School of Medicine, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Jennifer C Reid
- Michael G. DeGroote School of Medicine, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Wendy Ye
- Michael G. DeGroote School of Medicine, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Sean Vandersluis
- Michael G. DeGroote School of Medicine, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Paige Johnson
- Michael G. DeGroote School of Medicine, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Amro ElRafie
- Michael G. DeGroote School of Medicine, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Deanna P Porras
- Michael G. DeGroote School of Medicine, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Dimetri Xenocostas
- Michael G. DeGroote School of Medicine, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Andrew Leber
- Michael G. DeGroote School of Medicine, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Brian Leber
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Ronan Foley
- Department of Oncology, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Michael Trus
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Tobias Berg
- Department of Oncology, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Eri Kawata
- Department of Medicine, Division of Hematology, Schulich School of Medicine, University of Western Ontario, London, Ontario N6A 3K7, Canada
| | - Anargyros Xenocostas
- Department of Medicine, Division of Hematology, Schulich School of Medicine, University of Western Ontario, London, Ontario N6A 3K7, Canada
| | - Mickie Bhatia
- Michael G. DeGroote School of Medicine, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada.
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9
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Peretz CAC, Kennedy VE, Walia A, Delley CL, Koh A, Tran E, Clark IC, Hayford CE, D'Amato C, Xue Y, Fontanez KM, Roy R, Logan AC, Perl AE, Abate A, Olshen A, Smith CC. Multiomic Single Cell Sequencing Identifies Stemlike Nature of Mixed Phenotype Acute Leukemia and Provides Novel Risk Stratification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.15.540305. [PMID: 37292835 PMCID: PMC10245585 DOI: 10.1101/2023.05.15.540305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Mixed phenotype acute leukemia (MPAL) is a leukemia whose biologic drivers are poorly understood, therapeutic strategy remains unclear, and prognosis is poor. We performed multiomic single cell (SC) profiling of 14 newly diagnosed adult MPAL patients to characterize the immunophenotypic, genetic, and transcriptional landscapes of MPAL. We show that neither genetic profile nor transcriptome reliably correlate with specific MPAL immunophenotypes. However, progressive acquisition of mutations is associated with increased expression of immunophenotypic markers of immaturity. Using SC transcriptional profiling, we find that MPAL blasts express a stem cell-like transcriptional profile distinct from other acute leukemias and indicative of high differentiation potential. Further, patients with the highest differentiation potential demonstrated inferior survival in our dataset. A gene set score, MPAL95, derived from genes highly enriched in this cohort, is applicable to bulk RNA sequencing data and was predictive of survival in an independent patient cohort, suggesting utility for clinical risk stratification.
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Affiliation(s)
- Cheryl A C Peretz
- Divison of Hematology and Oncology, Department of Pediatrics, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Vanessa E Kennedy
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Anushka Walia
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Cyrille L Delley
- Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Andrew Koh
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Elaine Tran
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Iain C Clark
- Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | | | | | - Yi Xue
- Fluent Biosciences Inc., Watertown, MA
| | | | - Ritu Roy
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Aaron C Logan
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Alexander E Perl
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Adam Abate
- Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Adam Olshen
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Catherine C Smith
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
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10
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Heuts BMH, Arza-Apalategi S, Alkema SG, Tijchon E, Jussen L, Bergevoet SM, van der Reijden BA, Martens JHA. Inducible MLL-AF9 Expression Drives an AML Program during Human Pluripotent Stem Cell-Derived Hematopoietic Differentiation. Cells 2023; 12:cells12081195. [PMID: 37190104 DOI: 10.3390/cells12081195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
A t(9;11)(p22;q23) translocation produces the MLL-AF9 fusion protein, which is found in up to 25% of de novo AML cases in children. Despite major advances, obtaining a comprehensive understanding of context-dependent MLL-AF9-mediated gene programs during early hematopoiesis is challenging. Here, we generated a human inducible pluripotent stem cell (hiPSC) model with a doxycycline dose-dependent MLL-AF9 expression. We exploited MLL-AF9 expression as an oncogenic hit to uncover epigenetic and transcriptomic effects on iPSC-derived hematopoietic development and the transformation into (pre-)leukemic states. In doing so, we observed a disruption in early myelomonocytic development. Accordingly, we identified gene profiles that were consistent with primary MLL-AF9 AML and uncovered high-confidence MLL-AF9-associated core genes that are faithfully represented in primary MLL-AF9 AML, including known and presently unknown factors. Using single-cell RNA-sequencing, we identified an increase of CD34 expressing early hematopoietic progenitor-like cell states as well as granulocyte-monocyte progenitor-like cells upon MLL-AF9 activation. Our system allows for careful chemically controlled and stepwise in vitro hiPSC-derived differentiation under serum-free and feeder-free conditions. For a disease that currently lacks effective precision medicine, our system provides a novel entry-point into exploring potential novel targets for personalized therapeutic strategies.
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Affiliation(s)
- Branco M H Heuts
- Faculty of Science, Department of Molecular Biology, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - Saioa Arza-Apalategi
- Radboud University Medical Center, Department of Laboratory Medicine, Laboratory of Hematology, 6525 GA Nijmegen, The Netherlands
| | - Sinne G Alkema
- Faculty of Science, Department of Molecular Biology, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - Esther Tijchon
- Faculty of Science, Department of Molecular Biology, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - Laura Jussen
- Faculty of Science, Department of Molecular Biology, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - Saskia M Bergevoet
- Radboud University Medical Center, Department of Laboratory Medicine, Laboratory of Hematology, 6525 GA Nijmegen, The Netherlands
| | - Bert A van der Reijden
- Radboud University Medical Center, Department of Laboratory Medicine, Laboratory of Hematology, 6525 GA Nijmegen, The Netherlands
| | - Joost H A Martens
- Faculty of Science, Department of Molecular Biology, Radboud University, 6525 GA Nijmegen, The Netherlands
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11
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Xu J, Song F, Lyu H, Kobayashi M, Zhang B, Zhao Z, Hou Y, Wang X, Luan Y, Jia B, Stasiak L, Wong JHY, Wang Q, Jin Q, Jin Q, Fu Y, Yang H, Hardison RC, Dovat S, Platanias LC, Diao Y, Yang Y, Yamada T, Viny AD, Levine RL, Claxton D, Broach JR, Zheng H, Yue F. Subtype-specific 3D genome alteration in acute myeloid leukaemia. Nature 2022; 611:387-398. [PMID: 36289338 PMCID: PMC10060167 DOI: 10.1038/s41586-022-05365-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/20/2022] [Indexed: 11/09/2022]
Abstract
Acute myeloid leukaemia (AML) represents a set of heterogeneous myeloid malignancies, and hallmarks include mutations in epigenetic modifiers, transcription factors and kinases1-5. The extent to which mutations in AML drive alterations in chromatin 3D structure and contribute to myeloid transformation is unclear. Here we use Hi-C and whole-genome sequencing to analyse 25 samples from patients with AML and 7 samples from healthy donors. Recurrent and subtype-specific alterations in A/B compartments, topologically associating domains and chromatin loops were identified. RNA sequencing, ATAC with sequencing and CUT&Tag for CTCF, H3K27ac and H3K27me3 in the same AML samples also revealed extensive and recurrent AML-specific promoter-enhancer and promoter-silencer loops. We validated the role of repressive loops on their target genes by CRISPR deletion and interference. Structural variation-induced enhancer-hijacking and silencer-hijacking events were further identified in AML samples. Hijacked enhancers play a part in AML cell growth, as demonstrated by CRISPR screening, whereas hijacked silencers have a downregulating role, as evidenced by CRISPR-interference-mediated de-repression. Finally, whole-genome bisulfite sequencing of 20 AML and normal samples revealed the delicate relationship between DNA methylation, CTCF binding and 3D genome structure. Treatment of AML cells with a DNA hypomethylating agent and triple knockdown of DNMT1, DNMT3A and DNMT3B enabled the manipulation of DNA methylation to revert 3D genome organization and gene expression. Overall, this study provides a resource for leukaemia studies and highlights the role of repressive loops and hijacked cis elements in human diseases.
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Affiliation(s)
- Jie Xu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Penn State University, Hershey, PA, USA
| | - Fan Song
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Bioinformatics and Genomics Graduate Program, Huck Institutes of Life Sciences, Penn State University, State College, PA, USA
| | - Huijue Lyu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Mikoto Kobayashi
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Baozhen Zhang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Ziyu Zhao
- Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Ye Hou
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Xiaotao Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Yu Luan
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Bei Jia
- Department of Medicine, Division of Hematology and Oncology, Penn State Cancer Institute, Penn State University, Hershey, PA, USA
| | - Lena Stasiak
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Josiah Hiu-Yuen Wong
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Qixuan Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Qi Jin
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Qiushi Jin
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Yihao Fu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Hongbo Yang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Huck Institutes of Life Sciences, Penn State University, State College, PA, USA
| | - Sinisa Dovat
- Department of Medicine, Division of Hematology and Oncology, Penn State Cancer Institute, Penn State University, Hershey, PA, USA
| | - Leonidas C Platanias
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Medicine, Jesse Brown Veterans Affairs Medical Center, Chicago, IL, USA
| | - Yarui Diao
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Yue Yang
- Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Tomoko Yamada
- Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Aaron D Viny
- Division of Hematology/Oncology and Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA
| | - Ross L Levine
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David Claxton
- Department of Medicine, Division of Hematology and Oncology, Penn State Cancer Institute, Penn State University, Hershey, PA, USA
| | - James R Broach
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Penn State University, Hershey, PA, USA
| | - Hong Zheng
- Department of Medicine, Division of Hematology and Oncology, Penn State Cancer Institute, Penn State University, Hershey, PA, USA.
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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12
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Challenges in Cell Fate Acquisition to Scid-Repopulating Activity from Hemogenic Endothelium of hiPSCs Derived from AML Patients Using Forced Transcription Factor Expression. Cells 2022; 11:cells11121915. [PMID: 35741044 PMCID: PMC9221973 DOI: 10.3390/cells11121915] [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] [Received: 03/27/2022] [Revised: 06/05/2022] [Accepted: 06/08/2022] [Indexed: 12/10/2022] Open
Abstract
The generation of human hematopoietic stem cells (HSCs) from human pluripotent stem cells (hPSCs) represents a major goal in regenerative medicine and is believed would follow principles of early development. HSCs arise from a type of endothelial cell called a “hemogenic endothelium” (HE), and human HSCs are experimentally detected by transplantation into SCID or other immune-deficient mouse recipients, termed SCID-Repopulating Cells (SRC). Recently, SRCs were detected by forced expression of seven transcription factors (TF) (ERG, HOXA5, HOXA9, HOXA10, LCOR, RUNX1, and SPI1) in hPSC-derived HE, suggesting these factors are deficient in hPSC differentiation to HEs required to generate HSCs. Here we derived PECAM-1-, Flk-1-, and VE-cadherin-positive endothelial cells that also lack CD45 expression (PFVCD45−) which are solely responsible for hematopoietic output from iPSC lines reprogrammed from AML patients. Using HEs derived from AML patient iPSCs devoid of somatic leukemic aberrations, we sought to generate putative SRCs by the forced expression of 7TFs to model autologous HSC transplantation. The expression of 7TFs in hPSC-derived HE cells from an enhanced hematopoietic progenitor capacity was present in vitro, but failed to acquire SRC activity in vivo. Our findings emphasize the benefits of forced TF expression, along with the continued challenges in developing HSCs for autologous-based therapies from hPSC sources.
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13
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Morris V, Wang D, Li Z, Marion W, Hughes T, Sousa P, Harada T, Sui SH, Naumenko S, Kalfon J, Sensharma P, Falchetti M, Vinicius da Silva R, Candelli T, Schneider P, Margaritis T, Holstege FCP, Pikman Y, Harris M, Stam RW, Orkin SH, Koehler AN, Shalek AK, North TE, Pimkin M, Daley GQ, Lummertz da Rocha E, Rowe RG. Hypoxic, glycolytic metabolism is a vulnerability of B-acute lymphoblastic leukemia-initiating cells. Cell Rep 2022; 39:110752. [PMID: 35476984 PMCID: PMC9099058 DOI: 10.1016/j.celrep.2022.110752] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/24/2022] [Accepted: 04/07/2022] [Indexed: 02/06/2023] Open
Abstract
High-risk forms of B-acute lymphoblastic leukemia (B-ALL) remain a therapeutic challenge. Leukemia-initiating cells (LICs) self-renew and spark relapse and therefore have been the subject of intensive investigation; however, the properties of LICs in high-risk B-ALL are not well understood. Here, we use single-cell transcriptomics and quantitative xenotransplantation to understand LICs in MLL-rearranged (MLL-r) B-ALL. Compared with reported LIC frequencies in acute myeloid leukemia (AML), engraftable LICs in MLL-r B-ALL are abundant. Although we find that multipotent, self-renewing LICs are enriched among phenotypically undifferentiated B-ALL cells, LICs with the capacity to replenish the leukemic cellular diversity can emerge from more mature fractions. While inhibiting oxidative phosphorylation blunts blast proliferation, this intervention promotes LIC emergence. Conversely, inhibiting hypoxia and glycolysis impairs MLL-r B-ALL LICs, providing a therapeutic benefit in xenotransplantation systems. These findings provide insight into the aggressive nature of MLL-r B-ALL and provide a rationale for therapeutic targeting of hypoxia and glycolysis.
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Affiliation(s)
- Vivian Morris
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA
| | - Dahai Wang
- Stem Cell Transplantation Program, Department of Hematology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Zhiheng Li
- Stem Cell Transplantation Program, Department of Hematology, Boston Children's Hospital, Boston, MA 02115, USA
| | - William Marion
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA
| | - Travis Hughes
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Patricia Sousa
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA
| | - Taku Harada
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA
| | - Shannan Ho Sui
- Harvard Chan Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Sergey Naumenko
- Harvard Chan Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Jérémie Kalfon
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Prerana Sensharma
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Stem Cell Transplantation Program, Department of Hematology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Marcelo Falchetti
- Graduate Program of Pharmacology, Center for Biological Sciences, Federal University of Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil
| | - Renan Vinicius da Silva
- Graduate Program of Pharmacology, Center for Biological Sciences, Federal University of Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil
| | - Tito Candelli
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Pauline Schneider
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | | | | | - Yana Pikman
- Harvard Medical School, Boston, MA 02115, USA; Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA
| | - Marian Harris
- Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Ronald W Stam
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Stuart H Orkin
- Harvard Medical School, Boston, MA 02115, USA; Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Angela N Koehler
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alex K Shalek
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Trista E North
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Maxim Pimkin
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA
| | - George Q Daley
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Edroaldo Lummertz da Rocha
- Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis Santa Catarina 88040-900, Brazil
| | - R Grant Rowe
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Stem Cell Transplantation Program, Department of Hematology, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA.
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14
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Tien FM, Tsai CH, Huang SC, Liu JH, Chen CY, Kuo YY, Chuang YK, Tseng MH, Peng YL, Liu MC, Liu CW, Liao XW, Lin LI, Wu YS, Hou MF, Wu SJ, Hsu SC, Ko BS, Chou WC, Yao M, Hou HA, Tang JL, Tien HF. Distinct clinico-biological features in AML patients with low allelic ratio FLT3-ITD: role of allogeneic stem cell transplantation in first remission. Bone Marrow Transplant 2022; 57:95-105. [PMID: 34671120 DOI: 10.1038/s41409-021-01454-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 08/15/2021] [Accepted: 08/26/2021] [Indexed: 02/08/2023]
Abstract
The mutant burden of FLT3-ITD modulates its prognostic impact on patients with acute myeloid leukemia (AML). However, for patients with low allelic ratio (AR) FLT3-ITD (FLT3-ITDlow, AR < 0.5), clinical features, as well as genomic and transcriptomic profiles remain unclear, and evidence supporting allogeneic hematopoietic stem cell transplantation (allo-HSCT) in first complete remission (CR1) remains controversial. This study aimed to elucidate the genomic features, prognosis, and transplantation outcome of FLT3-ITDIow in AML patients with intermediate-risk cytogenetics. FLT3-ITDlow was associated with a negative enrichment of the leukemic stem cell signature, a marked enrichment of the RAS pathway, and with higher frequencies of RAS pathway mutations, different from those with FLT3-ITDhigh. Concurrent CEBPA double mutations were favorable prognostic factors, whereas MLL-PTD, and mutations in splicing factors were unfavorable prognostic factors in FLT3-ITDlow patients. Patients with FLT3-ITDlow had a shorter overall survival (OS) and event-free survival (EFS) than those with FLT3wt. Allo-HSCT in CR1 was associated with a significantly longer OS and EFS compared with postremission chemotherapy in patients with FLT3-ITDlow. In conclusion, FLT3-ITDlow is associated with different mutational and transcriptomic profiles compared with FLT3-ITDhigh. The presence of concomitant poor-risk mutations exert negative prognostic impacts in patients with FLT3-ITDlow, who markedly benefit from allo-HSCT in CR1.
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Affiliation(s)
- Feng-Ming Tien
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Department of Hematological Oncology, National Taiwan University Cancer Center, Taipei, Taiwan.,Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Cheng-Hong Tsai
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Sheng-Chuan Huang
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Jia-Hau Liu
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Department of Hematological Oncology, National Taiwan University Cancer Center, Taipei, Taiwan
| | - Chien-Yuan Chen
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Yuan-Yeh Kuo
- Tai-Chen Cell Therapy Center, National Taiwan University, Taipei, Taiwan
| | - Yi-Kuang Chuang
- Tai-Chen Cell Therapy Center, National Taiwan University, Taipei, Taiwan
| | - Mei-Hsuan Tseng
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Yen-Ling Peng
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Ming-Chih Liu
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Chia-Wen Liu
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Xiu-Wen Liao
- Tai-Chen Cell Therapy Center, National Taiwan University, Taipei, Taiwan
| | - Liang-In Lin
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yu-Sin Wu
- Department of Nursing, National Taiwan University Cancer Center, Taipei, Taiwan
| | - Mei-Fang Hou
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Department of Nursing, National Taiwan University Hospital, Taipei, Taiwan
| | - Shang-Ju Wu
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Szu-Chun Hsu
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Bor-Sheng Ko
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Department of Hematological Oncology, National Taiwan University Cancer Center, Taipei, Taiwan
| | - Wen-Chien Chou
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Ming Yao
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Hsin-An Hou
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.
| | - Jih-Luh Tang
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan. .,Department of Hematological Oncology, National Taiwan University Cancer Center, Taipei, Taiwan. .,Tai-Chen Cell Therapy Center, National Taiwan University, Taipei, Taiwan.
| | - Hwei-Fang Tien
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
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15
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CMAHP promotes metastasis by reducing ubiquitination of Snail and inducing angiogenesis via GM-CSF overexpression in gastric cancer. Oncogene 2022; 41:159-172. [PMID: 34716430 DOI: 10.1038/s41388-021-02087-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 12/18/2022]
Abstract
Pseudogenes are generally considered "junk" DNA or "genomic fossils" generated during the evolution process that lack biological activity. However, accumulating reports indicate that pseudogenes have biological functions critical for cancer development. Experiments from the current study showed marked overexpression of the cytidine monophospho-N-acetylneuraminic acid hydroxylase pseudogene (CMAHP) in gastric cancer, which was associated with poor overall survival. However, the mechanisms underlying the activity of CMAHP in tumor development are largely unknown. Gene Set Enrichment Analysis (GSEA) revealed that CMAHP-correlated genes are significantly involved in epithelial-mesenchymal transition (EMT) and angiogenesis. Functional studies further confirmed that CMAHP mediates metastasis and angiogenesis in vitro and in vivo. Furthermore, CMAHP promoted cancer cell migration, invasion, and metastasis through Snail overexpression, which decreased ubiquitination mediated by NF-κB signaling. Angiogenesis is known to be induced by granulocyte-macrophage colony-stimulating factor (GM-CSF) stimulation. CMAHP increased GM-CSF transactivation via promoting direct binding of c-Jun to the -1981/-1975 region of the GM-CSF promoter. Notably, CMAHP interacts with Histone H1.4 promoting histone acetylation to enhance c-Jun and RelA (p65) expression. Our collective findings provide novel evidence that CMAHP contributes to tumor progression and modulates metastasis and angiogenesis in gastric cancer.
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16
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Ueda T, Kanai A, Komuro A, Amano H, Ota K, Honda M, Kawazu M, Okada H. KDM4B promotes acute myeloid leukemia associated with AML1-ETO by regulating chromatin accessibility. FASEB Bioadv 2021; 3:1020-1033. [PMID: 34938963 PMCID: PMC8664044 DOI: 10.1096/fba.2021-00030] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 11/11/2022] Open
Abstract
Epigenetic alterations of chromatin structure affect chromatin accessibility and collaborate with genetic alterations in the development of cancer. Lysine demethylase 4B (KDM4B) has been identified as a JmjC domain-containing epigenetic modifier that possesses histone demethylase activity. Although recent studies have demonstrated that KDM4B positively regulates the pathogenesis of multiple types of solid tumors, the tissue specificity and context dependency have not been fully elucidated. In this study, we investigated gene expression profiles established from clinical samples and found that KDM4B is elevated specifically in acute myeloid leukemia (AML) associated with chromosomal translocation 8;21 [t(8;21)], which results in a fusion of the AML1 and the eight-twenty-one (ETO) genes to generate a leukemia oncogene, AML1-ETO fusion transcription factor. Short hairpin RNA-mediated KDM4B silencing significantly reduced cell proliferation in t(8;21)-positive AML cell lines. Meanwhile, KDM4B silencing suppressed the expression of AML1-ETO-inducible genes, and consistently perturbed chromatin accessibility of AML1-ETO-binding sites involving altered active enhancer marks and functional cis-regulatory elements. Notably, transduction of murine KDM4B orthologue mutants followed by KDM4B silencing demonstrated a requirement of methylated-histone binding modules for a proliferative surge. To address the role of KDM4B in leukemia development, we further generated and analyzed Kdm4b conditional knockout mice. As a result, Kdm4b deficiency attenuated clonogenic potential mediated by AML1-ETO and delayed leukemia progression in vivo. Thus, our results highlight a tumor-promoting role of KDM4B in AML associated with t(8;21).
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Affiliation(s)
- Takeshi Ueda
- Department of BiochemistryKindai University Faculty of MedicineOsakasayamaJapan
- Graduate School of Medical SciencesKindai University Faculty of MedicineOsakasayamaJapan
| | - Akinori Kanai
- Department of Molecular OncologyResearch Institute for Radiation Biology and MedicineHiroshima UniversityHiroshimaJapan
| | - Akiyoshi Komuro
- Department of BiochemistryKindai University Faculty of MedicineOsakasayamaJapan
| | - Hisayuki Amano
- Department of BiochemistryKindai University Faculty of MedicineOsakasayamaJapan
| | - Kazushige Ota
- Department of BiochemistryKindai University Faculty of MedicineOsakasayamaJapan
| | - Masahiko Honda
- Department of BiochemistryKindai University Faculty of MedicineOsakasayamaJapan
| | - Masahito Kawazu
- Division of Cellular SignalingNational Cancer Center Research InstituteTokyoJapan
| | - Hitoshi Okada
- Department of BiochemistryKindai University Faculty of MedicineOsakasayamaJapan
- Graduate School of Medical SciencesKindai University Faculty of MedicineOsakasayamaJapan
- Anti‐Aging CenterKindai UniversityHigashi‐OsakaJapan
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17
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Shukla S, Ying W, Gray F, Yao Y, Simes ML, Zhao Q, Miao H, Cho HJ, González-Alonso P, Winkler A, Lund G, Purohit T, Kim E, Zhang X, Ray JM, He S, Nikolaidis C, Ndoj J, Wang J, Jaremko Ł, Jaremko M, Ryan RJH, Guzman ML, Grembecka J, Cierpicki T. Small-molecule inhibitors targeting Polycomb repressive complex 1 RING domain. Nat Chem Biol 2021; 17:784-793. [PMID: 34155404 PMCID: PMC8238916 DOI: 10.1038/s41589-021-00815-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 05/10/2021] [Indexed: 12/11/2022]
Abstract
Polycomb repressive complex 1 (PRC1) is an essential chromatin-modifying complex that monoubiquitinates histone H2A and is involved in maintaining the repressed chromatin state. Emerging evidence suggests PRC1 activity in various cancers, rationalizing the need for small-molecule inhibitors with well-defined mechanisms of action. Here, we describe the development of compounds that directly bind to RING1B-BMI1, the heterodimeric complex constituting the E3 ligase activity of PRC1. These compounds block the association of RING1B-BMI1 with chromatin and inhibit H2A ubiquitination. Structural studies demonstrate that these inhibitors bind to RING1B by inducing the formation of a hydrophobic pocket in the RING domain. Our PRC1 inhibitor, RB-3, decreases the global level of H2A ubiquitination and induces differentiation in leukemia cell lines and primary acute myeloid leukemia (AML) samples. In summary, we demonstrate that targeting the PRC1 RING domain with small molecules is feasible, and RB-3 represents a valuable chemical tool to study PRC1 biology.
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Affiliation(s)
- Shirish Shukla
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Weijiang Ying
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Felicia Gray
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yiwu Yao
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Miranda L Simes
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Qingjie Zhao
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Hongzhi Miao
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Hyo Je Cho
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | - Alyssa Winkler
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - George Lund
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Trupta Purohit
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - EunGi Kim
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Xiaotian Zhang
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Joshua M Ray
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Shihan He
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | - Juliano Ndoj
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Jingya Wang
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- MedImmune, LLC, Gaithersburg, MD, USA
| | - Łukasz Jaremko
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mariusz Jaremko
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Russell J H Ryan
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Monica L Guzman
- Division of Hematology and Medical Oncology, Leukemia Program, Weill Cornell Medicine/New York-Presbyterian Hospital, New York, NY, USA
| | - Jolanta Grembecka
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
| | - Tomasz Cierpicki
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
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18
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Albayrak E, Uslu M, Akgol S, Tuysuz EC, Kocabas F. Small molecule-mediated modulation of ubiquitination and neddylation improves HSC function ex vivo. J Cell Physiol 2021; 236:8122-8136. [PMID: 34101829 DOI: 10.1002/jcp.30466] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 05/04/2021] [Accepted: 05/27/2021] [Indexed: 11/07/2022]
Abstract
Hematopoietic stem cells (HSCs) are particularly characterized by their quiescence and self-renewal. Cell cycle regulators tightly control quiescence and self-renewal capacity. Studies suggest that modulation of ubiquitination and neddylation could contribute to HSC function via cyclin-dependent kinase inhibitors (CDKIs). S-phase kinase-associated protein 2 (SKP2) is responsible for ubiquitin-mediated proteolysis of CDKIs. Here, we modulated overall neddylation and SKP2-associated ubiquitination in HSCs by using SKP2-C25, an SKP2 inhibitor, and MLN4924 (Pevonedistat) as an inhibitor of the NEDD8 system. Treatments of SKP2-C25 and MLN4924 increased both murine and human stem and progenitor cell (HSPC) compartments. This is associated with the improved quiescence of murine HSC by upregulation of p27 and p57 CDKIs. A colony-forming unit assay showed an enhanced in vitro self-renewal potential post inhibition of ubiquitination and neddylation. In addition, MLN4924 triggered the mobilization of bone marrow HSPCs to peripheral blood. Intriguingly, MLN4924 treatment could decrease the proliferation of murine bone marrow mesenchymal stem cells or endothelial cells. These findings shed light on the contribution of SKP2, and associated ubiquitination and neddylation in HSC maintenance, self-renewal, and expansion.
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Affiliation(s)
- Esra Albayrak
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Merve Uslu
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Sezer Akgol
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Emre Can Tuysuz
- Department of Medical Genetics, Faculty of Medicine, Yeditepe University, Istanbul, Turkey
| | - Fatih Kocabas
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
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19
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Pacharne S, Dovey OM, Cooper JL, Gu M, Friedrich MJ, Rajan SS, Barenboim M, Collord G, Vijayabaskar MS, Ponstingl H, De Braekeleer E, Bautista R, Mazan M, Rad R, Tzelepis K, Wright P, Gozdecka M, Vassiliou GS. SETBP1 overexpression acts in the place of class-defining mutations to drive FLT3-ITD-mutant AML. Blood Adv 2021; 5:2412-2425. [PMID: 33956058 PMCID: PMC8114559 DOI: 10.1182/bloodadvances.2020003443] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 01/25/2021] [Indexed: 12/23/2022] Open
Abstract
Advances in cancer genomics have revealed genomic classes of acute myeloid leukemia (AML) characterized by class-defining mutations, such as chimeric fusion genes or in genes such as NPM1, MLL, and CEBPA. These class-defining mutations frequently synergize with internal tandem duplications in FLT3 (FLT3-ITDs) to drive leukemogenesis. However, ∼20% of FLT3-ITD-positive AMLs bare no class-defining mutations, and mechanisms of leukemic transformation in these cases are unknown. To identify pathways that drive FLT3-ITD mutant AML in the absence of class-defining mutations, we performed an insertional mutagenesis (IM) screening in Flt3-ITD mice, using Sleeping Beauty transposons. All mice developed acute leukemia (predominantly AML) after a median of 73 days. Analysis of transposon insertions in 38 samples from Flt3-ITD/IM leukemic mice identified recurrent integrations at 22 loci, including Setbp1 (20/38), Ets1 (11/38), Ash1l (8/38), Notch1 (8/38), Erg (7/38), and Runx1 (5/38). Insertions at Setbp1 led exclusively to AML and activated a transcriptional program similar, but not identical, to those of NPM1-mutant and MLL-rearranged AMLs. Guide RNA targeting of Setbp1 was highly detrimental to Flt3ITD/+/Setbp1IM+, but not to Flt3ITD/+/Npm1cA/+, AMLs. Also, analysis of RNA-sequencing data from hundreds of human AMLs revealed that SETBP1 expression is significantly higher in FLT3-ITD AMLs lacking class-defining mutations. These findings propose that SETBP1 overexpression collaborates with FLT3-ITD to drive a subtype of human AML. To identify genetic vulnerabilities of these AMLs, we performed genome-wide CRISPR-Cas9 screening in Flt3ITD/+/Setbp1IM+ AMLs and identified potential therapeutic targets, including Kdm1a, Brd3, Ezh2, and Hmgcr. Our study gives new insights into epigenetic pathways that can drive AMLs lacking class-defining mutations and proposes therapeutic approaches against such cases.
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Affiliation(s)
- Suruchi Pacharne
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Wellcome-Medical Research Center (MRC) Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Oliver M Dovey
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Jonathan L Cooper
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Muxin Gu
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Wellcome-Medical Research Center (MRC) Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Mathias J Friedrich
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Department of Medicine II, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
| | - Sandeep S Rajan
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- United Kingdom Dementia Research Institute, University of Cambridge, Cambridge, United Kingdom
| | - Maxim Barenboim
- Department of Pediatrics and Children's Cancer Research Center, Klinikum Rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Grace Collord
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Wellcome-Medical Research Center (MRC) Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - M S Vijayabaskar
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Wellcome-Medical Research Center (MRC) Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Hannes Ponstingl
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Etienne De Braekeleer
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Wellcome-Medical Research Center (MRC) Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Ruben Bautista
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Milena Mazan
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Research and Development Department, Selvita S.A., Krakow, Poland
| | - Roland Rad
- Department of Medicine II, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany; and
| | - Konstantinos Tzelepis
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Gurdon Institute
- Department of Pathology, and
| | | | - Malgorzata Gozdecka
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Wellcome-Medical Research Center (MRC) Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - George S Vassiliou
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Wellcome-Medical Research Center (MRC) Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, Cambridge University Hospitals National Health Service (NHS) Trust, Cambridge, United Kingdom
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20
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Molecular-Based Score inspired on metabolic signature improves prognostic stratification for myelodysplastic syndrome. Sci Rep 2021; 11:1675. [PMID: 33462268 PMCID: PMC7814118 DOI: 10.1038/s41598-020-80918-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/29/2020] [Indexed: 01/29/2023] Open
Abstract
Deregulated cellular energetics is formally incorporated as an emerging hallmark of cancer, however little is known about its processes in myelodysplastic syndromes (MDS). Using transcriptomic data of CD34+ cells from 159 MDS patients and 17 healthy donors, we selected 37 genes involved in cellular energetics and interrogated about its clinical and prognostic functions. Based on the low expression of ACLY, ANPEP, and PANK1, as well as high expression of PKM and SLC25A5, we constructed our Molecular-Based Score (MBS), that efficiently discriminated patients at three risks groups: favourable risk (n = 28; 3-year overall survival (OS): 100%); intermediate (n = 60; 76% [62-93%]) and adverse (n = 71; 35% [17-61%]). Adverse MBS risk was independently associated with inferior OS (HR = 10.1 [95% CI 1.26-81]; P = 0.029) in multivariable analysis using age, gender and the revised international prognostic score system as confounders. Transcriptional signature revealed that Favourable- and intermediate-risk patients presented enriched molecular programs related to mature myeloid progenitors, cell cycle progression, and oxidative phosphorylation, indicating that this cells differs in their origin, metabolic state, and cell cycle regulation, in comparison to the adverse-risk. Our study provides the first evidence that cellular energetics is transcriptionally deregulated in MDS CD34+ cells and establishes a new useful prognostic score based on the expression of five genes.
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21
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Capo V, Penna S, Merelli I, Barcella M, Scala S, Basso-Ricci L, Draghici E, Palagano E, Zonari E, Desantis G, Uva P, Cusano R, Sergi LS, Crisafulli L, Moshous D, Stepensky P, Drabko K, Kaya Z, Unal E, Gezdiric A, Menna G, Serafini M, Aiuti A, Locatelli SL, Carlo-Stella C, Schulz AS, Ficara F, Sobacchi C, Gentner B, Villa A. Expanded circulating hematopoietic stem/progenitor cells as novel cell source for the treatment of TCIRG1 osteopetrosis. Haematologica 2021; 106:74-86. [PMID: 31949009 PMCID: PMC7776247 DOI: 10.3324/haematol.2019.238261] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 01/09/2020] [Indexed: 11/16/2022] Open
Abstract
Allogeneic hematopoietic stem cell transplantation is the treatment of choice for autosomal recessive osteopetrosis caused by defects in the TCIRG1 gene. Despite recent progress in conditioning, a relevant number of patients are not eligible for allogeneic stem cell transplantation because of the severity of the disease and significant transplant-related morbidity. We exploited peripheral CD34+ cells, known to circulate at high frequency in the peripheral blood of TCIRG1-deficient patients, as a novel cell source for autologous transplantation of gene corrected cells. Detailed phenotypical analysis showed that circulating CD34+ cells have a cellular composition that resembles bone marrow, supporting their use in gene therapy protocols. Transcriptomic profile revealed enrichment in genes expressed by hematopoietic stem and progenitor cells (HSPCs). To overcome the limit of bone marrow harvest/ HSPC mobilization and serial blood drawings in TCIRG1 patients, we applied UM171-based ex-vivo expansion of HSPCs coupled with lentiviral gene transfer. Circulating CD34+ cells from TCIRG1-defective patients were transduced with a clinically-optimized lentiviral vector (LV) expressing TCIRG1 under the control of phosphoglycerate promoter and expanded ex vivo. Expanded cells maintained long-term engraftment capacity and multi-lineage repopulating potential when transplanted in vivo both in primary and secondary NSG recipients. Moreover, when CD34+ cells were differentiated in vitro, genetically corrected osteoclasts resorbed the bone efficiently. Overall, we provide evidence that expansion of circulating HSPCs coupled to gene therapy can overcome the limit of stem cell harvest in osteopetrotic patients, thus opening the way to future gene-based treatment of skeletal diseases caused by bone marrow fibrosis.
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Affiliation(s)
- Valentina Capo
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Sara Penna
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- DIMET, University of Milano-Bicocca, Monza, Italy
| | - Ivan Merelli
- Institute for Biomedical Technologies, National Research Council, Segrate, Italy
| | - Matteo Barcella
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Serena Scala
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Luca Basso-Ricci
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Elena Draghici
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Eleonora Palagano
- CNR-IRGB, Milan Unit, Milan, Italy
- Humanitas Clinical and Research Center - IRCCS, Rozzano, Italy
| | - Erika Zonari
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giacomo Desantis
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Paolo Uva
- CRS4, Science and Technology Park Polaris, Pula, Italy
| | | | - Lucia Sergi Sergi
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Laura Crisafulli
- CNR-IRGB, Milan Unit, Milan, Italy
- Humanitas Clinical and Research Center - IRCCS, Rozzano, Italy
| | - Despina Moshous
- Unite d'Immunologie, Hematologie et Rhumatologie Pediatriques (UIHR), Assistance Publique-Hopitaux de Paris, Hopital Necker-Enfants Malades, Paris, France
- INSERM UMR1163, Institut Imagine, Universite Paris Descartes-Sorbonne Paris Cite, Paris, France
| | - Polina Stepensky
- Department of Bone Marrow Transplantation and Cancer Immunotherapy, Hadassah University Hospital, Jerusalem, Israel
| | | | - Zühre Kaya
- Department of Pediatric Hematology, Gazi University, School of Medicine, Ankara, Turkey
| | - Ekrem Unal
- Erciyes University, Pediatric Hematology Oncology, Kayseri, Turkey
- Molecular Biology and Genetic Department, Gevher Nesibe Genom and Stem Cell Institution, Genome and Stem Cell Center (GENKOK), Erciyes University, Kayseri, Turkey
| | - Alper Gezdiric
- Department of Medical Genetics, Istanbul Health Science University, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul, Turkey
| | - Giuseppe Menna
- Hemato-Oncology Unit, Department of Oncology, Pausilipon Hospital, Naples, Italy
| | | | - Alessandro Aiuti
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Silvia Laura Locatelli
- Department of Oncology and Hematology, Humanitas Cancer Center, Humanitas Clinical and Research Center, Rozzano, Italy
| | - Carmelo Carlo-Stella
- Department of Oncology and Hematology, Humanitas Cancer Center, Humanitas Clinical and Research Center, Rozzano, Italy
- Department of Biomedical Sciences, Humanitas University, Rozzano, Italy
| | - Ansgar S. Schulz
- Department of Pediatrics and Adolescent Medicine, University Medical Center, Ulm, Germany
| | - Francesca Ficara
- CNR-IRGB, Milan Unit, Milan, Italy
- Humanitas Clinical and Research Center - IRCCS, Rozzano, Italy
| | - Cristina Sobacchi
- CNR-IRGB, Milan Unit, Milan, Italy
- Humanitas Clinical and Research Center - IRCCS, Rozzano, Italy
| | - Bernhard Gentner
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Anna Villa
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- CNR-IRGB, Milan Unit, Milan, Italy
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22
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Quintero A, Hübschmann D, Kurzawa N, Steinhauser S, Rentzsch P, Krämer S, Andresen C, Park J, Eils R, Schlesner M, Herrmann C. ShinyButchR: Interactive NMF-based decomposition workflow of genome-scale datasets. Biol Methods Protoc 2020; 5:bpaa022. [PMID: 33376806 PMCID: PMC7750682 DOI: 10.1093/biomethods/bpaa022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/25/2020] [Accepted: 10/26/2020] [Indexed: 11/12/2022] Open
Abstract
Non-negative matrix factorization (NMF) has been widely used for the analysis of genomic data to perform feature extraction and signature identification due to the interpretability of the decomposed signatures. However, running a basic NMF analysis requires the installation of multiple tools and dependencies, along with a steep learning curve and computing time. To mitigate such obstacles, we developed ShinyButchR, a novel R/Shiny application that provides a complete NMF-based analysis workflow, allowing the user to perform matrix decomposition using NMF, feature extraction, interactive visualization, relevant signature identification, and association to biological and clinical variables. ShinyButchR builds upon the also novel R package ButchR, which provides new TensorFlow solvers for algorithms of the NMF family, functions for downstream analysis, a rational method to determine the optimal factorization rank and a novel feature selection strategy.
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Affiliation(s)
| | | | | | | | - Philipp Rentzsch
- Computational Genome Biology, Berlin Institute of Health (BIH), Berlin, Germany
| | - Stephen Krämer
- Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carolin Andresen
- Computational Oncology, Molecular Diagnostics Program, National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
| | - Jeongbin Park
- Center for Digital Health, Berlin Institute of Health (BIH) and Charité – Universitätsmedizin Berlin, Germany
| | - Roland Eils
- Health Data Science Unit, Medical Faculty and BioQuant, University Heidelberg, Heidelberg, Germany
- Center for Digital Health, Berlin Institute of Health (BIH) and Charité – Universitätsmedizin Berlin, Germany
| | - Matthias Schlesner
- Present address: Chair of Biomedical Informatics, Data Mining and Data Analytics, Faculty of Computer Science, University of Augsburg, Germany
| | - Carl Herrmann
- Correspondence address. Health Data Science Unit, Medical Faculty and BioQuant, University Heidelberg, Heidelberg, Germany. Tel: +49 6221 5451249; Fax: +49 6221 545148. E-mail:
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23
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Spyrou N, Papapetrou EP. Studying leukemia stem cell properties and vulnerabilities with human iPSCs. Stem Cell Res 2020; 50:102117. [PMID: 33388708 PMCID: PMC8190184 DOI: 10.1016/j.scr.2020.102117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/16/2020] [Accepted: 12/04/2020] [Indexed: 12/17/2022] Open
Abstract
The reprogramming of cancer cells into induced pluripotent stem cells (iPSCs) can capture entire cancer genomes, and thus create genetically faithful models of human cancers. By providing stringent genetically clonal conditions, iPSC modeling can also unveil non-genetic sources of cancer heterogeneity and provide a unique opportunity to study them separately from genetic sources, as we recently showed in an iPSC-based model of acute myeloid leukemia (AML). Genetically clonal iPSCs, derived from a patient with AML, reproduce, upon hematopoietic differentiation, phenotypic and functional heterogeneity with all the hallmarks of a leukemia stem cell (LSC) hierarchy. Here we discuss the lessons that can be learned about the LSC state, its plasticity, stability and genetic and epigenetic determinants from iPSC modeling. We also discuss the practical and translational implications of exploiting AML-iPSCs to prospectively isolate large numbers of iLSCs for large-scale experiments, such as screens, and for discovery of new therapeutic targets specific to AML LSCs.
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Affiliation(s)
- Nikolaos Spyrou
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eirini P Papapetrou
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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24
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Hung SY, Lin CC, Hsu CL, Yao CY, Wang YH, Tsai CH, Hou HA, Chou WC, Tien HF. The expression levels of long non-coding RNA KIAA0125 are associated with distinct clinical and biological features in myelodysplastic syndromes. Br J Haematol 2020; 192:589-598. [PMID: 33249572 DOI: 10.1111/bjh.17231] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/20/2020] [Indexed: 12/16/2022]
Abstract
Long non-coding RNAs (lncRNAs) have important functions in cancer biology. Among them, lncRNA KIAA0125 is one of the genes proposed to play a critical role in leukaemia stem cell (LSC). In this study, we aimed to investigate the clinical relevance of the expression levels of lncRNA KIAA0125 in myelodysplastic syndromes (MDS), a disease with highly heterogeneous clinical and biological features. Using RNA arrays, we measured the expression of KIAA0125 in 176 primary MDS patients. We found that higher KIAA0125 expression was associated with higher risk MDS, based on the revised International Prognostic Scoring System (IPSS-R), mutations in ASXL1 and NRAS, and predicted poorer overall survival (OS) and leukaemia-free survival (LFS). Multivariate analysis revealed that higher KIAA0125 expression was an independent, unfavourable prognostic factor for OS and LFS, irrespective of IPSS-R and mutation status. Further global gene expression profile analysis suggested a close association of higher KIAA0125 expressions with LSC signatures. The expression of KIAA0125 may be a potential biomarker to guide the treatment choice in MDS patients, especially those with lower risk subtypes, in whom palliative treatment is usually used.
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Affiliation(s)
- Sheng-Yu Hung
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital Yunlin Branch, Yunlin, Taiwan
| | - Chien-Chin Lin
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei, Taiwan.,Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chia-Lang Hsu
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - Chi-Yuan Yao
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei, Taiwan.,Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Yu-Hung Wang
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Cheng-Hong Tsai
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Hsin-An Hou
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Wen-Chien Chou
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Hwei-Fang Tien
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
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25
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Distinct clinical and biological characteristics of acute myeloid leukemia with higher expression of long noncoding RNA KIAA0125. Ann Hematol 2020; 100:487-498. [PMID: 33225420 PMCID: PMC7817567 DOI: 10.1007/s00277-020-04358-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 11/18/2020] [Indexed: 12/12/2022]
Abstract
Expression of long non-coding RNA KIAA0125 has been incorporated in various gene expression signatures for prognostic prediction in acute myeloid leukemia (AML) patients, yet its functions and clinical significance remain unclear. This study aimed to investigate the clinical and biological characteristics of AML bearing different levels of KIAA0125. We profiled KIAA0125 expression levels in bone marrow cells from 347 de novo AML patients and found higher KIAA0125 expression was closely associated with RUNX1 mutation, but inversely correlated with t(8;21) and t(15;17) karyotypes. Among the 227 patients who received standard chemotherapy, those with higher KIAA0125 expression had a lower complete remission rate, shorter overall survival (OS) and disease-free survival (DFS) than those with lower expression. The prognostic significance was validated in both TCGA and GSE12417 cohorts. Subgroup analyses showed that higher KIAA0125 expression also predicted shorter DFS and OS in patients with normal karyotype or non-M3 AML. In multivariable analysis, higher KIAA0125 expression remained an adverse risk factor independent of age, WBC counts, karyotypes, and mutation patterns. Bioinformatics analyses revealed that higher KIAA0125 expression was associated with hematopoietic and leukemic stem cell signatures and ATP-binding cassette transporters, two predisposing factors for chemoresistance.
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26
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An induced pluripotent stem cell model of Fanconi anemia reveals mechanisms of p53-driven progenitor cell differentiation. Blood Adv 2020; 4:4679-4692. [PMID: 33002135 DOI: 10.1182/bloodadvances.2020001593] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 08/26/2020] [Indexed: 12/17/2022] Open
Abstract
Fanconi anemia (FA) is a disorder of DNA repair that manifests as bone marrow (BM) failure. The lack of accurate murine models of FA has refocused efforts toward differentiation of patient-derived induced pluripotent stem cells (IPSCs) to hematopoietic progenitor cells (HPCs). However, an intact FA DNA repair pathway is required for efficient IPSC derivation, hindering these efforts. To overcome this barrier, we used inducible complementation of FANCA-deficient IPSCs, which permitted robust maintenance of IPSCs. Modulation of FANCA during directed differentiation to HPCs enabled the production of FANCA-deficient human HPCs that recapitulated FA genotoxicity and hematopoietic phenotypes relative to isogenic FANCA-expressing HPCs. FANCA-deficient human HPCs underwent accelerated terminal differentiation driven by activation of p53/p21. We identified growth arrest specific 6 (GAS6) as a novel target of activated p53 in FANCA-deficient HPCs and modulate GAS6 signaling to rescue hematopoiesis in FANCA-deficient cells. This study validates our strategy to derive a sustainable, highly faithful human model of FA, uncovers a mechanism of HPC exhaustion in FA, and advances toward future cell therapy in FA.
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27
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Uslu M, Albayrak E, Kocabaş F. Temporal modulation of calcium sensing in hematopoietic stem cells is crucial for proper stem cell expansion and engraftment. J Cell Physiol 2020; 235:9644-9666. [PMID: 32394484 DOI: 10.1002/jcp.29777] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 04/25/2020] [Accepted: 04/29/2020] [Indexed: 12/11/2022]
Abstract
Hematopoietic stem cells (HSCs) are known to reside in a bone marrow (BM) niche, which is associated with relatively higher calcium content. HSCs sense and respond to calcium changes. However, how calcium-sensing components modulate HSC function and expansion is largely unknown. We investigated temporal modulation of calcium sensing and Ca2+ homeostasis during ex vivo HSC culture and in vivo. Murine BM-HSCs, human BM, and umbilical cord blood (UCB) mononuclear cells (MNCs) were treated with store-operated calcium entry (SOCE) inhibitors SKF 96365 hydrochloride (abbreviated as SKF) and 2-aminoethoxydiphenyl borate (2-APB). Besides, K+ channel inhibitor TEA chloride (abbreviated as TEA) was used to compare the relationship between calcium-activated potassium channel activities. Seven days of SKF treatment induced mouse and human ex vivo BM-HSC expansion as well as UCB-derived primitive HSC expansion. SKF treatment induced the surface expression of CaSR, CXCR4, and adhesion molecules on human hematopoietic stem and progenitor cells. HSCs expanded with SKF successfully differentiated into blood lineages in recipient animals and demonstrated a higher repopulation capability. Furthermore, modulation of SOCE in the BM-induced HSC content and differentially altered niche-related gene expression profile in vivo. Intriguingly, treatments with SOCE inhibitors SKF and 2-APB boosted the mouse BM mesenchymal stem cell (MSC) and human adipose-derived MSCs proliferation, whereas they did not affect the endothelial cell proliferation. These findings suggest that temporal modulation of calcium sensing is crucial in expansion and maintenance of murine HSCs, human HSCs, and mouse BM-MSCs function.
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Affiliation(s)
- Merve Uslu
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey.,Graduate School of Natural and Applied Sciences, Yeditepe University, Istanbul, Turkey
| | - Esra Albayrak
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey.,Graduate School of Natural and Applied Sciences, Yeditepe University, Istanbul, Turkey
| | - Fatih Kocabaş
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey.,Graduate School of Natural and Applied Sciences, Yeditepe University, Istanbul, Turkey
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28
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Ma Z, Xu J, Wu L, Wang J, Lin Q, Chowdhury FA, Mazumder MHH, Hu G, Li X, Du W. Hes1 deficiency causes hematopoietic stem cell exhaustion. Stem Cells 2020; 38:756-768. [PMID: 32129527 PMCID: PMC7260087 DOI: 10.1002/stem.3169] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/28/2020] [Accepted: 02/19/2020] [Indexed: 12/19/2022]
Abstract
The transcriptional repressor Hairy Enhancer of Split 1 (HES1) plays an essential role in the development of many organs by promoting the maintenance of stem/progenitor cells, controlling the reversibility of cellular quiescence, and regulating both cell fate decisions. Deletion of Hes1 in mice results in severe defects in multiple organs and is lethal in late embryogenesis. Here we have investigated the role of HES1 in hematopoiesis using a hematopoietic lineage‐specific Hes1 knockout mouse model. We found that while Hes1 is dispensable for steady‐state hematopoiesis, Hes1‐deficient hematopoietic stem cells (HSCs) undergo exhaustion under replicative stress. Loss of Hes1 upregulates the expression of genes involved in PPARγ signaling and fatty acid metabolism pathways, and augments fatty acid oxidation (FAO) in Hes1f/fVav1Cre HSCs and progenitors. Functionally, PPARγ targeting or FAO inhibition ameliorates the repopulating defects of Hes1f/fVav1Cre HSCs through improving quiescence in HSCs. Lastly, transcriptome analysis reveals that disruption of Hes1 in hematopoietic lineage alters expression of genes critical to HSC function, PPARγ signaling, and fatty acid metabolism. Together, our findings identify a novel role of HES1 in regulating stress hematopoiesis and provide mechanistic insight into the function of HES1 in HSC maintenance.
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Affiliation(s)
- Zhilin Ma
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia, USA.,Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, People's Republic of China
| | - Jian Xu
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia, USA.,Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, People's Republic of China
| | - Limei Wu
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia, USA
| | - Junjie Wang
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia, USA
| | - Qiqi Lin
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia, USA.,Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, People's Republic of China
| | - Fabliha A Chowdhury
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia, USA
| | - Md Habibul H Mazumder
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia, USA
| | - Gangqing Hu
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, West Virginia, USA.,Bioinformatics Core, West Virginia University, Morgantown, West Virginia, USA
| | - Xue Li
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia, USA.,Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, People's Republic of China
| | - Wei Du
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia, USA.,Alexander B. Osborn Hematopoietic Malignancy and Transplantation Program, West Virginia University Cancer Institute, Morgantown, West Virginia, USA
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29
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Khalaj M, Woolthuis CM, Hu W, Durham BH, Chu SH, Qamar S, Armstrong SA, Park CY. miR-99 regulates normal and malignant hematopoietic stem cell self-renewal. J Exp Med 2020; 214:2453-2470. [PMID: 28733386 PMCID: PMC5551568 DOI: 10.1084/jem.20161595] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 04/18/2017] [Accepted: 06/08/2017] [Indexed: 12/17/2022] Open
Abstract
The mechanisms that regulate self-renewal in hematopoietic stem cells (HSCs) and leukemia stem cells (LSCs) are poorly understood. Herein, Khalaj et al. identify microRNA-99 (miR-99) as a novel noncoding RNA critical for the maintenance of HSCs and LSCs and demonstrate that miR-99 mediates its role by suppressing multiple target genes, including HOXA1. The microRNA-99 (miR-99) family comprises a group of broadly conserved microRNAs that are highly expressed in hematopoietic stem cells (HSCs) and acute myeloid leukemia stem cells (LSCs) compared with their differentiated progeny. Herein, we show that miR-99 regulates self-renewal in both HSCs and LSCs. miR-99 maintains HSC long-term reconstitution activity by inhibiting differentiation and cell cycle entry. Moreover, miR-99 inhibition induced LSC differentiation and depletion in an MLL-AF9–driven mouse model of AML, leading to reduction in leukemia-initiating activity and improved survival in secondary transplants. Confirming miR-99’s role in established AML, miR-99 inhibition induced primary AML patient blasts to undergo differentiation. A forward genetic shRNA library screen revealed Hoxa1 as a critical mediator of miR-99 function in HSC maintenance, and this observation was independently confirmed in both HSCs and LSCs. Together, these studies demonstrate the importance of noncoding RNAs in the regulation of HSC and LSC function and identify miR-99 as a critical regulator of stem cell self-renewal.
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Affiliation(s)
- Mona Khalaj
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Graduate School of Medical Sciences, Cornell University, New York, NY
| | - Carolien M Woolthuis
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Wenhuo Hu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Benjamin H Durham
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - S Haihua Chu
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston, MA
| | - Sarah Qamar
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Graduate School of Medical Sciences, Cornell University, New York, NY
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston, MA
| | - Christopher Y Park
- Department of Pathology, New York University School of Medicine, New York, NY
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30
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Rowe RG, Lummertz da Rocha E, Sousa P, Missios P, Morse M, Marion W, Yermalovich A, Barragan J, Mathieu R, Jha DK, Fleming MD, North TE, Daley GQ. The developmental stage of the hematopoietic niche regulates lineage in MLL-rearranged leukemia. J Exp Med 2019; 216:527-538. [PMID: 30728174 PMCID: PMC6400531 DOI: 10.1084/jem.20181765] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 12/05/2018] [Accepted: 01/11/2019] [Indexed: 01/11/2023] Open
Abstract
Leukemia phenotypes vary with age of onset. Delineating mechanisms of age specificity in leukemia could improve disease models and uncover new therapeutic approaches. Here, we used heterochronic transplantation of leukemia driven by MLL/KMT2A translocations to investigate the contribution of the age of the hematopoietic microenvironment to age-specific leukemia phenotypes. When driven by MLL-AF9, leukemia cells in the adult microenvironment sustained a myeloid phenotype, whereas the neonatal microenvironment supported genesis of mixed early B cell/myeloid leukemia. In MLL-ENL leukemia, the neonatal microenvironment potentiated B-lymphoid differentiation compared with the adult. Ccl5 elaborated from adult marrow stroma inhibited B-lymphoid differentiation of leukemia cells, illuminating a mechanism of age-specific lineage commitment. Our study illustrates the contribution of the developmental stage of the hematopoietic microenvironment in defining the age specificity of leukemia.
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Affiliation(s)
- R Grant Rowe
- Stem Cell Program, Boston Children's Hospital, Boston, MA.,Division of Pediatric Hematology, Oncology, and Stem Cell Transplantation, Dana Farber Cancer Institute and Boston Children's Hospital, Boston, MA.,Harvard Medical School, Boston, MA
| | | | - Patricia Sousa
- Stem Cell Program, Boston Children's Hospital, Boston, MA
| | - Pavlos Missios
- Stem Cell Program, Boston Children's Hospital, Boston, MA
| | - Michael Morse
- Stem Cell Program, Boston Children's Hospital, Boston, MA
| | - William Marion
- Stem Cell Program, Boston Children's Hospital, Boston, MA
| | | | | | - Ronald Mathieu
- Flow Cytometry Core Facility, Boston Children's Hospital, Boston, MA
| | | | - Mark D Fleming
- Harvard Medical School, Boston, MA.,Department of Pathology, Boston Children's Hospital, Boston, MA
| | - Trista E North
- Stem Cell Program, Boston Children's Hospital, Boston, MA
| | - George Q Daley
- Stem Cell Program, Boston Children's Hospital, Boston, MA .,Harvard Medical School, Boston, MA.,Harvard Stem Cell Institute, Cambridge, MA
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31
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Yassin M, Aqaqe N, Yassin AA, van Galen P, Kugler E, Bernstein BE, Koren-Michowitz M, Canaani J, Nagler A, Lechman ER, Dick JE, Wienholds E, Izraeli S, Milyavsky M. A novel method for detecting the cellular stemness state in normal and leukemic human hematopoietic cells can predict disease outcome and drug sensitivity. Leukemia 2019; 33:2061-2077. [PMID: 30705411 DOI: 10.1038/s41375-019-0386-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 12/02/2018] [Accepted: 12/20/2018] [Indexed: 02/06/2023]
Abstract
Acute leukemia is an aggressive blood malignancy with low survival rates. A high expression of stem-like programs in leukemias predicts poor prognosis and is assumed to act in an aberrant fashion in the phenotypically heterogeneous leukemia stem cell (LSC) population. A lack of suitable genome engineering tools that can isolate LSCs based on their stemness precludes their comprehensive examination and full characterization. We hypothesized that tagging endogenous stemness-regulatory regions could generate a genome reporter for the putative leukemia stemness-state. Our analysis revealed that the ERG + 85 enhancer region can serve as a marker for stemness-state and a fluorescent lentiviral reporter was developed that can accurately recapitulate the endogenous activity. Using our novel reporter, we revealed cellular heterogeneity in several leukemia cell lines and patient-derived samples. Alterations in reporter activity were associated with transcriptomic and functional changes that were closely related to the hematopoietic stem cell (HSC) identity. Notably, the differentiation potential was skewed towards the erythro-megakaryocytic lineage. Moreover, an ERG + 85High fraction of AML cells could regenerate the original cellular heterogeneity and was enriched for LSCs. RNA-seq analysis coupled with in silico drug-screen analysis identified 4HPR as an effective inhibitor of ERG + 85High leukemia growth. We propose that further utilization of our novel molecular tool will identify crucial determinants of LSCs, thus providing a rationale for their therapeutic targeting.
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Affiliation(s)
- Muhammad Yassin
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Nasma Aqaqe
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Abed Alkader Yassin
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Peter van Galen
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Eitan Kugler
- Department of Pediatric Hemato-Oncology, Schneider Children Medical Center, Petah Tikva, Israel.,The Gene Development and Environment Pediatric Research Institute, Pediatric Hemato-Oncology, Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Department of Molecular Human Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Bradley E Bernstein
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, 02114, USA
| | | | - Jonathan Canaani
- Hematology Division, Chaim Sheba Medical Center, Tel-Hashomer, Israel
| | - Arnon Nagler
- Hematology Division, Chaim Sheba Medical Center, Tel-Hashomer, Israel
| | - Eric R Lechman
- Princess Margaret Cancer Centre, University Health Network and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Erno Wienholds
- Princess Margaret Cancer Centre, University Health Network and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Shai Izraeli
- Department of Pediatric Hemato-Oncology, Schneider Children Medical Center, Petah Tikva, Israel.,The Gene Development and Environment Pediatric Research Institute, Pediatric Hemato-Oncology, Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Department of Molecular Human Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Michael Milyavsky
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel.
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32
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Martinez-Soria N, McKenzie L, Draper J, Ptasinska A, Issa H, Potluri S, Blair HJ, Pickin A, Isa A, Chin PS, Tirtakusuma R, Coleman D, Nakjang S, Assi S, Forster V, Reza M, Law E, Berry P, Mueller D, Osborne C, Elder A, Bomken SN, Pal D, Allan JM, Veal GJ, Cockerill PN, Wichmann C, Vormoor J, Lacaud G, Bonifer C, Heidenreich O. The Oncogenic Transcription Factor RUNX1/ETO Corrupts Cell Cycle Regulation to Drive Leukemic Transformation. Cancer Cell 2018; 34:626-642.e8. [PMID: 30300583 PMCID: PMC6179967 DOI: 10.1016/j.ccell.2018.08.015] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 04/20/2018] [Accepted: 08/29/2018] [Indexed: 12/11/2022]
Abstract
Oncogenic transcription factors such as the leukemic fusion protein RUNX1/ETO, which drives t(8;21) acute myeloid leukemia (AML), constitute cancer-specific but highly challenging therapeutic targets. We used epigenomic profiling data for an RNAi screen to interrogate the transcriptional network maintaining t(8;21) AML. This strategy identified Cyclin D2 (CCND2) as a crucial transmitter of RUNX1/ETO-driven leukemic propagation. RUNX1/ETO cooperates with AP-1 to drive CCND2 expression. Knockdown or pharmacological inhibition of CCND2 by an approved drug significantly impairs leukemic expansion of patient-derived AML cells and engraftment in immunodeficient murine hosts. Our data demonstrate that RUNX1/ETO maintains leukemia by promoting cell cycle progression and identifies G1 CCND-CDK complexes as promising therapeutic targets for treatment of RUNX1/ETO-driven AML.
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Affiliation(s)
- Natalia Martinez-Soria
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Lynsey McKenzie
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Julia Draper
- Cancer Research UK Manchester Institute, Manchester M20 4GJ, UK
| | - Anetta Ptasinska
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Hasan Issa
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Sandeep Potluri
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Helen J Blair
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Anna Pickin
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Asmida Isa
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Paulynn Suyin Chin
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Ricky Tirtakusuma
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Daniel Coleman
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Sirintra Nakjang
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Salam Assi
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Victoria Forster
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Mojgan Reza
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Ed Law
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Philip Berry
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Dorothee Mueller
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Cameron Osborne
- Department of Medical & Molecular Genetics, King's College London, London SE1 9RT, UK
| | - Alex Elder
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Simon N Bomken
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Deepali Pal
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - James M Allan
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Gareth J Veal
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Peter N Cockerill
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Christian Wichmann
- Department of Transfusion Medicine, Cell Therapeutics and Hemostaseology, Ludwig-Maximilian University Hospital, Munich 80539, Germany
| | - Josef Vormoor
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK; Princess Maxima Center for Pediatric Oncology, Utrecht 3584CS, the Netherlands
| | - Georges Lacaud
- Cancer Research UK Manchester Institute, Manchester M20 4GJ, UK
| | - Constanze Bonifer
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK.
| | - Olaf Heidenreich
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK; Princess Maxima Center for Pediatric Oncology, Utrecht 3584CS, the Netherlands.
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33
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Alexander TB, Gu Z, Iacobucci I, Dickerson K, Choi JK, Xu B, Payne-Turner D, Yoshihara H, Loh ML, Horan J, Buldini B, Basso G, Elitzur S, de Haas V, Zwaan CM, Yeoh A, Reinhardt D, Tomizawa D, Kiyokawa N, Lammens T, De Moerloose B, Catchpoole D, Hori H, Moorman A, Moore AS, Hrusak O, Meshinchi S, Orgel E, Devidas M, Borowitz M, Wood B, Heerema NA, Carrol A, Yang YL, Smith MA, Davidsen TM, Hermida LC, Gesuwan P, Marra MA, Ma Y, Mungall AJ, Moore RA, Jones SJM, Valentine M, Janke LJ, Rubnitz JE, Pui CH, Ding L, Liu Y, Zhang J, Nichols KE, Downing JR, Cao X, Shi L, Pounds S, Newman S, Pei D, Guidry Auvil JM, Gerhard DS, Hunger SP, Inaba H, Mullighan CG. The genetic basis and cell of origin of mixed phenotype acute leukaemia. Nature 2018; 562:373-379. [PMID: 30209392 PMCID: PMC6195459 DOI: 10.1038/s41586-018-0436-0] [Citation(s) in RCA: 265] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 07/03/2018] [Indexed: 12/16/2022]
Abstract
Mixed phenotype acute leukaemia (MPAL) is a high-risk subtype of leukaemia with myeloid and lymphoid features, limited genetic characterization, and a lack of consensus regarding appropriate therapy. Here we show that the two principal subtypes of MPAL, T/myeloid (T/M) and B/myeloid (B/M), are genetically distinct. Rearrangement of ZNF384 is common in B/M MPAL, and biallelic WT1 alterations are common in T/M MPAL, which shares genomic features with early T-cell precursor acute lymphoblastic leukaemia. We show that the intratumoral immunophenotypic heterogeneity characteristic of MPAL is independent of somatic genetic variation, that founding lesions arise in primitive haematopoietic progenitors, and that individual phenotypic subpopulations can reconstitute the immunophenotypic diversity in vivo. These findings indicate that the cell of origin and founding lesions, rather than an accumulation of distinct genomic alterations, prime tumour cells for lineage promiscuity. Moreover, these findings position MPAL in the spectrum of immature leukaemias and provide a genetically informed framework for future clinical trials of potential treatments for MPAL.
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Affiliation(s)
- Thomas B Alexander
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pediatrics, University of North Carolina, Chapel Hill, NC, USA
| | - Zhaohui Gu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kirsten Dickerson
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - John K Choi
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Beisi Xu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Debbie Payne-Turner
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hiroki Yoshihara
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital and the Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA
| | - John Horan
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Department of Pediatrics, Atlanta, GA, USA
| | - Barbara Buldini
- Department of Women and Child Health, Hemato-Oncology Division, University of Padova, Padova, Italy
| | - Giuseppe Basso
- Department of Women and Child Health, Hemato-Oncology Division, University of Padova, Padova, Italy
| | - Sarah Elitzur
- Pediatric Hematology-Oncology, Schneider Children's Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Israel
| | | | - C Michel Zwaan
- Prinses Maxima Centre, Utrecht, The Netherlands
- Department of Pediatric Oncology, Erasmus MC-Sophia, Rotterdam, The Netherlands
| | - Allen Yeoh
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | | | - Daisuke Tomizawa
- Division of Leukemia and Lymphoma, Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Nobutaka Kiyokawa
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tim Lammens
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Barbara De Moerloose
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Daniel Catchpoole
- The Tumour Bank CCRU, The Kids Research Institute, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Hiroki Hori
- Department of Pediatrics, Mie University, Tsu, Japan
| | - Anthony Moorman
- Wolfson Childhood Cancer Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle-upon-Tyne, UK
| | - Andrew S Moore
- The University of Queensland Diamantina Institute & Children's Health, Brisbane, Queensland, Australia
| | - Ondrej Hrusak
- Department of Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Soheil Meshinchi
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA, USA
- Children's Oncology Group, Arcadia, CA, USA
| | - Etan Orgel
- Children's Center for Cancer and Blood Disease, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | | | | | - Brent Wood
- University of Washington, Seattle, WA, USA
| | - Nyla A Heerema
- The Ohio State University School of Medicine, Columbus, OH, USA
| | - Andrew Carrol
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - Yung-Li Yang
- Department of Laboratory Medicine and Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Malcolm A Smith
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD, USA
| | - Tanja M Davidsen
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD, USA
| | - Leandro C Hermida
- Office of Cancer Genomics, National Cancer Institute, Bethesda, MD, USA
| | - Patee Gesuwan
- Office of Cancer Genomics, National Cancer Institute, Bethesda, MD, USA
| | - Marco A Marra
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Yussanne Ma
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Andrew J Mungall
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Richard A Moore
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Marcus Valentine
- Cytogenetics Shared Resource, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Laura J Janke
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jeffrey E Rubnitz
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Liang Ding
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yu Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kim E Nichols
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - James R Downing
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xueyuan Cao
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Lei Shi
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Scott Newman
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Deqing Pei
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Daniela S Gerhard
- Office of Cancer Genomics, National Cancer Institute, Bethesda, MD, USA
| | - Stephen P Hunger
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Hiroto Inaba
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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Omrani MR, Yaqubi M, Mohammadnia A. Transcription Factors in Regulatory and Protein Subnetworks during Generation of Neural Stem Cells and Neurons from Direct Reprogramming of Non-fibroblastic Cell Sources. Neuroscience 2018; 380:63-77. [PMID: 29653196 DOI: 10.1016/j.neuroscience.2018.03.033] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 03/19/2018] [Accepted: 03/20/2018] [Indexed: 12/31/2022]
Abstract
Direct reprogramming of non-fibroblastic cells to the neuronal cell types including induced neurons (iNs) and induced neural stem cells (iNSCs) has provided an alternative approach for the direct reprogramming of fibroblasts to those cells. However, to increase the efficiency of the reprogramming process the underlying mechanisms should be clarified. In the current study, we analyzed the gene expression profiles of five different cellular conversions to understand the most significant molecular mechanisms and transcription factors (TFs) underlying each conversion. For each conversion, we found the list of differentially expressed genes (DEGs) and the list of differentially expressed TFs (DE-TFs) which regulate expression of DEGs. Moreover, we constructed gene regulatory networks based on the TF-binding sites' data and found the most central regulators and the most active part of the networks. Furthermore, protein complexes were identified from constructed protein-protein interaction networks for DE-TFs. Finally, we proposed a list of main regulators for each conversion; for example, in the direct conversion of epithelial-like cells (ECs) to iNSCs, combination of centrality with active modules or protein complex analyses highlighted the role of POU3F2, BACH1, AR, PBX1, SOX2 and NANOG genes in this conversion. To the best of our knowledge, this study is the first one that analyzed the direct conversion of non-fibroblastic cells toward iNs and iNSCs and we believe that the expression manipulation of identified genes may increase efficiency of these processes.
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Affiliation(s)
- Mohammad Reza Omrani
- National Institute of Genetics Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Moein Yaqubi
- Department of Psychiatry, Ludmer Centre for Neuroinformatics and Mental Health, Douglas Mental Health University Institute, McGill University, Montreal, Quebec, Canada.
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Li N, Yang Y, Liang C, Qiu Q, Pan C, Li M, Yang S, Chen L, Zhu X, Hu Y. Tmem30a Plays Critical Roles in Ensuring the Survival of Hematopoietic Cells and Leukemia Cells in Mice. THE AMERICAN JOURNAL OF PATHOLOGY 2018; 188:1457-1468. [PMID: 29574182 DOI: 10.1016/j.ajpath.2018.02.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 02/03/2018] [Accepted: 02/27/2018] [Indexed: 02/05/2023]
Abstract
The fundamental structure of eukaryotic cell plasma membrane is the phospholipid bilayer, which contains four major phospholipids. These phospholipids are asymmetrically distributed between the outer and inner leaflets. P4-ATPase flippase complexes play essential roles in ensuring this asymmetry. We found that conditional deletion of Tmem30a, the β subunit of P4-ATPase flippase complex, caused pancytopenia in mice. Tmem30a deficiency resulted in depletion of lineage-committed blood cells in the peripheral blood, spleen, and bone marrow. Ablation of Tmem30a also caused the depletion of hematopoietic stem cells (HSCs). HSC RNA sequencing results revealed that multiple biological processes and signal pathways were involved in the event, including mammalian target of rapamycin signaling, genes for HSC stemness, and genes responding to interferons. Our results also revealed that targeting Tmem30a signaling had therapeutic utility in BCR/ABL1-induced chronic myeloid leukemia.
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Affiliation(s)
- Ning Li
- Department of Thyroid Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China; State Key Laboratory of Biotherapy & Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yeming Yang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Cailing Liang
- Department of Thyroid Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China; State Key Laboratory of Biotherapy & Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Qiang Qiu
- Department of Thyroid Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China; State Key Laboratory of Biotherapy & Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Cong Pan
- Department of Thyroid Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China; State Key Laboratory of Biotherapy & Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Mengyuan Li
- Department of Thyroid Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China; State Key Laboratory of Biotherapy & Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Shengyong Yang
- State Key Laboratory of Biotherapy & Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lijuan Chen
- State Key Laboratory of Biotherapy & Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xianjun Zhu
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China; Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China; Chengdu Institute of Biology, Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, Sichuan, China.
| | - Yiguo Hu
- Department of Thyroid Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China; State Key Laboratory of Biotherapy & Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
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36
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Trentin L, Queudeville M, Eckhoff SM, Hasan N, Münch V, Boldrin E, Seyfried F, Enzenmüller S, Debatin KM, Meyer LH. Leukemia reconstitution in vivo is driven by cells in early cell cycle and low metabolic state. Haematologica 2018. [PMID: 29519870 PMCID: PMC6058781 DOI: 10.3324/haematol.2017.167502] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
In contrast to well-established hierarchical concepts of tumor stem cells, leukemia-initiating cells in B-cell precursor acute lymphoblastic leukemia have not yet been phenotypically identified. Different subpopulations, as defined by surface markers, have shown equal abilities to reconstitute leukemia upon transplantation into immunodeficient mice. Using a non-obese diabetes/severe combined immunodeficiency human acute lymphoblastic leukemia mouse model and cell cycle analysis annotating cells to distinct cycle phases, we functionally characterized leukemia-initiating cells and found that cells in all stages of the cell cycle are able to reconstitute leukemia in vivo, with early cycling cells (G1blow population) exhibiting the highest leukemia-initiating potential. Interestingly, cells of the G2/M compartment, i.e. dividing cells, were less effective in leukemia reconstitution. Moreover, G1blow cells were more resistant to spontaneous or drug-induced cell death in vitro, were enriched for stem cell signatures and were less metabolically active, as determined by lower levels of reactive oxygen species, compared to G2/M stage cells. Our data provide new information on the biological properties of leukemia-initiating cells in B-cell precursor acute lymphoblastic leukemia and underline the concept of a stochastic model of leukemogenesis.
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Affiliation(s)
- Luca Trentin
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Germany
| | - Manon Queudeville
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Germany
| | - Sarah Mirjam Eckhoff
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Germany
| | - Nabiul Hasan
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Germany
| | - Vera Münch
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Germany.,International Graduate School in Molecular Medicine, Ulm University, Germany
| | - Elena Boldrin
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Germany.,International Graduate School in Molecular Medicine, Ulm University, Germany
| | - Felix Seyfried
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Germany
| | - Stefanie Enzenmüller
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Germany
| | - Klaus-Michael Debatin
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Germany
| | - Lüder Hinrich Meyer
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Germany
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Germano G, Morello G, Aveic S, Pinazza M, Minuzzo S, Frasson C, Persano L, Bonvini P, Viola G, Bresolin S, Tregnago C, Paganin M, Pigazzi M, Indraccolo S, Basso G. ZNF521 sustains the differentiation block in MLL-rearranged acute myeloid leukemia. Oncotarget 2018; 8:26129-26141. [PMID: 28412727 PMCID: PMC5432245 DOI: 10.18632/oncotarget.15387] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 01/31/2017] [Indexed: 12/31/2022] Open
Abstract
Zinc finger protein 521 (ZNF521) is a multiple zinc finger transcription factor and a strong candidate as regulator of hematopoietic stem cell homeostasis. Recently, independent gene expression profile studies have evidenced a positive correlation between ZNF521 mRNA overexpression and MLL-rearranged acute myeloid leukemia (AML), leaving open the question on the role of ZNF521 in this subtype of leukemia. In this study, we sought to analyze the effect of ZNF521 depletion on MLL-rearranged AML cell lines and MLL-AF9 xenograft primary cells. Knockdown of ZNF521 with short-hairpin RNA (shRNA) led to decreased leukemia proliferation, reduced colony formation and caused cell cycle arrest in MLL-rearranged AML cell lines. Importantly, we showed that loss of ZNF521 substantially caused differentiation of both MLL-rearranged cell lines and primary cells. Moreover, gene profile analysis in ZNF521-silenced THP-1 cells revealed a loss of MLL-AF9-directed leukemic signature and an increase of the differentiation program. Finally, we determined that both MLL-AF9 and MLL-ENL fusion proteins directly interacted with ZNF521 promoter activating its transcription. In conclusion, our findings identify ZNF521 as a critical effector of MLL fusion proteins in blocking myeloid differentiation and highlight ZNF521 as a potential therapeutic target for this subtype of leukemia.
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Affiliation(s)
- Giuseppe Germano
- Foundation Institute of Pediatric Research Città della Speranza, Padova, Italy
| | - Giulia Morello
- Foundation Institute of Pediatric Research Città della Speranza, Padova, Italy
| | - Sanja Aveic
- Foundation Institute of Pediatric Research Città della Speranza, Padova, Italy
| | - Marica Pinazza
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Italy
| | - Sonia Minuzzo
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Italy
| | - Chiara Frasson
- Department of Woman and Child Health, University of Padova, Italy
| | - Luca Persano
- Foundation Institute of Pediatric Research Città della Speranza, Padova, Italy
| | - Paolo Bonvini
- Foundation Institute of Pediatric Research Città della Speranza, Padova, Italy
| | - Giampietro Viola
- Department of Woman and Child Health, University of Padova, Italy
| | - Silvia Bresolin
- Department of Woman and Child Health, University of Padova, Italy
| | - Claudia Tregnago
- Department of Woman and Child Health, University of Padova, Italy
| | | | - Martina Pigazzi
- Department of Woman and Child Health, University of Padova, Italy
| | - Stefano Indraccolo
- Immunology and Molecular Oncology Unit, Istituto Oncologico Veneto IRCCS, Padova, Italy
| | - Giuseppe Basso
- Department of Woman and Child Health, University of Padova, Italy
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Control of Human T-Cell Leukemia Virus Type 1 (HTLV-1) Infection by Eliminating Envelope Protein-Positive Cells with Recombinant Vesicular Stomatitis Viruses Encoding HTLV-1 Primary Receptor. J Virol 2018; 92:JVI.01885-17. [PMID: 29212930 PMCID: PMC5790936 DOI: 10.1128/jvi.01885-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 11/18/2017] [Indexed: 01/01/2023] Open
Abstract
Human T-cell leukemia virus type 1 (HTLV-1) infection causes adult T-cell leukemia (ATL), which is frequently resistant to currently available therapies and has a very poor prognosis. To prevent the development of ATL among carriers, it is important to control HTLV-1-infected cells in infected individuals. Therefore, the establishment of novel therapies with drugs specifically targeting infected cells is urgently required. This study aimed to develop a potential therapy by generating recombinant vesicular stomatitis viruses (rVSVs) that lack an envelope glycoprotein G and instead encode an HTLV-1 receptor with human glucose transporter 1 (GLUT1), neuropilin 1 (NRP1), or heparan sulfate proteoglycans (HSPGs), including syndecan 1 (SDC1), designated VSVΔG-GL, VSVΔG-NP, or VSVΔG-SD, respectively. In an attempt to enhance the infectivity of rVSV against HTLV-1-infected cells, we also constructed rVSVs with a combination of two or three receptor genes, designated VSVΔG-GLN and VSVΔG-GLNS, respectively. The present study demonstrates VSVΔG-GL, VSVΔG-NP, VSVΔG-GLN, and VSVΔG-GLNS have tropism for HTLV-1 envelope (Env)-expressing cells. Notably, the inoculation of VSVΔG-GL or VSVΔG-NP significantly eliminated HTLV-1-infected cells under the culture conditions. Furthermore, in an HTLV-1-infected humanized mouse model, VSVΔG-NP was capable of efficiently preventing HTLV-1-induced leukocytosis in the periphery and eliminating HTLV-1-infected Env-expressing cells in the lymphoid tissues. In summary, an rVSV engineered to express HTLV-1 primary receptor, especially human NRP1, may represent a drug candidate that has potential for the development of unique virotherapy against HTLV-1 de novo infection. IMPORTANCE Although several anti-ATL therapies are currently available, ATL is still frequently resistant to therapeutic approaches, and its prognosis remains poor. Control of HTLV-1 de novo infection or expansion of HTLV-1-infected cells in the carrier holds considerable promise for the prevention of ATL development. In this study, we developed rVSVs that specifically target and kill HTLV-1 Env-expressing cells (not ATL cells, which generally do not express Env in vivo) through replacement of the G gene with HTLV-1 receptor gene(s) in the VSV genome. Notably, an rVSV engineered to express human NRP1 controlled the number of HTLV-1-infected Env-expressing cells in vitro and in vivo, suggesting the present approach may be a promising candidate for novel anti-HTLV-1 virotherapy in HTLV-1 carriers, including as a prophylactic treatment against the development of ATL.
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Huizer K, Mustafa DAM, Spelt JC, Kros JM, Sacchetti A. Improving the characterization of endothelial progenitor cell subsets by an optimized FACS protocol. PLoS One 2017; 12:e0184895. [PMID: 28910385 PMCID: PMC5599045 DOI: 10.1371/journal.pone.0184895] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 09/01/2017] [Indexed: 02/07/2023] Open
Abstract
The characterization of circulating endothelial progenitor cells (EPCs) is fundamental to any study related to angiogenesis. Unfortunately, current literature lacks consistency in the definition of EPC subsets due to variations in isolation strategies and inconsistencies in the use of lineage markers. Here we address critical points in the identification of hematopoietic progenitor cells (HPCs), circulating endothelial cells (CECs), and culture-generated outgrowth endothelial cells (OECs) from blood samples of healthy adults (AB) and umbilical cord (UCB). Peripheral blood mononuclear cells (PBMCs) were enriched using a Ficoll-based gradient followed by an optimized staining and gating strategy to enrich for the target cells. Sorted EPC populations were subjected to RT-PCR for tracing the expression of markers beyond the limits of cell surface-based immunophenotyping. Using CD34, CD133 and c-kit staining, combined with FSC and SSC, we succeeded in the accurate and reproducible identification of four HPC subgroups and found significant differences in the respective populations in AB vs. UCB. Co-expression analysis of endothelial markers on HPCs revealed a complex pattern characterized by various subpopulations. CECs were identified by using CD34, KDR, CD45, and additional endothelial markers, and were subdivided according to their apoptotic state and expression of c-kit. Comparison of UCB-CECs vs. AB-CECs revealed significant differences in CD34 and KDR levels. OECs were grown from PBMC-fractions We found that viable c-kit+ CECs are a candidate circulating precursor for CECs. RT-PCR to angiogenic factors and receptors revealed that all EPC subsets expressed angiogenesis-related molecules. Taken together, the improvements in immunophenotyping and gating strategies resulted in accurate identification and comparison of better defined cell populations in a single procedure.
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Affiliation(s)
- Karin Huizer
- Department of Pathology, Erasmus MC, Rotterdam, The Netherlands
| | | | | | - Johan M. Kros
- Department of Pathology, Erasmus MC, Rotterdam, The Netherlands
- * E-mail:
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A Phase II Study of Arginine Deiminase (ADI-PEG20) in Relapsed/Refractory or Poor-Risk Acute Myeloid Leukemia Patients. Sci Rep 2017; 7:11253. [PMID: 28900115 PMCID: PMC5595917 DOI: 10.1038/s41598-017-10542-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 08/10/2017] [Indexed: 11/08/2022] Open
Abstract
Exogenous arginine is required for growth in some argininosuccinate synthetase (ASS)-deficient cancers. Arginine deiminase (ADI) inhibits growth in various ASS-deficient cancers by depleting arginine. The efficacy of pegylated ADI (ADI-PEG20) in relapsed/refractory/poor-risk acute myeloid leukemia (AML) was evaluated in 43 patients in a prospective, phase II trial (NCT01910012 (10/07/2013), https://clinicaltrials.gov/ct2/show/NCT01910012?term = ADI-PEG20&rank = 12). Despite almost all pre-treatment tumor samples showing ASS deficiency, the best response among 21 evaluable patients was complete response (CR) in 2 (9.5%) and stable disease in 7 (33.3%), yielding a disease control rate (DCR) of 42.9%. The response durations of the two patients with CR were 7.5 and 8.8 months. DCR was correlated with a median of 8 weeks of arginine depletion to ≤10 μM. Using whole transcriptome sequencing, we compared gene expression profiling of pre- and post-treatment bone marrow samples of the two responders and three non-responders. The expression levels of some markers for AML subtypes and c-MYC regulated genes were considered potential predictors of response to ADI-PEG20. These results suggest that ASS deficiency is a prerequisite but not a sufficient condition for response to ADI-PEG20 monotherapy in AML. Predictive biomarkers and mechanistic explorations will be critical for identifying appropriate patients for future AML trials of ADI-PEG20.
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41
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Vu LP, Prieto C, Amin EM, Chhangawala S, Krivtsov A, Calvo-Vidal MN, Chou T, Chow A, Minuesa G, Park SM, Barlowe TS, Taggart J, Tivnan P, Deering RP, Chu LP, Kwon JA, Meydan C, Perales-Paton J, Arshi A, Gönen M, Famulare C, Patel M, Paietta E, Tallman MS, Lu Y, Glass J, Garret-Bakelman FE, Melnick A, Levine R, Al-Shahrour F, Järås M, Hacohen N, Hwang A, Garippa R, Lengner CJ, Armstrong SA, Cerchietti L, Cowley GS, Root D, Doench J, Leslie C, Ebert BL, Kharas MG. Functional screen of MSI2 interactors identifies an essential role for SYNCRIP in myeloid leukemia stem cells. Nat Genet 2017; 49:866-875. [PMID: 28436985 PMCID: PMC5508533 DOI: 10.1038/ng.3854] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 03/31/2017] [Indexed: 12/15/2022]
Abstract
The identity of the RNA-binding proteins (RBPs) that govern cancer stem cells remains poorly characterized. The MSI2 RBP is a central regulator of translation of cancer stem cell programs. Through proteomic analysis of the MSI2-interacting RBP network and functional shRNA screening, we identified 24 genes required for in vivo leukemia. Syncrip was the most differentially required gene between normal and myeloid leukemia cells. SYNCRIP depletion increased apoptosis and differentiation while delaying leukemogenesis. Gene expression profiling of SYNCRIP-depleted cells demonstrated a loss of the MLL and HOXA9 leukemia stem cell program. SYNCRIP and MSI2 interact indirectly though shared mRNA targets. SYNCRIP maintains HOXA9 translation, and MSI2 or HOXA9 overexpression rescued the effects of SYNCRIP depletion. Altogether, our data identify SYNCRIP as a new RBP that controls the myeloid leukemia stem cell program. We propose that targeting these RBP complexes might provide a novel therapeutic strategy in leukemia.
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Affiliation(s)
- Ly P Vu
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, and Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Camila Prieto
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, and Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York, USA
| | - Elianna M Amin
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, and Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Sagar Chhangawala
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York, USA.,Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Andrei Krivtsov
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - M Nieves Calvo-Vidal
- Department of Medicine, Division of Hematology/Oncology, Weill Cornell Medical College, New York, New York, USA
| | - Timothy Chou
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, and Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Arthur Chow
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, and Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Gerard Minuesa
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, and Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Sun Mi Park
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, and Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Trevor S Barlowe
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, and Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - James Taggart
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, and Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Patrick Tivnan
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, and Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Lisa P Chu
- Division of Hematology, Brigham and Woman's Hospital, Boston, Massachusetts, USA
| | | | - Cem Meydan
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA
| | - Javier Perales-Paton
- Translational Bioinformatics Unit, Clinical Research Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Arora Arshi
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Mithat Gönen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Christopher Famulare
- Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Minal Patel
- Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Elisabeth Paietta
- Department of Medicine, Montefiore Medical Center, Bronx, New York, USA
| | - Martin S Tallman
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Hospital, New York, New York, USA
| | - Yuheng Lu
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jacob Glass
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Hospital, New York, New York, USA
| | - Francine E Garret-Bakelman
- Department of Medicine and Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA.,Division of Hematology and Medical Oncology, Departments of Medicine and Pharmacology, Weill Cornell Medical College, Cornell University, New York, New York, USA
| | - Ari Melnick
- Division of Hematology and Medical Oncology, Departments of Medicine and Pharmacology, Weill Cornell Medical College, Cornell University, New York, New York, USA
| | - Ross Levine
- Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Fatima Al-Shahrour
- Translational Bioinformatics Unit, Clinical Research Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Marcus Järås
- Department of Clinical Genetics, Lund University, Lund, Sweden
| | - Nir Hacohen
- Harvard Medical School, Boston, Massachusetts, USA
| | - Alexia Hwang
- RNAi Core, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ralph Garippa
- RNAi Core, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Christopher J Lengner
- Department of Animal Biology, Department of Cell and Developmental Biology, and Institute for Regenerative Medicine, Schools of Veterinary Medicine and Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Scott A Armstrong
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Leandro Cerchietti
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Glenn S Cowley
- Discovery Sciences, Janssen Research and Development, Spring House, Pennsylvania, USA
| | - David Root
- Broad Institute, Boston, Massachusetts, USA
| | | | - Christina Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Benjamin L Ebert
- Division of Hematology, Brigham and Woman's Hospital, Boston, Massachusetts, USA
| | - Michael G Kharas
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, and Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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42
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Cao Q, Gearhart MD, Gery S, Shojaee S, Yang H, Sun H, Lin DC, Bai JW, Mead M, Zhao Z, Chen Q, Chien WW, Alkan S, Alpermann T, Haferlach T, Müschen M, Bardwell VJ, Koeffler HP. BCOR regulates myeloid cell proliferation and differentiation. Leukemia 2016; 30:1155-65. [PMID: 26847029 PMCID: PMC5131645 DOI: 10.1038/leu.2016.2] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 12/03/2015] [Accepted: 12/18/2015] [Indexed: 02/05/2023]
Abstract
BCOR is a component of a variant Polycomb group repressive complex 1 (PRC1). Recently, we and others reported recurrent somatic BCOR loss-of-function mutations in myelodysplastic syndrome and acute myelogenous leukemia (AML). However, the role of BCOR in normal hematopoiesis is largely unknown. Here, we explored the function of BCOR in myeloid cells using myeloid murine models with Bcor conditional loss-of-function or overexpression alleles. Bcor mutant bone marrow cells showed significantly higher proliferation and differentiation rates with upregulated expression of Hox genes. Mutation of Bcor reduced protein levels of RING1B, an H2A ubiquitin ligase subunit of PRC1 family complexes and reduced H2AK119ub upstream of upregulated HoxA genes. Global RNA expression profiling in murine cells and AML patient samples with BCOR loss-of-function mutation suggested that loss of BCOR expression is associated with enhanced cell proliferation and myeloid differentiation. Our results strongly suggest that BCOR plays an indispensable role in hematopoiesis by inhibiting myeloid cell proliferation and differentiation and offer a mechanistic explanation for how BCOR regulates gene expression such as Hox genes.
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Affiliation(s)
- Qi Cao
- Department of Hematology and Oncology, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Micah D. Gearhart
- Department of Genetics, Cell Biology and Development and Masonic Cancer Center, University of Minnesota, Minneapolis, MN
| | - Sigal Gery
- Department of Hematology and Oncology, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Seyedmehdi Shojaee
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Haibo Sun
- Department of Hematology and Oncology, Cedars-Sinai Medical Center, Los Angeles, CA
| | - De-chen Lin
- Department of Hematology and Oncology, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Jing-wen Bai
- Department of Hematology and Oncology, Cedars-Sinai Medical Center, Los Angeles, CA
- Changjiang Scholar’s Laboratory and Cancer Research Center, Shantou University Medical College, Shantou, China
| | - Monica Mead
- Department of Hematology and Oncology, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Zhiqiang Zhao
- Department of Hematology and Oncology, Cedars-Sinai Medical Center, Los Angeles, CA
- Department of Musculoskeletal Oncology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Qi Chen
- Department of Endocrinology, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Wen-wen Chien
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Serhan Alkan
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA
| | | | | | - Markus Müschen
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA
| | - Vivian J. Bardwell
- Department of Genetics, Cell Biology and Development and Masonic Cancer Center, University of Minnesota, Minneapolis, MN
| | - H. Phillip Koeffler
- Department of Hematology and Oncology, Cedars-Sinai Medical Center, Los Angeles, CA
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- National University Cancer Institute of Singapore, National University Hospital, Singapore
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43
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A six gene expression signature defines aggressive subtypes and predicts outcome in childhood and adult acute lymphoblastic leukemia. Oncotarget 2016; 6:16527-42. [PMID: 26001296 PMCID: PMC4599287 DOI: 10.18632/oncotarget.4113] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 04/22/2015] [Indexed: 11/25/2022] Open
Abstract
Abnormal gene expression in cancer represents an under-explored source of cancer markers and therapeutic targets. In order to identify gene expression signatures associated with survival in acute lymphoblastic leukemia (ALL), a strategy was designed to search for aberrant gene activity, which consists of applying several filters to transcriptomic datasets from two pediatric ALL studies. Six genes whose expression in leukemic blasts was associated with prognosis were identified:three genes predicting poor prognosis (AK022211, FASTKD1 and STARD4) and three genes associated with a favorable outcome (CAMSAP1, PCGF6 and SH3RF3). Combining the expression of these 6 genes could successfully predict prognosis not only in the two discovery pediatric ALL studies, but also in two independent validation cohorts of adult patients, one from a publicly available study and one consisting of 62 newly recruited Chinese patients. Moreover, our data demonstrate that our six gene based test is particularly efficient in stratifying MLL or BCR.ABL negative patients. Finally, common biological traits characterizing aggressive forms of ALL in both children and adults were found, including features of dormant hematopoietic stem cells, suggesting new therapeutic strategies.
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44
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Rashed RA, Kadry DY, El Taweel M, Abd El Wahab N, Abd El Hameed T. Relation of BAALC and ERG Gene Expression with Overall Survival in Acute Myeloid Leukemia Cases. Asian Pac J Cancer Prev 2015; 16:7875-82. [PMID: 26625814 DOI: 10.7314/apjcp.2015.16.17.7875] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The objectives of this study were to evaluate the expression of brain and acute leukemia, cytoplasmic (BAALC) gene and erythroblast transformation-specific related gene (ERG) in de novo cases of acute myeloid leukemia (AML) and identify roles in disease progression and outcome. MATERIALS AND METHODS This study included 50 newly diagnosed AML patients, along with 10 apparently healthy normal controls. BAALC and ERG expression was detected in the bone marrow of both patients and controls using real-time RT-PCR. RESULTS BAALC and ERG expression was detected in 52% of cases but not in any controls. There was a statistically significant correlation between BAALC and ERG gene expression and age (p- value=0.004 and 0.019, respectively). No statistical significance was noted for sex, lymphadenopathy, hepatomegaly, splenomegaly, other hematological findings, immunophenotyping and FAB sub-classification except for ERG gene and FAB (p-value=0.058). A statistical significant correlation was found between response to treatment with ERG expression (p-value=0.028) and age (p-value=0.014). A statistically significant variation in overall survival was evident with patient age, BM blast cells, FAB subgroups, BAALC and ERG expression (p-value= <0.001, 0.045, 0.041, <0.008 and 0.025 respectively). CONCLUSIONS Our results suggest that BAALC and ERG genes are specific significant molecular markers in AML disease progression, response to treatment and survival.
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Affiliation(s)
- Reham A Rashed
- Clinical Pathology, Medicine, National Cancer Institute, Cairo, Egypt E-mail :
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45
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Cruickshank VA, Sroczynska P, Sankar A, Miyagi S, Rundsten CF, Johansen JV, Helin K. SWI/SNF Subunits SMARCA4, SMARCD2 and DPF2 Collaborate in MLL-Rearranged Leukaemia Maintenance. PLoS One 2015; 10:e0142806. [PMID: 26571505 PMCID: PMC4646637 DOI: 10.1371/journal.pone.0142806] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 10/27/2015] [Indexed: 12/23/2022] Open
Abstract
Alterations in chromatin structure caused by deregulated epigenetic mechanisms collaborate with underlying genetic lesions to promote cancer. SMARCA4/BRG1, a core component of the SWI/SNF ATP-dependent chromatin-remodelling complex, has been implicated by its mutational spectrum as exerting a tumour-suppressor function in many solid tumours; recently however, it has been reported to sustain leukaemogenic transformation in MLL-rearranged leukaemia in mice. Here we further explore the role of SMARCA4 and the two SWI/SNF subunits SMARCD2/BAF60B and DPF2/BAF45D in leukaemia. We observed the selective requirement for these proteins for leukaemic cell expansion and self-renewal in-vitro as well as in leukaemia. Gene expression profiling in human cells of each of these three factors suggests that they have overlapping functions in leukaemia. The gene expression changes induced by loss of the three proteins demonstrate that they are required for the expression of haematopoietic stem cell associated genes but in contrast to previous results obtained in mouse cells, the three proteins are not required for the expression of c-MYC regulated genes.
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Affiliation(s)
- V. Adam Cruickshank
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
- Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Patrycja Sroczynska
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
- Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Aditya Sankar
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
- Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Satoru Miyagi
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
- Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
- The Danish Stem Cell Centre (Danstem), University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Carsten Friis Rundsten
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Jens Vilstrup Johansen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Kristian Helin
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
- Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
- The Danish Stem Cell Centre (Danstem), University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
- * E-mail:
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46
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Viny AD, Ott CJ, Spitzer B, Rivas M, Meydan C, Papalexi E, Yelin D, Shank K, Reyes J, Chiu A, Romin Y, Boyko V, Thota S, Maciejewski JP, Melnick A, Bradner JE, Levine RL. Dose-dependent role of the cohesin complex in normal and malignant hematopoiesis. J Exp Med 2015; 212:1819-32. [PMID: 26438361 PMCID: PMC4612085 DOI: 10.1084/jem.20151317] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Accepted: 09/04/2015] [Indexed: 01/18/2023] Open
Abstract
Cohesin complex members have recently been identified as putative tumor suppressors in hematologic and epithelial malignancies. The cohesin complex guides chromosome segregation; however, cohesin mutant leukemias do not show genomic instability. We hypothesized that reduced cohesin function alters chromatin structure and disrupts cis-regulatory architecture of hematopoietic progenitors. We investigated the consequences of Smc3 deletion in normal and malignant hematopoiesis. Biallelic Smc3 loss induced bone marrow aplasia with premature sister chromatid separation and revealed an absolute requirement for cohesin in hematopoietic stem cell (HSC) function. In contrast, Smc3 haploinsufficiency increased self-renewal in vitro and in vivo, including competitive transplantation. Smc3 haploinsufficiency reduced coordinated transcriptional output, including reduced expression of transcription factors and other genes associated with lineage commitment. Smc3 haploinsufficiency cooperated with Flt3-ITD to induce acute leukemia in vivo, with potentiated Stat5 signaling and altered nucleolar topology. These data establish a dose dependency for cohesin in regulating chromatin structure and HSC function.
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Affiliation(s)
- Aaron D Viny
- Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Department of Pathology, Molecular Cytology Core Facility, and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065 Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Department of Pathology, Molecular Cytology Core Facility, and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Christopher J Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215 Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Barbara Spitzer
- Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Department of Pathology, Molecular Cytology Core Facility, and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Martin Rivas
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065
| | - Cem Meydan
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065
| | - Efthymia Papalexi
- Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Department of Pathology, Molecular Cytology Core Facility, and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Dana Yelin
- Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Department of Pathology, Molecular Cytology Core Facility, and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065 Department of Medicine, Rabin Medical Center, Beilinson Campus, Petah Tikvah 49100, Israel
| | - Kaitlyn Shank
- Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Department of Pathology, Molecular Cytology Core Facility, and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Jaime Reyes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
| | - April Chiu
- Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Department of Pathology, Molecular Cytology Core Facility, and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Yevgeniy Romin
- Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Department of Pathology, Molecular Cytology Core Facility, and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Vitaly Boyko
- Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Department of Pathology, Molecular Cytology Core Facility, and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Swapna Thota
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195
| | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195
| | - Ari Melnick
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215 Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Ross L Levine
- Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Department of Pathology, Molecular Cytology Core Facility, and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065 Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Department of Pathology, Molecular Cytology Core Facility, and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065 Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Department of Pathology, Molecular Cytology Core Facility, and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065
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47
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Khaznadar Z, Boissel N, Agaugué S, Henry G, Cheok M, Vignon M, Geromin D, Cayuela JM, Castaigne S, Pautas C, Raffoux E, Lachuer J, Sigaux F, Preudhomme C, Dombret H, Dulphy N, Toubert A. Defective NK Cells in Acute Myeloid Leukemia Patients at Diagnosis Are Associated with Blast Transcriptional Signatures of Immune Evasion. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2015; 195:2580-90. [PMID: 26246143 DOI: 10.4049/jimmunol.1500262] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 07/08/2015] [Indexed: 01/29/2023]
Abstract
Acute myeloid leukemia (AML) is a heterogeneous group of malignancies that may be sensitive to the NK cell antitumor response. However, NK cells are frequently defective in AML. In this study, we found in an exploratory cohort (n = 46) that NK cell status at diagnosis of AML separated patients in two groups with a different clinical outcome. Patients with a deficient NK cell profile, including reduced expression of some activating NK receptors (e.g., DNAX accessory molecule-1, NKp46, and NKG2D) and decreased IFN-γ production, had a significantly higher risk of relapse (p = 0.03) independently of cytogenetic classification in multivariate analysis. Patients with defective NK cells showed a profound gene expression decrease in AML blasts for cytokine and chemokine signaling (e.g., IL15, IFNGR1, IFNGR2, and CXCR4), Ag processing (e.g., HLA-DRA, HLA-DRB1, and CD74) and adhesion molecule pathways (e.g., PVR and ICAM1). A set of 388 leukemic classifier genes defined in the exploratory cohort was independently validated in a multicentric cohort of 194 AML patients. In total, these data evidenced the interplay between NK cells and AML blasts at diagnosis allowing an immune-based stratification of AML patients independently of clinical classifications.
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MESH Headings
- Adult
- Aged
- Antigens, CD/immunology
- Cell Adhesion Molecules/immunology
- Cytotoxicity, Immunologic/immunology
- Female
- HLA-DR alpha-Chains/immunology
- HLA-DRB1 Chains/immunology
- Humans
- Interferon-gamma/biosynthesis
- Interleukin-15/biosynthesis
- Killer Cells, Natural/immunology
- Leukemia, Myeloid, Acute/diagnosis
- Leukemia, Myeloid, Acute/immunology
- Male
- Middle Aged
- Receptors, CXCR4/biosynthesis
- Receptors, Interferon/biosynthesis
- Receptors, Natural Killer Cell/metabolism
- Sialyltransferases/immunology
- Tumor Escape/genetics
- Tumor Escape/immunology
- Young Adult
- Interferon gamma Receptor
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Affiliation(s)
- Zena Khaznadar
- INSERM, Unité Mixte de Recherche-S1160, 75010 Paris, France; Institut Universitaire d'Hématologie, Université Paris Diderot, Sorbonne Paris Cité, 75010 Paris, France
| | - Nicolas Boissel
- Institut Universitaire d'Hématologie, Université Paris Diderot, Sorbonne Paris Cité, 75010 Paris, France; Service d'Hématologie Adulte, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Louis, 75010 Paris, France; Université Paris Diderot, Sorbonne Paris Cité, EA3518, 75010 Paris, France
| | - Sophie Agaugué
- INSERM, Unité Mixte de Recherche-S1160, 75010 Paris, France; Institut Universitaire d'Hématologie, Université Paris Diderot, Sorbonne Paris Cité, 75010 Paris, France
| | - Guylaine Henry
- Laboratoire d'Immunologie et Histocompatibilité, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Louis, 75010 Paris, France
| | - Meyling Cheok
- INSERM, Unité Mixte de Recherche-S1172, 59045 Lille, France; Laboratoire d'Hématologie, Centre de Biologie-Pathologie Centre Hospitalier Régional Universitaire Lille, Université de Lille, 59000 Lille, France
| | - Marguerite Vignon
- INSERM, Unité Mixte de Recherche-S1160, 75010 Paris, France; Institut Universitaire d'Hématologie, Université Paris Diderot, Sorbonne Paris Cité, 75010 Paris, France
| | - Daniela Geromin
- Institut Universitaire d'Hématologie, Université Paris Diderot, Sorbonne Paris Cité, 75010 Paris, France; Laboratoire d'Hématologie Biologique, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Louis, 75010 Paris, France; Tumorothèque, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Louis, 75010 Paris, France
| | - Jean-Michel Cayuela
- Institut Universitaire d'Hématologie, Université Paris Diderot, Sorbonne Paris Cité, 75010 Paris, France; Laboratoire d'Hématologie Biologique, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Louis, 75010 Paris, France; Tumorothèque, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Louis, 75010 Paris, France
| | - Sylvie Castaigne
- Université de Versailles-Saint Quentin, 78000 Versailles, France
| | - Cécile Pautas
- Université Paris-Est Créteil, 94000 Créteil, France; Service d'Hématologie Clinique, Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, 94000 Créteil, France
| | - Emmanuel Raffoux
- Service d'Hématologie Adulte, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Louis, 75010 Paris, France; Université Paris Diderot, Sorbonne Paris Cité, EA3518, 75010 Paris, France
| | - Joel Lachuer
- INSERM, Unité Mixte de Recherche-S1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Centre National pour la Recherche Scientifique, Unité Mixte de Recherche-5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Unité Mixte de Recherche-S1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université de Lyon, 69000 Lyon, France; and ProfileXpert, 69008 Lyon, France
| | - François Sigaux
- Institut Universitaire d'Hématologie, Université Paris Diderot, Sorbonne Paris Cité, 75010 Paris, France
| | - Claude Preudhomme
- INSERM, Unité Mixte de Recherche-S1172, 59045 Lille, France; Laboratoire d'Hématologie, Centre de Biologie-Pathologie Centre Hospitalier Régional Universitaire Lille, Université de Lille, 59000 Lille, France
| | - Hervé Dombret
- Institut Universitaire d'Hématologie, Université Paris Diderot, Sorbonne Paris Cité, 75010 Paris, France; Service d'Hématologie Adulte, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Louis, 75010 Paris, France; Université Paris Diderot, Sorbonne Paris Cité, EA3518, 75010 Paris, France
| | - Nicolas Dulphy
- INSERM, Unité Mixte de Recherche-S1160, 75010 Paris, France; Institut Universitaire d'Hématologie, Université Paris Diderot, Sorbonne Paris Cité, 75010 Paris, France; Laboratoire d'Immunologie et Histocompatibilité, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Louis, 75010 Paris, France;
| | - Antoine Toubert
- INSERM, Unité Mixte de Recherche-S1160, 75010 Paris, France; Institut Universitaire d'Hématologie, Université Paris Diderot, Sorbonne Paris Cité, 75010 Paris, France; Laboratoire d'Immunologie et Histocompatibilité, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Louis, 75010 Paris, France;
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Kohlscheen S, Wintterle S, Schwarzer A, Kamp C, Brugman MH, Breuer DC, Büsche G, Baum C, Modlich U. Inhibition of Thrombopoietin/Mpl Signaling in Adult Hematopoiesis Identifies New Candidates for Hematopoietic Stem Cell Maintenance. PLoS One 2015; 10:e0131866. [PMID: 26147434 PMCID: PMC4493002 DOI: 10.1371/journal.pone.0131866] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 05/11/2015] [Indexed: 01/23/2023] Open
Abstract
Thrombopoietin (Thpo) signals via its receptor Mpl and regulates megakaryopoiesis, hematopoietic stem cell (HSC) maintenance and post-transplant expansion. Mpl expression is tightly controlled and deregulation of Thpo/Mpl-signaling is linked to hematological disorders. Here, we constructed an intracellular-truncated, signaling-deficient Mpl protein which is presented on the cell surface (dnMpl). The transplantation of bone marrow cells retrovirally transduced to express dnMpl into wildtype mice induced thrombocytopenia, and a progressive loss of HSC. The aplastic BM allowed the engraftment of a second BM transplant without further conditioning. Functional analysis of the truncated Mpl in vitro and in vivo demonstrated no internalization after Thpo binding and the inhibition of Thpo/Mpl-signaling in wildtype cells due to dominant-negative (dn) effects by receptor competition with wildtype Mpl for Thpo binding. Intracellular inhibition of Mpl could be excluded as the major mechanism by the use of a constitutive-dimerized dnMpl. To further elucidate the molecular changes induced by Thpo/Mpl-inhibition on the HSC-enriched cell population in the BM, we performed gene expression analysis of Lin-Sca1+cKit+ (LSK) cells isolated from mice transplanted with dnMpl transduced BM cells. The gene expression profile supported the exhaustion of HSC due to increased cell cycle progression and identified new and known downstream effectors of Thpo/Mpl-signaling in HSC (namely TIE2, ESAM1 and EPCR detected on the HSC-enriched LSK cell population). We further compared gene expression profiles in LSK cells of dnMpl mice with human CD34+ cells of aplastic anemia patients and identified similar deregulations of important stemness genes in both cell populations. In summary, we established a novel way of Thpo/Mpl inhibition in the adult mouse and performed in depth analysis of the phenotype including gene expression profiling.
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Affiliation(s)
- Saskia Kohlscheen
- Research Group for Gene Modification in Stem Cells, LOEWE Center for Cell and Gene Therapy Frankfurt/Main and the Paul-Ehrlich-Institute, Langen, Germany
- Institute of Experimental Hematology; Hannover Medical School, Hannover, Germany
| | - Sabine Wintterle
- Institute of Experimental Hematology; Hannover Medical School, Hannover, Germany
| | - Adrian Schwarzer
- Institute of Experimental Hematology; Hannover Medical School, Hannover, Germany
| | - Christel Kamp
- Department of Biostatistik, Paul-Ehrlich-Institute, Langen, Germany
| | - Martijn H. Brugman
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, ZA Leiden, The Netherlands
| | - Daniel C. Breuer
- Institute of Experimental Hematology; Hannover Medical School, Hannover, Germany
| | - Guntram Büsche
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Christopher Baum
- Institute of Experimental Hematology; Hannover Medical School, Hannover, Germany
| | - Ute Modlich
- Research Group for Gene Modification in Stem Cells, LOEWE Center for Cell and Gene Therapy Frankfurt/Main and the Paul-Ehrlich-Institute, Langen, Germany
- Institute of Experimental Hematology; Hannover Medical School, Hannover, Germany
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49
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Levine JH, Simonds EF, Bendall SC, Davis KL, Amir EAD, Tadmor MD, Litvin O, Fienberg HG, Jager A, Zunder ER, Finck R, Gedman AL, Radtke I, Downing JR, Pe'er D, Nolan GP. Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis. Cell 2015; 162:184-97. [PMID: 26095251 DOI: 10.1016/j.cell.2015.05.047] [Citation(s) in RCA: 1334] [Impact Index Per Article: 148.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 03/16/2015] [Accepted: 05/04/2015] [Indexed: 12/20/2022]
Abstract
Acute myeloid leukemia (AML) manifests as phenotypically and functionally diverse cells, often within the same patient. Intratumor phenotypic and functional heterogeneity have been linked primarily by physical sorting experiments, which assume that functionally distinct subpopulations can be prospectively isolated by surface phenotypes. This assumption has proven problematic, and we therefore developed a data-driven approach. Using mass cytometry, we profiled surface and intracellular signaling proteins simultaneously in millions of healthy and leukemic cells. We developed PhenoGraph, which algorithmically defines phenotypes in high-dimensional single-cell data. PhenoGraph revealed that the surface phenotypes of leukemic blasts do not necessarily reflect their intracellular state. Using hematopoietic progenitors, we defined a signaling-based measure of cellular phenotype, which led to isolation of a gene expression signature that was predictive of survival in independent cohorts. This study presents new methods for large-scale analysis of single-cell heterogeneity and demonstrates their utility, yielding insights into AML pathophysiology.
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Affiliation(s)
- Jacob H Levine
- Departments of Biological Sciences and Systems Biology, Columbia University, New York, NY 10027, USA
| | - Erin F Simonds
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Sean C Bendall
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Kara L Davis
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - El-ad D Amir
- Departments of Biological Sciences and Systems Biology, Columbia University, New York, NY 10027, USA
| | - Michelle D Tadmor
- Departments of Biological Sciences and Systems Biology, Columbia University, New York, NY 10027, USA
| | - Oren Litvin
- Departments of Biological Sciences and Systems Biology, Columbia University, New York, NY 10027, USA
| | - Harris G Fienberg
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Astraea Jager
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Eli R Zunder
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Rachel Finck
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Amanda L Gedman
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Ina Radtke
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - James R Downing
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Dana Pe'er
- Departments of Biological Sciences and Systems Biology, Columbia University, New York, NY 10027, USA.
| | - Garry P Nolan
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA.
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50
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Antileukemia activity of the novel peptidic CXCR4 antagonist LY2510924 as monotherapy and in combination with chemotherapy. Blood 2015; 126:222-32. [PMID: 26031918 DOI: 10.1182/blood-2015-02-628677] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 05/21/2015] [Indexed: 12/12/2022] Open
Abstract
Targeting the stromal cell-derived factor 1α (SDF-1α)/C-X-C chemokine receptor type 4 (CXCR4) axis has been shown to be a promising therapeutic approach to overcome chemoresistance in acute myeloid leukemia (AML). We investigated the antileukemia efficacy of a novel peptidic CXCR4 antagonist, LY2510924, in preclinical models of AML. LY2510924 rapidly and durably blocked surface CXCR4 and inhibited stromal cell-derived factor 1 (SDF-1)α-induced chemotaxis and prosurvival signals of AML cells at nanomolar concentrations more effectively than the small-molecule CXCR4 antagonist AMD3100. In vitro, LY2510924 chiefly inhibited the proliferation of AML cells with little induction of cell death and reduced protection against chemotherapy by stromal cells. In mice with established AML, LY2510924 caused initial mobilization of leukemic cells into the circulation followed by reduction in total tumor burden. LY2510924 had antileukemia effects as monotherapy as well as in combination with chemotherapy. Gene expression profiling of AML cells isolated from LY2510924-treated mice demonstrated changes consistent with loss of SDF-1α/CXCR4 signaling and suggested reduced proliferation and induction of differentiation, which was proved by showing the attenuation of multiple prosurvival pathways such as PI3K/AKT, MAPK, and β-catenin and myeloid differentiation in vivo. Effective disruption of the SDF-1α/CXCR4 axis by LY2510924 may translate into effective antileukemia therapy in future clinical applications.
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