1
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Longitudinal single-cell profiling of chemotherapy response in acute myeloid leukemia. Nat Commun 2023; 14:1285. [PMID: 36890137 PMCID: PMC9995364 DOI: 10.1038/s41467-023-36969-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/22/2023] [Indexed: 03/10/2023] Open
Abstract
Acute myeloid leukemia may be characterized by a fraction of leukemia stem cells (LSCs) that sustain disease propagation eventually leading to relapse. Yet, the contribution of LSCs to early therapy resistance and AML regeneration remains controversial. We prospectively identify LSCs in AML patients and xenografts by single-cell RNA sequencing coupled with functional validation by a microRNA-126 reporter enriching for LSCs. Through nucleophosmin 1 (NPM1) mutation calling or chromosomal monosomy detection in single-cell transcriptomes, we discriminate LSCs from regenerating hematopoiesis, and assess their longitudinal response to chemotherapy. Chemotherapy induced a generalized inflammatory and senescence-associated response. Moreover, we observe heterogeneity within progenitor AML cells, some of which proliferate and differentiate with expression of oxidative-phosphorylation (OxPhos) signatures, while others are OxPhos (low) miR-126 (high) and display enforced stemness and quiescence features. miR-126 (high) LSCs are enriched at diagnosis in chemotherapy-refractory AML and at relapse, and their transcriptional signature robustly stratifies patients for survival in large AML cohorts.
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2
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Lipids and the cancer stemness regulatory system in acute myeloid leukemia. Essays Biochem 2022; 66:333-344. [PMID: 35996953 DOI: 10.1042/ebc20220028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/30/2022] [Accepted: 08/08/2022] [Indexed: 12/17/2022]
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease of impaired myeloid differentiation and a caricature of normal hematopoiesis. Leukemic stem cells (LSCs) are responsible for long-term clonal propagation in AML just as hematopoietic stem cells (HSCs) sustain lifelong hematopoiesis. LSCs are often resistant to standard chemotherapy and are responsible for clinical relapse. Although AML is highly heterogeneous, determinants of stemness are prognostic for AML patient survival and can predict AML drug sensitivity. Therefore, one way to overcome challenges preventing efficacious treatment outcomes is to target LSC stemness. Metabolomic and lipidomic studies of serum and cells from AML patients are emerging to complement genomic, transcriptomic, epigenetic, and proteomic data sets to characterize and stratify AML. Recent studies have shown the value of fractionating LSCs versus blasts when characterizing metabolic pathways and implicate the importance of lipid balance to LSCs function. As more extensive metabolic studies coupled to functional in vivo assays are conducted on highly purified HSCs, bulk AML, and LSCs, the similarities and differences in lipid homeostasis in stem-like versus more mature AML subtypes as well as from normal HSCs are emerging. Here, we discuss the latest findings from studies of lipid function in LSCs, with a focus on sphingolipids (SLs) as stemness/lineage fate mediators in AML, and the balance of fatty acid anabolism and catabolism fueling metabolic flexibility and drug resistance in AML. We also discuss how designing successful strategies to target lipid vulnerabilities and improve AML patient survival should take into consideration the hierarchical nature of AML.
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3
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Gudmundsson KO, Du Y. Quiescence regulation by normal haematopoietic stem cells and leukaemia stem cells. FEBS J 2022. [PMID: 35514133 DOI: 10.1111/febs.16472] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 03/21/2022] [Accepted: 05/03/2022] [Indexed: 11/30/2022]
Abstract
The haematopoietic system is maintained by rare haematopoietic stem cells (HSCs), which are quiescent most of the time and only divide occasionally to self-renew and/or to undergo commitment to clonal expansion via the generation of highly proliferative progenitor cells. The latter is responsible for the generation of all mature cells of the system through subsequent lineage commitment and terminal differentiation. Cells with similar properties also exist in leukaemias and are known as leukaemia stem cells (LSCs). Quiescence provides essential protection for both HSC and LSC from cytotoxic stress and DNA damage and, in the case of LSCs, likely causes therapy resistance and disease relapse in leukaemia patients. Specific inhibition of LSC quiescence has been considered a promising strategy for eliminating LSCs and curing leukaemias. Although the understanding of mechanisms responsible for quiescence maintenance in these cells remains limited, particularly for LSCs, recent studies have suggested potential differences in their dependency on certain pathways and their levels of stress and DNA damage caused by increased cycling. Such differences likely stem from oncogenic mutations in LSCs and could be specifically exploited for the elimination of LSCs while sparing normal HSCs in the future.
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Affiliation(s)
- Kristbjorn Orri Gudmundsson
- Basic Science Program Leidos Biomedical Research Inc. Frederick National Laboratory for Cancer Research in the Mouse Cancer Genetics Program Center for Cancer Research NCI Frederick MD USA
| | - Yang Du
- Department of Pediatrics Uniformed Services University of the Health Sciences Bethesda MD USA
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4
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p21-Activated kinases as promising therapeutic targets in hematological malignancies. Leukemia 2022; 36:315-326. [PMID: 34697424 DOI: 10.1038/s41375-021-01451-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/30/2021] [Accepted: 10/07/2021] [Indexed: 01/12/2023]
Abstract
The p21-Activated Kinases (PAKs) are a family of six serine/threonine kinases that were originally identified as downstream effectors of the Rho GTPases Cdc42 and Rac. Since the first PAK was discovered in 1994, studies have revealed their fundamental and biological importance in the development of physiological systems. Within the cell, PAKs also play significant roles in regulating essential cellular processes such as cytoskeletal dynamics, gene expression, cell survival, and cell cycle progression. These processes are often deregulated in numerous cancers when different PAKs are overexpressed or amplified at the chromosomal level. Furthermore, PAKs modulate multiple oncogenic signaling pathways which facilitate apoptosis escape, uncontrolled proliferation, and drug resistance. There is growing insight into the critical roles of PAKs in regulating steady-state hematopoiesis, including the properties of hematopoietic stem cells (HSC), and the initiation and progression of hematological malignancies. This review will focus on the most recent studies that provide experimental evidence showing how specific PAKs regulate the properties of leukemic stem cells (LSCs) and drug-resistant cells to initiate and maintain hematological malignancies. The current understanding of the molecular and cellular mechanisms by which the PAKs operate in specific human leukemia or lymphomas will be discussed. From a translational point of view, PAKs have been suggested to be critical therapeutic targets and potential prognosis markers; thus, this review will also discuss current therapeutic strategies against hematological malignancies using existing small-molecule PAK inhibitors, as well as promising combination treatments, to sensitize drug-resistant cells to conventional therapies. The challenges of toxicity and non-specific targeting associated with some PAK inhibitors, as well as how future approaches for PAK inhibition to overcome these limitations, will also be addressed.
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5
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A primary hierarchically organized patient-derived model enables in depth interrogation of stemness driven by the coding and non-coding genome. Leukemia 2022; 36:2690-2704. [PMID: 36131042 PMCID: PMC9613464 DOI: 10.1038/s41375-022-01697-9] [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: 06/01/2022] [Revised: 08/23/2022] [Accepted: 09/01/2022] [Indexed: 11/30/2022]
Abstract
Many cancers are organized as cellular hierarchies sustained by cancer stem cells (CSC), whose eradication is crucial for achieving long-term remission. Difficulties to isolate and undertake in vitro and in vivo experimental studies of rare CSC under conditions that preserve their original properties currently constitute a bottleneck for identifying molecular mechanisms involving coding and non-coding genomic regions that govern stemness. We focussed on acute myeloid leukemia (AML) as a paradigm of the CSC model and developed a patient-derived system termed OCI-AML22 that recapitulates the cellular hierarchy driven by leukemia stem cells (LSC). Through classical flow sorting and functional analyses, we established that a single phenotypic population is highly enriched for LSC. The LSC fraction can be easily isolated and serially expanded in culture or in xenografts while faithfully recapitulating functional, transcriptional and epigenetic features of primary LSCs. A novel non-coding regulatory element was identified with a new computational approach using functionally validated primary AML LSC fractions and its role in LSC stemness validated through efficient CRISPR editing using methods optimized for OCI-AML22 LSC. Collectively, OCI-AML22 constitutes a valuable resource to uncover mechanisms governing CSC driven malignancies.
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6
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Nguyen P, Chien S, Dai J, Monnat RJ, Becker PS, Kueh HY. Unsupervised discovery of dynamic cell phenotypic states from transmitted light movies. PLoS Comput Biol 2021; 17:e1009626. [PMID: 34968384 PMCID: PMC8754342 DOI: 10.1371/journal.pcbi.1009626] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 01/12/2022] [Accepted: 11/09/2021] [Indexed: 11/26/2022] Open
Abstract
Identification of cell phenotypic states within heterogeneous populations, along with elucidation of their switching dynamics, is a central challenge in modern biology. Conventional single-cell analysis methods typically provide only indirect, static phenotypic readouts. Transmitted light images, on the other hand, provide direct morphological readouts and can be acquired over time to provide a rich data source for dynamic cell phenotypic state identification. Here, we describe an end-to-end deep learning platform, UPSIDE (Unsupervised Phenotypic State IDEntification), for discovering cell states and their dynamics from transmitted light movies. UPSIDE uses the variational auto-encoder architecture to learn latent cell representations, which are then clustered for state identification, decoded for feature interpretation, and linked across movie frames for transition rate inference. Using UPSIDE, we identified distinct blood cell types in a heterogeneous dataset. We then analyzed movies of patient-derived acute myeloid leukemia cells, from which we identified stem-cell associated morphological states as well as the transition rates to and from these states. UPSIDE opens up the use of transmitted light movies for systematic exploration of cell state heterogeneity and dynamics in biology and medicine.
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Affiliation(s)
- Phuc Nguyen
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington, United States of America
| | - Sylvia Chien
- Division of Hematology, University of Washington, Seattle, Washington, United States of America
| | - Jin Dai
- Division of Hematology, University of Washington, Seattle, Washington, United States of America
| | - Raymond J. Monnat
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, United States of America
| | - Pamela S. Becker
- Division of Hematology, University of Washington, Seattle, Washington, United States of America
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Division of Hematology/Oncology, Department of Medicine, University of California, Irvine, California, United States of America
- Chao Family Comprehensive Cancer Center Cancer Research Institute, University of California, Irvine, California, United States of America
| | - Hao Yuan Kueh
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington, United States of America
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, United States of America
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7
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Pessoa Rodrigues C, Akhtar A. Differential H4K16ac levels ensure a balance between quiescence and activation in hematopoietic stem cells. SCIENCE ADVANCES 2021; 7:eabi5987. [PMID: 34362741 PMCID: PMC8346211 DOI: 10.1126/sciadv.abi5987] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/21/2021] [Indexed: 05/13/2023]
Abstract
Hematopoietic stem cells (HSCs) are able to reconstitute the bone marrow while retaining their self-renewal property. Individual HSCs demonstrate heterogeneity in their repopulating capacities. Here, we found that the levels of the histone acetyltransferase MOF (males absent on the first) and its target modification histone H4 lysine 16 acetylation are heterogeneous among HSCs and influence their proliferation capacities. The increased proliferative capacities of MOF-depleted cells are linked to their expression of CD93. The CD93+ HSC subpopulation simultaneously shows transcriptional features of quiescent HSCs and functional features of active HSCs. CD93+ HSCs were expanded and exhibited an enhanced proliferative advantage in Mof +/- animals reminiscent of a premalignant state. Accordingly, low MOF and high CD93 levels correlate with poor survival and increased proliferation capacity in leukemia. Collectively, our study indicates H4K16ac as an important determinant for HSC heterogeneity, which is linked to the onset of monocytic disorders.
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Affiliation(s)
- Cecilia Pessoa Rodrigues
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
- International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Freiburg, Germany
| | - Asifa Akhtar
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
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8
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TFEB-mediated endolysosomal activity controls human hematopoietic stem cell fate. Cell Stem Cell 2021; 28:1838-1850.e10. [PMID: 34343492 DOI: 10.1016/j.stem.2021.07.003] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/15/2021] [Accepted: 06/23/2021] [Indexed: 12/17/2022]
Abstract
It is critical to understand how human quiescent long-term hematopoietic stem cells (LT-HSCs) sense demand from daily and stress-mediated cues and then transition into bioenergetically active progeny to differentiate and meet these cellular needs. However, the demand-adapted regulatory circuits of these early steps of hematopoiesis are largely unknown. Here we show that lysosomes, sophisticated nutrient-sensing and signaling centers, are regulated dichotomously by transcription factor EB (TFEB) and MYC to balance catabolic and anabolic processes required for activating LT-HSCs and guiding their lineage fate. TFEB-mediated induction of the endolysosomal pathway causes membrane receptor degradation, limiting LT-HSC metabolic and mitogenic activation, promoting quiescence and self-renewal, and governing erythroid-myeloid commitment. In contrast, MYC engages biosynthetic processes while repressing lysosomal catabolism, driving LT-HSC activation. Our study identifies TFEB-mediated control of lysosomal activity as a central regulatory hub for proper and coordinated stem cell fate determination.
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9
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Subedi A, Liu Q, Ayyathan DM, Sharon D, Cathelin S, Hosseini M, Xu C, Voisin V, Bader GD, D'Alessandro A, Lechman ER, Dick JE, Minden MD, Wang JCY, Chan SM. Nicotinamide phosphoribosyltransferase inhibitors selectively induce apoptosis of AML stem cells by disrupting lipid homeostasis. Cell Stem Cell 2021; 28:1851-1867.e8. [PMID: 34293334 DOI: 10.1016/j.stem.2021.06.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 05/05/2021] [Accepted: 06/22/2021] [Indexed: 12/29/2022]
Abstract
Current treatments for acute myeloid leukemia (AML) are often ineffective in eliminating leukemic stem cells (LSCs), which perpetuate the disease. Here, we performed a metabolic drug screen to identify LSC-specific vulnerabilities and found that nicotinamide phosphoribosyltransferase (NAMPT) inhibitors selectively killed LSCs, while sparing normal hematopoietic stem and progenitor cells. Treatment with KPT-9274, a NAMPT inhibitor, suppressed the conversion of saturated fatty acids to monounsaturated fatty acids, a reaction catalyzed by the stearoyl-CoA desaturase (SCD) enzyme, resulting in apoptosis of AML cells. Transcriptomic analysis of LSCs treated with KPT-9274 revealed an upregulation of sterol regulatory-element binding protein (SREBP)-regulated genes, including SCD, which conferred partial protection against NAMPT inhibitors. Inhibition of SREBP signaling with dipyridamole enhanced the cytotoxicity of KPT-9274 on LSCs in vivo. Our work demonstrates that altered lipid homeostasis plays a key role in NAMPT inhibitor-induced apoptosis and identifies NAMPT inhibition as a therapeutic strategy for targeting LSCs in AML.
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Affiliation(s)
- Amit Subedi
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Qiang Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Dhanoop M Ayyathan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - David Sharon
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Severine Cathelin
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Mohsen Hosseini
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Changjiang Xu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON, Canada
| | - Veronique Voisin
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON, Canada
| | - Gary D Bader
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON, Canada
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO, USA
| | - Eric R Lechman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Medicine, University of Toronto, ON, Canada; Division of Medical Oncology and Hematology, Department of Medicine, University Health Network, Toronto, ON, Canada
| | - Jean C Y Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Medicine, University of Toronto, ON, Canada; Division of Medical Oncology and Hematology, Department of Medicine, University Health Network, Toronto, ON, Canada
| | - Steven M Chan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Medicine, University of Toronto, ON, Canada; Division of Medical Oncology and Hematology, Department of Medicine, University Health Network, Toronto, ON, Canada.
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10
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Schoof EM, Furtwängler B, Üresin N, Rapin N, Savickas S, Gentil C, Lechman E, Keller UAD, Dick JE, Porse BT. Quantitative single-cell proteomics as a tool to characterize cellular hierarchies. Nat Commun 2021; 12:3341. [PMID: 34099695 PMCID: PMC8185083 DOI: 10.1038/s41467-021-23667-y] [Citation(s) in RCA: 189] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 05/11/2021] [Indexed: 02/06/2023] Open
Abstract
Large-scale single-cell analyses are of fundamental importance in order to capture biological heterogeneity within complex cell systems, but have largely been limited to RNA-based technologies. Here we present a comprehensive benchmarked experimental and computational workflow, which establishes global single-cell mass spectrometry-based proteomics as a tool for large-scale single-cell analyses. By exploiting a primary leukemia model system, we demonstrate both through pre-enrichment of cell populations and through a non-enriched unbiased approach that our workflow enables the exploration of cellular heterogeneity within this aberrant developmental hierarchy. Our approach is capable of consistently quantifying ~1000 proteins per cell across thousands of individual cells using limited instrument time. Furthermore, we develop a computational workflow (SCeptre) that effectively normalizes the data, integrates available FACS data and facilitates downstream analysis. The approach presented here lays a foundation for implementing global single-cell proteomics studies across the world.
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Affiliation(s)
- Erwin M Schoof
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark.
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Canada.
| | - Benjamin Furtwängler
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nil Üresin
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nicolas Rapin
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Simonas Savickas
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Coline Gentil
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Eric Lechman
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Ulrich Auf dem Keller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Bo T Porse
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
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11
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Horizontal meta-analysis identifies common deregulated genes across AML subgroups providing a robust prognostic signature. Blood Adv 2021; 4:5322-5335. [PMID: 33108456 DOI: 10.1182/bloodadvances.2020002042] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 09/11/2020] [Indexed: 12/14/2022] Open
Abstract
Advances in transcriptomics have improved our understanding of leukemic development and helped to enhance the stratification of patients. The tendency of transcriptomic studies to combine AML samples, regardless of cytogenetic abnormalities, could lead to bias in differential gene expression analysis because of the differential representation of AML subgroups. Hence, we performed a horizontal meta-analysis that integrated transcriptomic data on AML from multiple studies, to enrich the less frequent cytogenetic subgroups and to uncover common genes involved in the development of AML and response to therapy. A total of 28 Affymetrix microarray data sets containing 3940 AML samples were downloaded from the Gene Expression Omnibus database. After stringent quality control, transcriptomic data on 1534 samples from 11 data sets, covering 10 AML cytogenetically defined subgroups, were retained and merged with the data on 198 healthy bone marrow samples. Differentially expressed genes between each cytogenetic subgroup and normal samples were extracted, enabling the unbiased identification of 330 commonly deregulated genes (CODEGs), which showed enriched profiles of myeloid differentiation, leukemic stem cell status, and relapse. Most of these genes were downregulated, in accordance with DNA hypermethylation. CODEGs were then used to create a prognostic score based on the weighted sum of expression of 22 core genes (CODEG22). The score was validated with microarray data of 5 independent cohorts and by quantitative real time-polymerase chain reaction in a cohort of 142 samples. CODEG22-based stratification of patients, globally and into subpopulations of cytologically healthy and elderly individuals, may complement the European LeukemiaNet classification, for a more accurate prediction of AML outcomes.
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12
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A latent subset of human hematopoietic stem cells resists regenerative stress to preserve stemness. Nat Immunol 2021; 22:723-734. [PMID: 33958784 DOI: 10.1038/s41590-021-00925-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 03/25/2021] [Indexed: 11/09/2022]
Abstract
Continuous supply of immune cells throughout life relies on the delicate balance in the hematopoietic stem cell (HSC) pool between long-term maintenance and meeting the demands of both normal blood production and unexpected stress conditions. Here we identified distinct subsets of human long-term (LT)-HSCs that responded differently to regeneration-mediated stress: an immune checkpoint ligand CD112lo subset that exhibited a transient engraftment restraint (termed latency) before contributing to hematopoietic reconstitution and a primed CD112hi subset that responded rapidly. This functional heterogeneity and CD112 expression are regulated by INKA1 through direct interaction with PAK4 and SIRT1, inducing epigenetic changes and defining an alternative state of LT-HSC quiescence that serves to preserve self-renewal and regenerative capacity upon regeneration-mediated stress. Collectively, our data uncovered the molecular intricacies underlying HSC heterogeneity and self-renewal regulation and point to latency as an orchestrated physiological response that balances blood cell demands with preserving a stem cell reservoir.
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13
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Abstract
Haematopoietic stem and progenitor cells (HSPCs) are defined as unspecialized cells that give rise to more differentiated cells. In a similar way, leukaemic stem and progenitor cells (LSPCs) are defined as unspecialized leukaemic cells, which can give rise to more differentiated cells. Leukaemic cells carry leukaemic mutations/variants and have clear differentiation abnormalities. Pre-leukaemic HSPCs (PreL-HSPCs) carry pre-leukaemic mutations/variants (pLMs) and are capable of producing mature functional cells, which will carry the same variants. Under the roof of LSPCs, one can find a broad range of cell types genetic and disease phenotypes. Present-day knowledge suggests that this phenotypic heterogeneity is the result of interactions between the cell of origin, the genetic background and the microenvironment background. The combination of these attributes will define the LSPC phenotype, frequency, differentiation capacity and evolutionary trajectory. Importantly, as LSPCs are leukaemia-initiating cells that sustain clinical remission and are the source of relapse, an improved understanding of LSPCs phenotype would offer better clinical opportunities for the treatment and hopefully prevention of human leukaemia. The current review will focus on LSPCs attributes in the context of human haematologic malignancies.
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Affiliation(s)
- L I Shlush
- From the, Liran Shlush's Lab - Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - T Feldman
- From the, Liran Shlush's Lab - Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
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14
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Xie SZ, Kaufmann KB, Wang W, Chan-Seng-Yue M, Gan OI, Laurenti E, Garcia-Prat L, Takayanagi SI, Ng SWK, Xu C, Zeng AGX, Jin L, McLeod J, Wagenblast E, Mitchell A, Kennedy JA, Liu Q, Boutzen H, Kleinau M, Jargstorf J, Holmes G, Zhang Y, Voisin V, Bader GD, Wang JCY, Hannun YA, Luberto C, Schroeder T, Minden MD, Dick JE. Sphingosine-1-phosphate receptor 3 potentiates inflammatory programs in normal and leukemia stem cells to promote differentiation. Blood Cancer Discov 2021; 2:32-53. [PMID: 33458693 PMCID: PMC7116590 DOI: 10.1158/2643-3230.bcd-20-0155] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/27/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022] Open
Abstract
Acute myeloid leukemia (AML) is a caricature of normal hematopoiesis, driven from leukemia stem cells (LSC) that share some hematopoietic stem cell (HSC) programs including responsiveness to inflammatory signaling. Although inflammation dysregulates mature myeloid cells and influences stemness programs and lineage determination in HSC by activating stress myelopoiesis, such roles in LSC are poorly understood. Here, we show that S1PR3, a receptor for the bioactive lipid sphingosine-1-phosphate, is a central regulator which drives myeloid differentiation and activates inflammatory programs in both HSC and LSC. S1PR3-mediated inflammatory signatures varied in a continuum from primitive to mature myeloid states across AML patient cohorts, each with distinct phenotypic and clinical properties. S1PR3 was high in LSC and blasts of mature myeloid samples with linkages to chemosensitivity, while S1PR3 activation in primitive samples promoted LSC differentiation leading to eradication. Our studies open new avenues for therapeutic target identification specific for each AML subset.
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Affiliation(s)
- Stephanie Z Xie
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
| | - Kerstin B Kaufmann
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Weijia Wang
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Michelle Chan-Seng-Yue
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Olga I Gan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Elisa Laurenti
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Laura Garcia-Prat
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Shin-Ichiro Takayanagi
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Cell Therapy Project, R&D Division, Kirin Holdings Company, Limited, Kanagawa, Japan
| | - Stanley W K Ng
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - ChangJiang Xu
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Andy G X Zeng
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Liqing Jin
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jessica McLeod
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Elvin Wagenblast
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Amanda Mitchell
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - James A Kennedy
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Division of Medical Oncology and Hematology, Department of Medicine, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Qiang Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Héléna Boutzen
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Melissa Kleinau
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Joseph Jargstorf
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Gareth Holmes
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Yang Zhang
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Veronique Voisin
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jean C Y Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Division of Medical Oncology and Hematology, Department of Medicine, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Yusuf A Hannun
- Stony Brook Cancer Center and Departments of Medicine, Biochemistry, and Pathology, Stony Brook University, Stony Brook, New York
| | - Chiara Luberto
- Department of Physiology and Biophysics, Stony Brook School of Medicine, Stony Brook, New York
| | - Timm Schroeder
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Division of Medical Oncology and Hematology, Department of Medicine, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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15
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Mejia-Ramirez E, Florian MC. Understanding intrinsic hematopoietic stem cell aging. Haematologica 2019; 105:22-37. [PMID: 31806687 PMCID: PMC6939535 DOI: 10.3324/haematol.2018.211342] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 11/14/2019] [Indexed: 01/03/2023] Open
Abstract
Hematopoietic stem cells (HSC) sustain blood production over the entire life-span of an organism. It is of extreme importance that these cells maintain self-renewal and differentiation potential over time in order to preserve homeostasis of the hematopoietic system. Many of the intrinsic aspects of HSC are affected by the aging process resulting in a deterioration in their potential, independently of their microenvironment. Here we review recent findings characterizing most of the intrinsic aspects of aged HSC, ranging from phenotypic to molecular alterations. Historically, DNA damage was thought to be the main cause of HSC aging. However, over recent years, many new findings have defined an increasing number of biological processes that intrinsically change with age in HSC. Epigenetics and chromatin architecture, together with autophagy, proteostasis and metabolic changes, and how they are interconnected, are acquiring growing importance for understanding the intrinsic aging of stem cells. Given the increase in populations of older subjects worldwide, and considering that aging is the primary risk factor for most diseases, understanding HSC aging becomes particularly relevant also in the context of hematologic disorders, such as myelodysplastic syndromes and acute myeloid leukemia. Research on intrinsic mechanisms responsible for HSC aging is providing, and will continue to provide, new potential molecular targets to possibly ameliorate or delay aging of the hematopoietic system and consequently improve the outcome of hematologic disorders in the elderly. The niche-dependent contributions to hematopoietic aging are discussed in another review in this same issue of the Journal.
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Affiliation(s)
- Eva Mejia-Ramirez
- Center for Regenerative Medicine in Barcelona (CMRB), Bellvitge Institute for Biomedical Research (IDIBELL), Barcelona, Spain.,Center for Networked Biomedical Research on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, 28029, Spain
| | - Maria Carolina Florian
- Center for Regenerative Medicine in Barcelona (CMRB), Bellvitge Institute for Biomedical Research (IDIBELL), Barcelona, Spain .,Institute of Molecular Medicine and Stem Cell Aging, Ulm University, Ulm, Germany EM-R and MCF contributed equally to this work
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16
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Xie SZ, Garcia-Prat L, Voisin V, Ferrari R, Gan OI, Wagenblast E, Kaufmann KB, Zeng AGX, Takayanagi SI, Patel I, Lee EK, Jargstorf J, Holmes G, Romm G, Pan K, Shoong M, Vedi A, Luberto C, Minden MD, Bader GD, Laurenti E, Dick JE. Sphingolipid Modulation Activates Proteostasis Programs to Govern Human Hematopoietic Stem Cell Self-Renewal. Cell Stem Cell 2019; 25:639-653.e7. [PMID: 31631013 PMCID: PMC6838675 DOI: 10.1016/j.stem.2019.09.008] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 07/09/2019] [Accepted: 09/23/2019] [Indexed: 12/30/2022]
Abstract
Cellular stress responses serve as crucial decision points balancing persistence or culling of hematopoietic stem cells (HSCs) for lifelong blood production. Although strong stressors cull HSCs, the linkage between stress programs and self-renewal properties that underlie human HSC maintenance remains unknown, particularly at quiescence exit when HSCs must also dynamically shift metabolic state. Here, we demonstrate distinct wiring of the sphingolipidome across the human hematopoietic hierarchy and find that genetic or pharmacologic modulation of the sphingolipid enzyme DEGS1 regulates lineage differentiation. Inhibition of DEGS1 in hematopoietic stem and progenitor cells during the transition from quiescence to cellular activation with N-(4-hydroxyphenyl) retinamide activates coordinated stress pathways that coalesce on endoplasmic reticulum stress and autophagy programs to maintain immunophenotypic and functional HSCs. Thus, our work identifies a linkage between sphingolipid metabolism, proteostatic quality control systems, and HSC self-renewal and provides therapeutic targets for improving HSC-based cellular therapeutics.
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Affiliation(s)
- Stephanie Z Xie
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada.
| | - Laura Garcia-Prat
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Veronique Voisin
- The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada
| | - Robin Ferrari
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Olga I Gan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Elvin Wagenblast
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Kerstin B Kaufmann
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Andy G X Zeng
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A8, Canada
| | - Shin-Ichiro Takayanagi
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada; R&D Division, Kyowa Kirin Co., Ltd., Tokyo 194-8533, Japan
| | - Ishita Patel
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Esther K Lee
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Joseph Jargstorf
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Gareth Holmes
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Guy Romm
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Kristele Pan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Michelle Shoong
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Aditi Vedi
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Department of Haematology, University of Cambridge, Cambridge, UK
| | - Chiara Luberto
- Department of Physiology and Biophysics, Stony Brook University School of Medicine, Stony Brook, NY 11794, USA
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada; Division of Medical Oncology and Hematology, Department of Medicine, University Health Network, Toronto, ON, Canada; Department of Medicine, University of Toronto, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A8, Canada
| | - Elisa Laurenti
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Department of Haematology, University of Cambridge, Cambridge, UK
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A8, Canada.
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17
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Long noncoding RNA MIAT promotes the progression of acute myeloid leukemia by negatively regulating miR-495. Leuk Res 2019; 87:106265. [PMID: 31698307 DOI: 10.1016/j.leukres.2019.106265] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 10/21/2019] [Accepted: 10/23/2019] [Indexed: 12/13/2022]
Abstract
Acute myeloid leukemia (AML) is a malignant myeloid hematopoietic stem and progenitor cell disease. Studies have shown that the long noncoding RNA (lncRNA) myocardial infarction associated transcript (MIAT) is abundantly expressed in multiple human solid tumors. However, the expression and role of MIAT in AML has not been explored previously. In this study, we find that MIAT is overexpressed in AML patient specimens and AML cell lines. Importantly, upregulation of MIAT is closely related with poor clinical outcome. Further investigations reveal that knockdown of MIAT inhibits the colony formation and proliferation, meanwhile, accelerates the apoptosis of AML cells in vitro. Consistently, MIAT knockdown slows AML progression in immunodeficient mice. Mechanistically, we confirm that MIAT can function as a sponge to inhibit microRNA-495 (miR-495), a tumor suppressor, in AML cells. Collectively, our results demonstrate that MIAT is involved in promoting the progression of AML, at least partly, through negative regulation of miR-495, and therefore provide a promising target for treatment of AML.
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