1
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Ling B, Xu Y, Qian S, Xiang Z, Xuan S, Wu J. Regulation of hematopoietic stem cells differentiation, self-renewal, and quiescence through the mTOR signaling pathway. Front Cell Dev Biol 2023; 11:1186850. [PMID: 37228652 PMCID: PMC10203478 DOI: 10.3389/fcell.2023.1186850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 04/28/2023] [Indexed: 05/27/2023] Open
Abstract
Hematopoietic stem cells (HSCs) are important for the hematopoietic system because they can self-renew to increase their number and differentiate into all the blood cells. At a steady state, most of the HSCs remain in quiescence to preserve their capacities and protect themselves from damage and exhaustive stress. However, when there are some emergencies, HSCs are activated to start their self-renewal and differentiation. The mTOR signaling pathway has been shown as an important signaling pathway that can regulate the differentiation, self-renewal, and quiescence of HSCs, and many types of molecules can regulate HSCs' these three potentials by influencing the mTOR signaling pathway. Here we review how mTOR signaling pathway regulates HSCs three potentials, and introduce some molecules that can work as the regulator of HSCs' these potentials through the mTOR signaling. Finally, we outline the clinical significance of studying the regulation of HSCs three potentials through the mTOR signaling pathway and make some predictions.
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Affiliation(s)
- Bai Ling
- Department of Pharmacy, The Yancheng Clinical College of Xuzhou Medical University, The First People’s Hospital of Yancheng, Yancheng, Jiangsu, China
| | - Yunyang Xu
- Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Siyuan Qian
- The Second School of Clinical Medicine, Wenzhou Medical University, Wenzhou, China
| | - Ze Xiang
- Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shihai Xuan
- Department of Laboratory Medicine, The People’s Hospital of Dongtai City, Dongtai, China
| | - Jian Wu
- Department of Clinical Laboratory, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu, China
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2
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Clarke ML, Lemma RB, Walton DS, Volpe G, Noyvert B, Gabrielsen OS, Frampton J. MYB insufficiency disrupts proteostasis in hematopoietic stem cells, leading to age-related neoplasia. Blood 2023; 141:1858-1870. [PMID: 36603185 PMCID: PMC10646772 DOI: 10.1182/blood.2022019138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 01/07/2023] Open
Abstract
MYB plays a key role in gene regulation throughout the hematopoietic hierarchy and is critical for the maintenance of normal hematopoietic stem cells (HSC). Acquired genetic dysregulation of MYB is involved in the etiology of a number of leukemias, although inherited noncoding variants of the MYB gene are a susceptibility factor for many hematological conditions, including myeloproliferative neoplasms (MPN). The mechanisms that connect variations in MYB levels to disease predisposition, especially concerning age dependency in disease initiation, are completely unknown. Here, we describe a model of Myb insufficiency in mice that leads to MPN, myelodysplasia, and leukemia in later life, mirroring the age profile of equivalent human diseases. We show that this age dependency is intrinsic to HSC, involving a combination of an initial defective cellular state resulting from small effects on the expression of multiple genes and a progressive accumulation of further subtle changes. Similar to previous studies showing the importance of proteostasis in HSC maintenance, we observed altered proteasomal activity and elevated proliferation indicators, followed by elevated ribosome activity in young Myb-insufficient mice. We propose that these alterations combine to cause an imbalance in proteostasis, potentially creating a cellular milieu favoring disease initiation.
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Affiliation(s)
- Mary L. Clarke
- Institute of Cancer & Genomic Sciences, College of Medical & Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Roza B. Lemma
- Department of Biosciences, University of Oslo, Oslo, Norway
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo, Oslo, Norway
| | - David S. Walton
- Institute of Cancer & Genomic Sciences, College of Medical & Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Giacomo Volpe
- Institute of Cancer & Genomic Sciences, College of Medical & Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Boris Noyvert
- Institute of Cancer & Genomic Sciences, College of Medical & Dental Sciences, University of Birmingham, Birmingham, United Kingdom
- CRUK Birmingham Centre and Centre for Computational Biology, University of Birmingham, Birmingham, United Kingdom
| | | | - Jon Frampton
- Institute of Cancer & Genomic Sciences, College of Medical & Dental Sciences, University of Birmingham, Birmingham, United Kingdom
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3
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Wang X, Liu S, Yu J. Multi-lineage Differentiation from Hematopoietic Stem Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1442:159-175. [PMID: 38228964 DOI: 10.1007/978-981-99-7471-9_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
The hematopoietic stem cells (HSCs) have the ability to differentiate and give rise to all mature blood cells. Commitment to differentiation progressively limits the self-renewal potential of the original HSCs by regulating the level of lineage-specific gene expression. In this review, we will summarize the current understanding of the molecular mechanisms underlying HSC differentiation toward erythroid, myeloid, and lymphocyte lineages. Moreover, we will decipher how the single-cell technologies advance the lineage-biased HSC subpopulations and their differentiation potential.
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Affiliation(s)
- Xiaoshuang Wang
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing, China.
- The Institute of Blood Transfusion, Chinese Academy of Medical Sciences / Peking Union Medical College, Chengdu, China.
| | - Siqi Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing, China
| | - Jia Yu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing, China.
- The Institute of Blood Transfusion, Chinese Academy of Medical Sciences / Peking Union Medical College, Chengdu, China.
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4
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Heuts BMH, Arza-Apalategi S, Frölich S, Bergevoet SM, van den Oever SN, van Heeringen SJ, van der Reijden BA, Martens JHA. Identification of transcription factors dictating blood cell development using a bidirectional transcription network-based computational framework. Sci Rep 2022; 12:18656. [PMID: 36333382 PMCID: PMC9636203 DOI: 10.1038/s41598-022-21148-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/23/2022] [Indexed: 11/06/2022] Open
Abstract
Advanced computational methods exploit gene expression and epigenetic datasets to predict gene regulatory networks controlled by transcription factors (TFs). These methods have identified cell fate determining TFs but require large amounts of reference data and experimental expertise. Here, we present an easy to use network-based computational framework that exploits enhancers defined by bidirectional transcription, using as sole input CAGE sequencing data to correctly predict TFs key to various human cell types. Next, we applied this Analysis Algorithm for Networks Specified by Enhancers based on CAGE (ANANSE-CAGE) to predict TFs driving red and white blood cell development, and THP-1 leukemia cell immortalization. Further, we predicted TFs that are differentially important to either cell line- or primary- associated MLL-AF9-driven gene programs, and in primary MLL-AF9 acute leukemia. Our approach identified experimentally validated as well as thus far unexplored TFs in these processes. ANANSE-CAGE will be useful to identify transcription factors that are key to any cell fate change using only CAGE-seq data as input.
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Affiliation(s)
- B. M. H. Heuts
- grid.5590.90000000122931605Department of Molecular Biology, Faculty of Science, RIMLS, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - S. Arza-Apalategi
- grid.10417.330000 0004 0444 9382Department of Laboratory Medicine, Laboratory of Hematology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - S. Frölich
- grid.5590.90000000122931605Department of Molecular Developmental Biology, Faculty of Science, RIMLS, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - S. M. Bergevoet
- grid.10417.330000 0004 0444 9382Department of Laboratory Medicine, Laboratory of Hematology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - S. N. van den Oever
- grid.5590.90000000122931605Department of Molecular Biology, Faculty of Science, RIMLS, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - S. J. van Heeringen
- grid.5590.90000000122931605Department of Molecular Developmental Biology, Faculty of Science, RIMLS, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - B. A. van der Reijden
- grid.10417.330000 0004 0444 9382Department of Laboratory Medicine, Laboratory of Hematology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - J. H. A. Martens
- grid.5590.90000000122931605Department of Molecular Biology, Faculty of Science, RIMLS, Radboud University, 6525 GA Nijmegen, The Netherlands
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5
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Chen Z, Guo Q, Song G, Hou Y. Molecular regulation of hematopoietic stem cell quiescence. Cell Mol Life Sci 2022; 79:218. [PMID: 35357574 PMCID: PMC11072845 DOI: 10.1007/s00018-022-04200-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 02/07/2022] [Accepted: 02/07/2022] [Indexed: 12/19/2022]
Abstract
Hematopoietic stem cells (HSCs) are primarily dormant in a cell-cycle quiescence state to preserve their self-renewal capacity and long-term maintenance, which is essential for the homeostasis of hematopoietic system. Dysregulation of quiescence causes HSC dysfunction and may result in aberrant hematopoiesis (e.g., myelodysplastic syndrome and bone marrow failure syndromes) and leukemia transformation. Accumulating evidence indicates that both intrinsic molecular networks and extrinsic signals regulate HSC quiescence, including cell-cycle regulators, transcription factors, epigenetic factors, and niche factors. Further, the transition between quiescence and activation of HSCs is a continuous developmental path driven by cell metabolism (e.g., protein synthesis, glycolysis, oxidative phosphorylation, and autophagy). Elucidating the complex regulatory networks of HSC quiescence will expand the knowledge of HSC hemostasis and benefit for clinical HSC use. Here, we review the current understanding and progression on the molecular and metabolic regulation of HSC quiescence, providing a more complete picture regarding the mechanisms of HSC quiescence maintenance.
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Affiliation(s)
- Zhe Chen
- Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, China
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Qian Guo
- Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, China
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Guanbin Song
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
| | - Yu Hou
- Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, China.
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China.
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6
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Mayer IM, Hoelbl-Kovacic A, Sexl V, Doma E. Isolation, Maintenance and Expansion of Adult Hematopoietic Stem/Progenitor Cells and Leukemic Stem Cells. Cancers (Basel) 2022; 14:cancers14071723. [PMID: 35406494 PMCID: PMC8996967 DOI: 10.3390/cancers14071723] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Transplantation of adult hematopoietic stem cells is an important therapeutic tool to help patients suffering from diverse hematological disorders. All types of blood cells can develop from a single hematopoietic stem cell underlining their enormous potential. Intense efforts are ongoing to generate “engraftable” human hematopoietic stem cells to treat hematopoietic diseases and to understand the molecular machinery driving them. Leukemic stem cells represent a low frequency subpopulation of leukemia cells that possess stem cell properties. They can instigate, maintain, and serially propagate leukemia in vivo, while they retain the capacity to differentiate into committed progenitors. Leukemic stem cells are unaffected by many therapeutic strategies and represent the major cause of relapse. We here describe all methods to maintain and expand murine and human hematopoietic cells in culture and describe their specific advantages. These methods are also employed to understand the biology of leukemic stem cells and to identify novel therapeutic strategies. Abstract Hematopoietic stem cells (HSCs) are rare, self-renewing cells that perch on top of the hematopoietic tree. The HSCs ensure the constant supply of mature blood cells in a tightly regulated process producing peripheral blood cells. Intense efforts are ongoing to optimize HSC engraftment as therapeutic strategy to treat patients suffering from hematopoietic diseases. Preclinical research paves the way by developing methods to maintain, manipulate and expand HSCs ex vivo to understand their regulation and molecular make-up. The generation of a sufficient number of transplantable HSCs is the Holy Grail for clinical therapy. Leukemia stem cells (LSCs) are characterized by their acquired stem cell characteristics and are responsible for disease initiation, progression, and relapse. We summarize efforts, that have been undertaken to increase the number of long-term (LT)-HSCs and to prevent differentiation towards committed progenitors in ex vivo culture. We provide an overview and compare methods currently available to isolate, maintain and enrich HSC subsets, progenitors and LSCs and discuss their individual advantages and drawbacks.
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7
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Rg1 Protects Hematopoietic Stem Cells from LiCl-Induced Oxidative Stress via Wnt Signaling Pathway. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:2875583. [PMID: 35388306 PMCID: PMC8977299 DOI: 10.1155/2022/2875583] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 01/09/2022] [Accepted: 02/11/2022] [Indexed: 11/22/2022]
Abstract
Background Ginsenoside Rg1 is a major component of ginseng with antioxidative and antiaging effects, which is a traditional Chinese medicine. In this study, we investigated the potential spillover and mechanism of action of Rg1 on LiCl-driven hematopoietic stem cell aging. Results Collect the purified Sca-1+ hematopoietic cells for differentiation ability detection and biochemical and molecular labeling. The experiment found that Rg1 plays an antiaging role in reversing the SA-β-gal staining associated with LiCl-induced hematopoietic stem cell senescence, the increase in p53 and p21 proteins, and sustained DNA damage. At the same time, Rg1 protects hematopoietic cells from the reduced differentiation ability caused by LiCl. In addition, Rg1 increased the excessive inhibition of intracellular GSK-3β protein, resulting in the maintenance of β-catenin protein levels in hematopoietic cells after LiCl treatment. Then, the target gene level of β-catenin can be maintained. Conclusions Rg1 exerts the pharmacological effect of maintaining the activity of GSK-3β in Sca-1+ hematopoietic cells, enhances the antioxidant potential of cells, improves the redox homeostasis, and thus protects cells from the decline in differentiation ability caused by aging. This study provides a potential therapeutic strategy to reduce stem cell pool failure caused by chronic oxidative damage to hematopoietic stem cells.
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8
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Böttcher L, Antulov-Fantulin N, Asikis T. AI Pontryagin or how artificial neural networks learn to control dynamical systems. Nat Commun 2022; 13:333. [PMID: 35039488 PMCID: PMC8763915 DOI: 10.1038/s41467-021-27590-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 11/26/2021] [Indexed: 11/10/2022] Open
Abstract
The efficient control of complex dynamical systems has many applications in the natural and applied sciences. In most real-world control problems, both control energy and cost constraints play a significant role. Although such optimal control problems can be formulated within the framework of variational calculus, their solution for complex systems is often analytically and computationally intractable. To overcome this outstanding challenge, we present AI Pontryagin, a versatile control framework based on neural ordinary differential equations that automatically learns control signals that steer high-dimensional dynamical systems towards a desired target state within a specified time interval. We demonstrate the ability of AI Pontryagin to learn control signals that closely resemble those found by corresponding optimal control frameworks in terms of control energy and deviation from the desired target state. Our results suggest that AI Pontryagin is capable of solving a wide range of control and optimization problems, including those that are analytically intractable.
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Affiliation(s)
- Lucas Böttcher
- Computational Social Science, Frankfurt School of Finance and Management, Frankfurt am Main, 60322, Germany.
- Department of Computational Medicine, University of California, Los Angeles, 90095-1766, Los Angeles, USA.
| | | | - Thomas Asikis
- Computational Social Science, ETH Zurich, 8092, Zurich, Switzerland.
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9
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Randhawa V, Kumar M. An integrated network analysis approach to identify potential key genes, transcription factors, and microRNAs regulating human hematopoietic stem cell aging. Mol Omics 2021; 17:967-984. [PMID: 34605522 DOI: 10.1039/d1mo00199j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hematopoietic stem cells (HSCs) undergo functional deterioration with increasing age that causes loss of their self-renewal and regenerative potential. Despite various efforts, significant success in identifying molecular regulators of HSC aging has not been achieved, one prime reason being the non-availability of appropriate human HSC samples. To demonstrate the scope of integrating and re-analyzing the HSC transcriptomics data available, we used existing tools and databases to structure a sequential data analysis pipeline to predict potential candidate genes, transcription factors, and microRNAs simultaneously. This sequential approach comprises (i) collecting matched young and aged mice HSC sample datasets, (ii) identifying differentially expressed genes, (iii) identifying human homologs of differentially expressed genes, (iv) inferring gene co-expression network modules, and (v) inferring the microRNA-transcription factor-gene regulatory network. Systems-level analyses of HSC interaction networks provided various insights based on which several candidates were predicted. For example, 16 HSC aging-related candidate genes were predicted (e.g., CD38, BRCA1, AGTR1, GSTM1, etc.) from GCN analysis. Following this, the shortest path distance-based analyses of the regulatory network predicted several novel candidate miRNAs and TFs. Among these, miR-124-3p was a common regulator in candidate gene modules, while TFs MYC and SP1 were identified to regulate various candidate genes. Based on the regulatory interactions among candidate genes, TFs, and miRNAs, a potential regulation model of biological processes in each of the candidate modules was predicted, which provided systems-level insights into the molecular complexity of each module to regulate HSC aging.
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Affiliation(s)
- Vinay Randhawa
- Virology Unit and Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific & Industrial Research, Chandigarh-160036, India.
| | - Manoj Kumar
- Virology Unit and Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific & Industrial Research, Chandigarh-160036, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
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10
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Wu F, Chen Z, Liu J, Hou Y. The Akt-mTOR network at the interface of hematopoietic stem cell homeostasis. Exp Hematol 2021; 103:15-23. [PMID: 34464661 DOI: 10.1016/j.exphem.2021.08.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 12/15/2022]
Abstract
Hematopoietic stem cells (HSCs) are immature blood cells that exhibit multilineage differentiation capacity. Homeostasis is critical for HSC potential and lifelong hematopoiesis, and HSC homeostasis is tightly governed by both intrinsic molecular networks and microenvironmental signals. The evolutionarily conserved serine/threonine protein kinase B (PKB, also referred to as Akt)-mammalian target of rapamycin (mTOR) pathway is universal to nearly all multicellular organisms and plays an integral role in most cellular processes. Emerging evidence has revealed a central role of the Akt-mTOR network in HSC homeostasis, because it responds to multiple intracellular and extracellular signals and regulates various downstream targets, eventually affecting several cellular processes, including the cell cycle, mitochondrial metabolism, and protein synthesis. Dysregulated Akt-mTOR signaling greatly affects HSC self-renewal, maintenance, differentiation, survival, autophagy, and aging, as well as transformation of HSCs to leukemia stem cells. Here, we review recent works and provide an advanced understanding of how the Akt-mTOR network regulates HSC homeostasis, thus offering insights into future clinical applications.
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Affiliation(s)
- Feng Wu
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Zhe Chen
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Jingbo Liu
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China.
| | - Yu Hou
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China.
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11
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A robust approach for the generation of functional hematopoietic progenitor cell lines to model leukemic transformation. Blood Adv 2021; 5:39-53. [PMID: 33570624 DOI: 10.1182/bloodadvances.2020003022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 11/20/2020] [Indexed: 12/21/2022] Open
Abstract
Studies of molecular mechanisms of hematopoiesis and leukemogenesis are hampered by the unavailability of progenitor cell lines that accurately mimic the situation in vivo. We now report a robust method to generate and maintain LSK (Lin-, Sca-1+, c-Kit+) cells, which closely resemble MPP1 cells. HPCLSKs reconstitute hematopoiesis in lethally irradiated recipient mice over >8 months. Upon transformation with different oncogenes including BCR/ABL, FLT3-ITD, or MLL-AF9, their leukemic counterparts maintain stem cell properties in vitro and recapitulate leukemia formation in vivo. The method to generate HPCLSKs can be applied to transgenic mice, and we illustrate it for CDK6-deficient animals. Upon BCR/ABLp210 transformation, HPCLSKsCdk6-/- induce disease with a significantly enhanced latency and reduced incidence, showing the importance of CDK6 in leukemia formation. Studies of the CDK6 transcriptome in murine HPCLSK and human BCR/ABL+ cells have verified that certain pathways depend on CDK6 and have uncovered a novel CDK6-dependent signature, suggesting a role for CDK6 in leukemic progenitor cell homing. Loss of CDK6 may thus lead to a defect in homing. The HPCLSK system represents a unique tool for combined in vitro and in vivo studies and enables the production of large quantities of genetically modifiable hematopoietic or leukemic stem/progenitor cells.
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12
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Abstract
In this issue, Le Coz et al. (2021. J. Exp. Med.https://doi.org/10.1084/jem.20201750) describe a novel immunodeficiency syndrome caused by mutations in SPI1. Through a series of in-depth studies, the authors provide insights into how SPI1 affects blood lineage specification, highlighting the important role of master transcription factors as cellular fate determinants.
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Affiliation(s)
- Lara Wahlster
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA.,Broad Institute of MIT and Harvard, Cambridge, MA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA.,Broad Institute of MIT and Harvard, Cambridge, MA
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13
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McKenna DH, Stroncek DF. Cellular Engineering. Transfus Med 2021. [DOI: 10.1002/9781119599586.ch19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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14
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Rothenberg EV. Logic and lineage impacts on functional transcription factor deployment for T-cell fate commitment. Biophys J 2021; 120:4162-4181. [PMID: 33838137 PMCID: PMC8516641 DOI: 10.1016/j.bpj.2021.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/22/2021] [Accepted: 04/02/2021] [Indexed: 11/19/2022] Open
Abstract
Transcription factors are the major agents that read the regulatory sequence information in the genome to initiate changes in expression of specific genes, both in development and in physiological activation responses. Their actions depend on site-specific DNA binding and are largely guided by their individual DNA target sequence specificities. However, their action is far more conditional in a real developmental context than would be expected for simple reading of local genomic DNA sequence, which is common to all cells in the organism. They are constrained by slow-changing chromatin states and by interactions with other transcription factors, which affect their occupancy patterns of potential sites across the genome. These mechanisms lead to emergent discontinuities in function even for transcription factors with minimally changing expression. This is well revealed by diverse lineages of blood cells developing throughout life from hematopoietic stem cells, which use overlapping combinations of transcription factors to drive strongly divergent gene regulation programs. Here, using development of T lymphocytes from hematopoietic multipotent progenitor cells as a focus, recent evidence is reviewed on how binding specificity and dynamics, transcription factor cooperativity, and chromatin state changes impact the effective regulatory functions of key transcription factors including PU.1, Runx1, Notch-RBPJ, and Bcl11b.
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Affiliation(s)
- Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California.
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15
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Edginton-White B, Bonifer C. The transcriptional regulation of normal and malignant blood cell development. FEBS J 2021; 289:1240-1255. [PMID: 33511785 DOI: 10.1111/febs.15735] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/11/2021] [Accepted: 01/26/2021] [Indexed: 11/27/2022]
Abstract
Development of multicellular organisms requires the differential usage of our genetic information to change one cell fate into another. This process drives the appearance of different cell types that come together to form specialized tissues sustaining a healthy organism. In the last decade, by moving away from studying single genes toward a global view of gene expression control, a revolution has taken place in our understanding of how genes work together and how cells communicate to translate the information encoded in the genome into a body plan. The development of hematopoietic cells has long served as a paradigm of development in general. In this review, we highlight how transcription factors and chromatin components work together to shape the gene regulatory networks controlling gene expression in the hematopoietic system and to drive blood cell differentiation. In addition, we outline how this process goes astray in blood cancers. We also touch upon emerging concepts that place these processes firmly into their associated subnuclear structures adding another layer of the control of differential gene expression.
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Affiliation(s)
- Benjamin Edginton-White
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, UK
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, UK
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16
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Investigation of a new oxazolidine derivative in human resistance acute leukemia cells: deciphering its mechanism of action by label-free proteomic. Naunyn Schmiedebergs Arch Pharmacol 2021; 394:1153-1166. [PMID: 33475759 DOI: 10.1007/s00210-020-02024-8] [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: 05/18/2019] [Accepted: 11/10/2020] [Indexed: 10/22/2022]
Abstract
The present study aimed to evaluate the mechanism of action of the antineoplastic activity of an oxazolidine derivative, LPSF/NB-3 (5-(4-cloro-benzilideno)-3-etil-2-tioxo-oxazolidin-4-ona). Cytotoxicity assays were performed in peripheral blood mononuclear cells (PBMCs) and resistant acute leukemia cell line (HL-60/MX1) by the MTT method. LPSF/NB-3 exhibited cytotoxicity in HL-60/MX1, but it was not toxic to healthy cells in the highest dose tested (100 μM). The protein extract of HL-60/MX1 cells treated with LPSF/NB-3 was subjected to proteomic analysis using two-dimensional chromatography coupled to mass spectrometry. We could identify a total of 2652 proteins, in which 633 were statistically modulated. Within the group of protein considered for the quantitative analysis with the established criteria, 262 were differentially expressed, 146 with increased expression and 116 with decreased expression in the sample treated with LPSF/NB-3 compared to the control. The following differentially expressed pathways were found: involving regulation of the cytoskeleton, DNA damage, and transduce cellular signals. Networks that were highlighted are related to the immune system. The ELISA technique was used to assess the immunomodulatory potential of LPSF/NB-3 in PBMCs. We observed significant decrease of IFNγ (p < 0.01) and dose-response pattern of the cytokines IL-6, IL-17A, IL-22, and IL-10. Therefore, results suggest that LPSF/NB-3 appears to modulate important pathways, including cell cycle and immune system regulatory pathways.
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Rothenberg EV, Göttgens B. How haematopoiesis research became a fertile ground for regulatory network biology as pioneered by Eric Davidson. Curr Opin Hematol 2021; 28:1-10. [PMID: 33229891 PMCID: PMC7755131 DOI: 10.1097/moh.0000000000000628] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PURPOSE OF REVIEW This historical perspective reviews how work of Eric H. Davidson was a catalyst and exemplar for explaining haematopoietic cell fate determination through gene regulation. RECENT FINDINGS Researchers studying blood and immune cells pioneered many of the early mechanistic investigations of mammalian gene regulatory processes. These efforts included the characterization of complex gene regulatory sequences exemplified by the globin and T-cell/B-cell receptor gene loci, as well as the identification of many key regulatory transcription factors through the fine mapping of chromosome translocation breakpoints in leukaemia patients. As the repertoire of known regulators expanded, assembly into gene regulatory network models became increasingly important, not only to account for the truism that regulatory genes do not function in isolation but also to devise new ways of extracting biologically meaningful insights from even more complex information. Here we explore how Eric H. Davidson's pioneering studies of gene regulatory network control in nonvertebrate model organisms have had an important and lasting impact on research into blood and immune cell development. SUMMARY The intellectual framework developed by Davidson continues to contribute to haematopoietic research, and his insistence on demonstrating logic and causality still challenges the frontier of research today.
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Affiliation(s)
- Ellen V. Rothenberg
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Berthold Göttgens
- Wellcome and MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge CB2 0AW, UK
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18
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Lin L, Hwang BJ, Li N, Googe P, Diaz LA, Miao E, Vilen B, Thomas NE, Ting J, Liu Z. Non-Cell-Autonomous Activity of the Hemidesmosomal Protein BP180/Collagen XVII in Granulopoiesis in Humanized NC16A Mice. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2020; 205:2786-2794. [PMID: 32998984 PMCID: PMC7658030 DOI: 10.4049/jimmunol.2000784] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/03/2020] [Indexed: 12/27/2022]
Abstract
BP180 (also termed type XVII collagen) is a hemidesmosomal protein and plays a critical role in cell-cell matrix adhesion in the skin; however, its other biological functions are largely unclear. In this study, we generated a BP180 functional-deficient mouse strain by deleting its extracellular domain of humanized NC16A (termed ΔNC16A mice). We found that BP180 is expressed by bone marrow mesenchymal stem cells (BM-MSC), and its functional deficiency leads to myeloid hyperplasia. Altered granulopoiesis in ΔNC16A mice is through bone marrow stromal cells evidenced by bone marrow transplantation. Furthermore, the level of G-CSF in bone marrow and circulation were significantly increased in ΔNC16A mice as compared with wild-type mice. The increased G-CSF was accompanied by an increased activation of the NF-κB signaling pathway in bone marrow and BM-MSC of ΔNC16A mice. Blockade of G-CSF restored normal granulopoiesis in ΔNC16A mice. Inhibition of NF-κB signaling pathway significantly reduces the release of G-CSF from ΔNC16A BM-MSC in vitro and the level of serum G-CSF in ΔNC16A mice. To our knowledge, these findings provide the first direct evidence that BP180 plays an important role in granulopoiesis through regulating NF-κB signaling pathway in BM-MSC.
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Affiliation(s)
- Lin Lin
- Department of Dermatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Oral Biology Program, School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Bin-Jin Hwang
- Department of Dermatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599; and
| | - Ning Li
- Department of Dermatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Paul Googe
- Department of Dermatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Luis A Diaz
- Department of Dermatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Ed Miao
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599; and
| | - Barbara Vilen
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599; and
| | - Nancy E Thomas
- Department of Dermatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Jenny Ting
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Zhi Liu
- Department of Dermatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599;
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599; and
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19
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Liggett LA, Sankaran VG. Unraveling Hematopoiesis through the Lens of Genomics. Cell 2020; 182:1384-1400. [PMID: 32946781 PMCID: PMC7508400 DOI: 10.1016/j.cell.2020.08.030] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/14/2020] [Accepted: 08/17/2020] [Indexed: 01/07/2023]
Abstract
Hematopoiesis has long served as a paradigm of stem cell biology and tissue homeostasis. In the past decade, the genomics revolution has ushered in powerful new methods for investigating the hematopoietic system that have provided transformative insights into its biology. As part of the advances in genomics, increasingly accurate deep sequencing and novel methods of cell tracking have revealed hematopoiesis to be more of a continuous and less of a discrete and punctuated process than originally envisioned. In part, this continuous nature of hematopoiesis is made possible by the emergent outcomes of vast, interconnected regulatory networks that influence cell fates and lineage commitment. It is also becoming clear how these mechanisms are modulated by genetic variation present throughout the population. This review describes how these recently uncovered complexities are reshaping our concept of tissue development and homeostasis while opening up a more comprehensive future understanding of hematopoiesis.
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Affiliation(s)
- L Alexander Liggett
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
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20
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Kucinski I, Gottgens B. Advancing Stem Cell Research through Multimodal Single-Cell Analysis. Cold Spring Harb Perspect Biol 2020; 12:a035725. [PMID: 31932320 PMCID: PMC7328456 DOI: 10.1101/cshperspect.a035725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Technological advances play a key role in furthering our understanding of stem cell biology, and advancing the prospects of regenerative therapies. Highly parallelized methods, developed in the last decade, can profile DNA, RNA, or proteins in thousands of cells and even capture data across two or more modalities (multiomics). This allows unbiased and precise definition of molecular cell states, thus allowing classification of cell types, tracking of differentiation trajectories, and discovery of underlying mechanisms. Despite being based on destructive techniques, novel experimental and bioinformatic approaches enable embedding and extraction of temporal information, which is essential for deconvolution of complex data and establishing cause and effect relationships. Here, we provide an overview of recent studies pertinent to stem cell biology, followed by an outlook on how further advances in single-cell molecular profiling and computational analysis have the potential to shape the future of both basic and translational research.
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Affiliation(s)
- Iwo Kucinski
- Wellcome-MRC Cambridge Stem Cell Institute and Department of Haematology, University of Cambridge, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge CB2 0AW, United Kingdom
| | - Berthold Gottgens
- Wellcome-MRC Cambridge Stem Cell Institute and Department of Haematology, University of Cambridge, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge CB2 0AW, United Kingdom
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21
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Gillespie MA, Palii CG, Sanchez-Taltavull D, Shannon P, Longabaugh WJR, Downes DJ, Sivaraman K, Espinoza HM, Hughes JR, Price ND, Perkins TJ, Ranish JA, Brand M. Absolute Quantification of Transcription Factors Reveals Principles of Gene Regulation in Erythropoiesis. Mol Cell 2020; 78:960-974.e11. [PMID: 32330456 PMCID: PMC7344268 DOI: 10.1016/j.molcel.2020.03.031] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 02/20/2020] [Accepted: 03/25/2020] [Indexed: 12/11/2022]
Abstract
Dynamic cellular processes such as differentiation are driven by changes in the abundances of transcription factors (TFs). However, despite years of studies, our knowledge about the protein copy number of TFs in the nucleus is limited. Here, by determining the absolute abundances of 103 TFs and co-factors during the course of human erythropoiesis, we provide a dynamic and quantitative scale for TFs in the nucleus. Furthermore, we establish the first gene regulatory network of cell fate commitment that integrates temporal protein stoichiometry data with mRNA measurements. The model revealed quantitative imbalances in TFs' cross-antagonistic relationships that underlie lineage determination. Finally, we made the surprising discovery that, in the nucleus, co-repressors are dramatically more abundant than co-activators at the protein level, but not at the RNA level, with profound implications for understanding transcriptional regulation. These analyses provide a unique quantitative framework to understand transcriptional regulation of cell differentiation in a dynamic context.
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Affiliation(s)
| | - Carmen G Palii
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H8L6, Canada
| | - Daniel Sanchez-Taltavull
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H8L6, Canada; Visceral Surgery and Medicine, Inselspital, Bern University Hospital, Department for BioMedical Research, University of Bern, Murtenstrasse 35, 3008 Bern, Switzerland
| | - Paul Shannon
- Institute for Systems Biology, Seattle, WA 98109, USA
| | | | - Damien J Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Karthi Sivaraman
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada
| | | | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | | | - Theodore J Perkins
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H8L6, Canada.
| | - Jeffrey A Ranish
- Institute for Systems Biology, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
| | - Marjorie Brand
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H8L6, Canada.
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22
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Shokouhian M, Bagheri M, Poopak B, Chegeni R, Davari N, Saki N. Altering chromatin methylation patterns and the transcriptional network involved in regulation of hematopoietic stem cell fate. J Cell Physiol 2020; 235:6404-6423. [PMID: 32052445 DOI: 10.1002/jcp.29642] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 01/31/2020] [Indexed: 12/15/2022]
Abstract
Hematopoietic stem cells (HSCs) are quiescent cells with self-renewal capacity and potential multilineage development. Various molecular regulatory mechanisms such as epigenetic modifications and transcription factor (TF) networks play crucial roles in establishing a balance between self-renewal and differentiation of HSCs. Histone/DNA methylations are important epigenetic modifications involved in transcriptional regulation of specific lineage HSCs via controlling chromatin structure and accessibility of DNA. Also, TFs contribute to either facilitation or inhibition of gene expression through binding to enhancer or promoter regions of DNA. As a result, epigenetic factors and TFs regulate the activation or repression of HSCs genes, playing a central role in normal hematopoiesis. Given the importance of histone/DNA methylation and TFs in gene expression regulation, their aberrations, including changes in HSCs-related methylation of histone/DNA and TFs (e.g., CCAAT-enhancer-binding protein α, phosphatase and tensin homolog deleted on the chromosome 10, Runt-related transcription factor 1, signal transducers and activators of transcription, and RAS family proteins) could disrupt HSCs fate. Herewith, we summarize how dysregulations in the expression of genes related to self-renewal, proliferation, and differentiation of HSCs caused by changes in epigenetic modifications and transcriptional networks lead to clonal expansion and leukemic transformation.
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Affiliation(s)
- Mohammad Shokouhian
- Department of Hematology and Blood Transfusion, School of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Marziye Bagheri
- Thalassemia and Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Behzad Poopak
- Department of Hematology, Faculty of Paramedical Sciences, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Rouzbeh Chegeni
- Michener Institute of Education at University Health Network, Toronto, Canada
| | - Nader Davari
- Thalassemia and Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Najmaldin Saki
- Thalassemia and Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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23
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Wang L, Gao S, Wang H, Xue C, Liu X, Yuan H, Wang Z, Chen S, Chen Z, de Thé H, Zhang Y, Zhang W, Zhu J, Zhou J. Interferon regulatory factor 2 binding protein 2b regulates neutrophil versus macrophage fate during zebrafish definitive myelopoiesis. Haematologica 2020; 105:325-337. [PMID: 31123027 PMCID: PMC7012491 DOI: 10.3324/haematol.2019.217596] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 05/20/2019] [Indexed: 12/15/2022] Open
Abstract
Aproper choice of neutrophil-macrophage progenitor cell fate is essential for the generation of adequate myeloid subpopulations during embryonic development and in adulthood. The network governing neutrophil-macrophage progenitor cell fate has several key determinants, such as myeloid master regulators CCAAT enhancer binding protein alpha (C/EBPα) and spleen focus forming virus proviral integration oncogene (PU.1). Nevertheless, more regulators remain to be identified and characterized. To ensure balanced commitment of neutrophil-macrophage progenitors toward each lineage, the interplay among these determinants is not only synergistic, but also antagonistic. Depletion of interferon regulatory factor 2 binding protein 2b (Irf2bp2b), a well-known negative transcription regulator, results in a bias in neutrophil-macrophage progenitor cell fate in favor of macrophages at the expense of neutrophils during the stage of definitive myelopoiesis in zebrafish embryos. Mechanistic studies indicate that Irf2bp2b acts as a downstream target of C/EBPα, repressing PU.1 expression, and that SUMOylation confers the repressive function of Irf2bp2b. Thus, Irf2bp2b is a novel determinant in the choice of fate of neutrophil-macrophage progenitor cells.
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Affiliation(s)
- Luxiang Wang
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuo Gao
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haihong Wang
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chang Xue
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaohui Liu
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hao Yuan
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zixuan Wang
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Saijuan Chen
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhu Chen
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hugues de Thé
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Université de Paris 7/INSERM/CNRS UMR 944/7212, Equipe Labellisée No. 11 Ligue Nationale Contre le Cancer, Hôpital St. Louis, Paris, France
| | - Yiyue Zhang
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou, China
| | - Wenqing Zhang
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou, China
| | - Jun Zhu
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China .,Université de Paris 7/INSERM/CNRS UMR 944/7212, Equipe Labellisée No. 11 Ligue Nationale Contre le Cancer, Hôpital St. Louis, Paris, France
| | - Jun Zhou
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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24
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Zimta AA, Tomuleasa C, Sahnoune I, Calin GA, Berindan-Neagoe I. Long Non-coding RNAs in Myeloid Malignancies. Front Oncol 2019; 9:1048. [PMID: 31681586 PMCID: PMC6813191 DOI: 10.3389/fonc.2019.01048] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 09/26/2019] [Indexed: 12/19/2022] Open
Abstract
Acute myeloid leukemia (AML) represents 80% of adult leukemias and 15-20% of childhood leukemias. AML are characterized by the presence of 20% blasts or more in the bone marrow, or defining cytogenetic abnormalities. Laboratory diagnoses of myelodysplastic syndromes (MDS) depend on morphological changes based on dysplasia in peripheral blood and bone marrow, including peripheral blood smears, bone marrow aspirate smears, and bone marrow biopsies. As leukemic cells are not functional, the patient develops anemia, neutropenia, and thrombocytopenia, leading to fatigue, recurrent infections, and hemorrhage. The genetic background and associated mutations in AML blasts determine the clinical course of the disease. Over the last decade, non-coding RNAs transcripts that do not codify for proteins but play a role in regulation of functions have been shown to have multiple applications in the diagnosis, prognosis and therapeutic approach of various types of cancers, including myeloid malignancies. After a comprehensive review of current literature, we found reports of multiple long non-coding RNAs (lncRNAs) that can differentiate between AML types and how their exogenous modulation can dramatically change the behavior of AML cells. These lncRNAs include: H19, LINC00877, RP11-84C10, CRINDE, RP11848P1.3, ZNF667-AS1, AC111000.4-202, SFMBT2, LINC02082-201, MEG3, AC009495.2, PVT1, HOTTIP, SNHG5, and CCAT1. In addition, by performing an analysis on available AML data in The Cancer Genome Atlas (TCGA), we found 10 lncRNAs with significantly differential expression between patients in favorable, intermediate/normal, or poor cytogenetic risk categories. These are: DANCR, PRDM16-DT, SNHG6, OIP5-AS1, SNHG16, JPX, FTX, KCNQ1OT1, TP73-AS1, and GAS5. The identification of a molecular signature based on lncRNAs has the potential for have deep clinical significance, as it could potentially help better define the evolution from low-grade MDS to high-grade MDS to AML, changing the course of therapy. This would allow clinicians to provide a more personalized, patient-tailored therapeutic approach, moving from transfusion-based therapy, as is the case for low-grade MDS, to the introduction of azacytidine-based chemotherapy or allogeneic stem cell transplantation, which is the current treatment for high-grade MDS.
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Affiliation(s)
- Alina-Andreea Zimta
- MedFuture - Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ciprian Tomuleasa
- Department of Hematology, Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Department of Hematology, Ion Chiricuta Clinical Cancer Center, Cluj-Napoca, Romania
| | - Iman Sahnoune
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - George A. Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ioana Berindan-Neagoe
- MedFuture - Research Center for Advanced Medicine, Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Department of Functional Genomics and Experimental Pathology, Ion Chiricuta Clinical Cancer Center, Cluj-Napoca, Romania
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25
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Qian P, De Kumar B, He XC, Nolte C, Gogol M, Ahn Y, Chen S, Li Z, Xu H, Perry JM, Hu D, Tao F, Zhao M, Han Y, Hall K, Peak A, Paulson A, Zhao C, Venkatraman A, Box A, Perera A, Haug JS, Parmely T, Li H, Krumlauf R, Li L. Retinoid-Sensitive Epigenetic Regulation of the Hoxb Cluster Maintains Normal Hematopoiesis and Inhibits Leukemogenesis. Cell Stem Cell 2019; 22:740-754.e7. [PMID: 29727682 DOI: 10.1016/j.stem.2018.04.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 09/15/2017] [Accepted: 04/13/2018] [Indexed: 12/16/2022]
Abstract
Hox genes modulate the properties of hematopoietic stem cells (HSCs) and reacquired Hox expression in progenitors contributes to leukemogenesis. Here, our transcriptome and DNA methylome analyses revealed that Hoxb cluster and retinoid signaling genes are predominantly enriched in LT-HSCs, and this coordinate regulation of Hoxb expression is mediated by a retinoid-dependent cis-regulatory element, distal element RARE (DERARE). Deletion of the DERARE reduced Hoxb expression, resulting in changes to many downstream signaling pathways (e.g., non-canonical Wnt signaling) and loss of HSC self-renewal and reconstitution capacity. DNA methyltransferases mediate DNA methylation on the DERARE, leading to reduced Hoxb cluster expression. Acute myeloid leukemia patients with DNMT3A mutations exhibit DERARE hypomethylation, elevated HOXB expression, and adverse outcomes. CRISPR-Cas9-mediated specific DNA methylation at DERARE attenuated HOXB expression and alleviated leukemogenesis. Collectively, these findings demonstrate pivotal roles for retinoid signaling and the DERARE in maintaining HSCs and preventing leukemogenesis by coordinate regulation of Hoxb genes.
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Affiliation(s)
- Pengxu Qian
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Bony De Kumar
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Xi C He
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Christof Nolte
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Madelaine Gogol
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Youngwook Ahn
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Shiyuan Chen
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Zhenrui Li
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Hanzhang Xu
- Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - John M Perry
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Deqing Hu
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Tianjin Medical University School of Basic Medicine, Tian Jin 300070, China
| | - Fang Tao
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Meng Zhao
- Key Laboratory of Stem Cells and Tissue Engineering, Sun Yat-Sen University, Ministry of Education, Guangzhou, Guangdong 510080, China
| | - Yingli Han
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Kate Hall
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Allison Peak
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Ariel Paulson
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Chongbei Zhao
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | | | - Andrew Box
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Anoja Perera
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jeffrey S Haug
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Tari Parmely
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Hua Li
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - Linheng Li
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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26
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Han X, Wei Y, Wang H, Wang F, Ju Z, Li T. Nonsense-mediated mRNA decay: a 'nonsense' pathway makes sense in stem cell biology. Nucleic Acids Res 2019; 46:1038-1051. [PMID: 29272451 PMCID: PMC5814811 DOI: 10.1093/nar/gkx1272] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 12/09/2017] [Indexed: 01/04/2023] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a highly conserved post-transcriptional regulatory mechanism of gene expression in eukaryotes. Originally, NMD was identified as an RNA surveillance machinery in degrading 'aberrant' mRNA species with premature termination codons. Recent studies indicate that NMD regulates the stability of natural gene transcripts that play significant roles in cell functions. Although components and action modes of the NMD machinery in degrading its RNA targets have been extensively studied with biochemical and structural approaches, the biological roles of NMD remain to be defined. Stem cells are rare cell populations, which play essential roles in tissue homeostasis and hold great promises in regenerative medicine. Stem cells self-renew to maintain the cellular identity and differentiate into somatic lineages with specialized functions to sustain tissue integrity. Transcriptional regulations and epigenetic modulations have been extensively implicated in stem cell biology. However, post-transcriptional regulatory mechanisms, such as NMD, in stem cell regulation are largely unknown. In this paper, we summarize the recent findings on biological roles of NMD factors in embryonic and tissue-specific stem cells. Furthermore, we discuss the possible mechanisms of NMD in regulating stem cell fates.
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Affiliation(s)
- Xin Han
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Yanling Wei
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Hua Wang
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Feilong Wang
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Zhenyu Ju
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Tangliang Li
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
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27
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Chan TE, Stumpf MPH, Babtie AC. Gene Regulatory Network Inference from Single-Cell Data Using Multivariate Information Measures. Cell Syst 2019; 5:251-267.e3. [PMID: 28957658 PMCID: PMC5624513 DOI: 10.1016/j.cels.2017.08.014] [Citation(s) in RCA: 283] [Impact Index Per Article: 56.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 04/26/2017] [Accepted: 08/24/2017] [Indexed: 12/03/2022]
Abstract
While single-cell gene expression experiments present new challenges for data processing, the cell-to-cell variability observed also reveals statistical relationships that can be used by information theory. Here, we use multivariate information theory to explore the statistical dependencies between triplets of genes in single-cell gene expression datasets. We develop PIDC, a fast, efficient algorithm that uses partial information decomposition (PID) to identify regulatory relationships between genes. We thoroughly evaluate the performance of our algorithm and demonstrate that the higher-order information captured by PIDC allows it to outperform pairwise mutual information-based algorithms when recovering true relationships present in simulated data. We also infer gene regulatory networks from three experimental single-cell datasets and illustrate how network context, choices made during analysis, and sources of variability affect network inference. PIDC tutorials and open-source software for estimating PID are available. PIDC should facilitate the identification of putative functional relationships and mechanistic hypotheses from single-cell transcriptomic data. PIDC infers gene regulatory networks from single-cell transcriptomic data Multivariate information measures and context in PIDC improve network inference Heterogeneity in single-cell data carries information about gene-gene interactions Fast, efficient, open-source software is made freely available
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Affiliation(s)
- Thalia E Chan
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Michael P H Stumpf
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK; MRC London Institute of Medical Sciences, Hammersmith Campus, Imperial College London, London W12 0NN, UK.
| | - Ann C Babtie
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
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28
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Kidoya H, Muramatsu F, Shimamura T, Jia W, Satoh T, Hayashi Y, Naito H, Kunisaki Y, Arai F, Seki M, Suzuki Y, Osawa T, Akira S, Takakura N. Regnase-1-mediated post-transcriptional regulation is essential for hematopoietic stem and progenitor cell homeostasis. Nat Commun 2019; 10:1072. [PMID: 30842549 PMCID: PMC6403248 DOI: 10.1038/s41467-019-09028-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 02/18/2019] [Indexed: 02/06/2023] Open
Abstract
The balance between self-renewal and differentiation of hematopoietic stem and progenitor cells (HSPCs) maintains hematopoietic homeostasis, failure of which can lead to hematopoietic disorder. HSPC fate is controlled by signals from the bone marrow niche resulting in alteration of the stem cell transcription network. Regnase-1, a member of the CCCH zinc finger protein family possessing RNAse activity, mediates post-transcriptional regulatory activity through degradation of target mRNAs. The precise function of Regnase-1 has been explored in inflammation-related cytokine expression but its function in hematopoiesis has not been elucidated. Here, we show that Regnase-1 regulates self-renewal of HSPCs through modulating the stability of Gata2 and Tal1 mRNA. In addition, we found that dysfunction of Regnase-1 leads to the rapid onset of abnormal hematopoiesis. Thus, our data reveal that Regnase-1-mediated post-transcriptional regulation is required for HSPC maintenance and suggest that it represents a leukemia tumor suppressor.
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Affiliation(s)
- Hiroyasu Kidoya
- Department of Signal Transduction, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Osaka, Suita,, 565-0871, Japan.
| | - Fumitaka Muramatsu
- Department of Signal Transduction, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Osaka, Suita,, 565-0871, Japan
| | - Teppei Shimamura
- Division of Systems Biology, Graduate School of Medicine, Nagoya University, 65 Tsurumai-cho, Nagoya, Showa-ku,, 466-8550, Japan
| | - Weizhen Jia
- Department of Signal Transduction, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Osaka, Suita,, 565-0871, Japan
| | - Takashi Satoh
- Department of Host Defense, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Osaka, Suita, 565-0871, Japan
| | - Yumiko Hayashi
- Department of Signal Transduction, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Osaka, Suita,, 565-0871, Japan
| | - Hisamichi Naito
- Department of Signal Transduction, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Osaka, Suita,, 565-0871, Japan
| | - Yuya Kunisaki
- Department of Stem Cell Biology and Medicine/Cancer Stem Cell Research, Kyushu University, 3-1-1 Maidashi, Fukuoka, Higashi-ku, 812-8582, Japan
| | - Fumio Arai
- Department of Stem Cell Biology and Medicine/Cancer Stem Cell Research, Kyushu University, 3-1-1 Maidashi, Fukuoka, Higashi-ku, 812-8582, Japan
| | - Masahide Seki
- Department of Medical Genome Sciences Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan
| | - Tsuyoshi Osawa
- Division of Integrative Nutriomics and Oncology, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Tokyo, Meguro-ku, 153-8904, Japan
| | - Shizuo Akira
- Department of Host Defense, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Osaka, Suita, 565-0871, Japan.,Laboratory of Host Defense, World Premier Institute Immunology Frontier Research Center, Osaka University, Osaka, 565-0871, Japan
| | - Nobuyuki Takakura
- Department of Signal Transduction, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Osaka, Suita,, 565-0871, Japan.
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29
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Dony L, He F, Stumpf MPH. Parametric and non-parametric gradient matching for network inference: a comparison. BMC Bioinformatics 2019; 20:52. [PMID: 30683048 PMCID: PMC6346534 DOI: 10.1186/s12859-018-2590-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 12/21/2018] [Indexed: 11/24/2022] Open
Abstract
Background Reverse engineering of gene regulatory networks from time series gene-expression data is a challenging problem, not only because of the vast sets of candidate interactions but also due to the stochastic nature of gene expression. We limit our analysis to nonlinear differential equation based inference methods. In order to avoid the computational cost of large-scale simulations, a two-step Gaussian process interpolation based gradient matching approach has been proposed to solve differential equations approximately. Results We apply a gradient matching inference approach to a large number of candidate models, including parametric differential equations or their corresponding non-parametric representations, we evaluate the network inference performance under various settings for different inference objectives. We use model averaging, based on the Bayesian Information Criterion (BIC), to combine the different inferences. The performance of different inference approaches is evaluated using area under the precision-recall curves. Conclusions We found that parametric methods can provide comparable, and often improved inference compared to non-parametric methods; the latter, however, require no kinetic information and are computationally more efficient. Electronic supplementary material The online version of this article (10.1186/s12859-018-2590-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Leander Dony
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.,Institute of Computational Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, 85764, Germany.,Max Planck Institute of Psychiatry, Kraepelinstr. 2-10, Munich, 80804, Germany
| | - Fei He
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.,School of Computing, Electronics, and Mathematics, Coventry University, Coventry, CV1 2JH, UK
| | - Michael P H Stumpf
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK. .,Melbourne Integrative Genomics, School of BioScience & School of Mathematics and Statistics, University of Melbourne, Parkville Melbourne, 3010, Australia.
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30
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Abstract
Hematopoietic stem cells (HSCs) reside at the apex of the hematopoietic hierarchy, possessing the ability to self-renew and differentiate toward all mature blood lineages. Along with more specialized progenitor cells, HSCs have an essential role in maintaining a healthy blood system. Incorrect regulation of cell fate decisions in stem/progenitor cells can lead to an imbalance of mature blood cell populations-a situation seen in diseases such as leukemia. Transcription factors, acting as part of complex regulatory networks, are known to play an important role in regulating hematopoietic cell fate decisions. Yet, discovering the interactions present in these networks remains a big challenge. Here, we discuss a computational method that uses single-cell gene expression data to reconstruct Boolean gene regulatory network models and show how this technique can be applied to enhance our understanding of transcriptional regulation in hematopoiesis.
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Affiliation(s)
- Fiona K Hamey
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Berthold Göttgens
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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31
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Janssens DH, Wu SJ, Sarthy JF, Meers MP, Myers CH, Olson JM, Ahmad K, Henikoff S. Automated in situ chromatin profiling efficiently resolves cell types and gene regulatory programs. Epigenetics Chromatin 2018; 11:74. [PMID: 30577869 PMCID: PMC6302505 DOI: 10.1186/s13072-018-0243-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 12/03/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Our understanding of eukaryotic gene regulation is limited by the complexity of protein-DNA interactions that comprise the chromatin landscape and by inefficient methods for characterizing these interactions. We recently introduced CUT&RUN, an antibody-targeted nuclease cleavage method that profiles DNA-binding proteins, histones and chromatin-modifying proteins in situ with exceptional sensitivity and resolution. RESULTS Here, we describe an automated CUT&RUN platform and apply it to characterize the chromatin landscapes of human cells. We find that automated CUT&RUN profiles of histone modifications crisply demarcate active and repressed chromatin regions, and we develop a continuous metric to identify cell-type-specific promoter and enhancer activities. We test the ability of automated CUT&RUN to profile frozen tumor samples and find that our method readily distinguishes two pediatric glioma xenografts by their subtype-specific gene expression programs. CONCLUSIONS The easy, cost-effective workflow makes automated CUT&RUN an attractive tool for high-throughput characterization of cell types and patient samples.
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Affiliation(s)
- Derek H Janssens
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98109, USA
| | - Steven J Wu
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98109, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, 98195, USA
| | - Jay F Sarthy
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98109, USA
- Cancer and Blood Disorder Center, Seattle Children's Hospital, 4800 Sand Point Way, Seattle, WA, 98105, USA
| | - Michael P Meers
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98109, USA
| | - Carrie H Myers
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98109, USA
| | - James M Olson
- Cancer and Blood Disorder Center, Seattle Children's Hospital, 4800 Sand Point Way, Seattle, WA, 98105, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98109, USA
| | - Kami Ahmad
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98109, USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98109, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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32
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A metabolic interplay coordinated by HLX regulates myeloid differentiation and AML through partly overlapping pathways. Nat Commun 2018; 9:3090. [PMID: 30082823 PMCID: PMC6078963 DOI: 10.1038/s41467-018-05311-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Accepted: 06/29/2018] [Indexed: 02/07/2023] Open
Abstract
The H2.0-like homeobox transcription factor (HLX) regulates hematopoietic differentiation and is overexpressed in Acute Myeloid Leukemia (AML), but the mechanisms underlying these functions remain unclear. We demonstrate here that HLX overexpression leads to a myeloid differentiation block both in zebrafish and human hematopoietic stem and progenitor cells (HSPCs). We show that HLX overexpression leads to downregulation of genes encoding electron transport chain (ETC) components and upregulation of PPARδ gene expression in zebrafish and human HSPCs. HLX overexpression also results in AMPK activation. Pharmacological modulation of PPARδ signaling relieves the HLX-induced myeloid differentiation block and rescues HSPC loss upon HLX knockdown but it has no effect on AML cell lines. In contrast, AMPK inhibition results in reduced viability of AML cell lines, but minimally affects myeloid progenitors. This newly described role of HLX in regulating the metabolic state of hematopoietic cells may have important therapeutic implications. HLX transcription factor regulates haematopoietic stem and progenitor cell (HSPC) differentiation and is overexpressed in acute myeloid leukemia. Here the authors show that HLX overexpression leads to myeloid differentiation block in zebrafish and human HSPCs by direct regulation of metabolic pathways.
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33
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Grinenko T, Eugster A, Thielecke L, Ramasz B, Krüger A, Dietz S, Glauche I, Gerbaulet A, von Bonin M, Basak O, Clevers H, Chavakis T, Wielockx B. Hematopoietic stem cells can differentiate into restricted myeloid progenitors before cell division in mice. Nat Commun 2018; 9:1898. [PMID: 29765026 PMCID: PMC5954009 DOI: 10.1038/s41467-018-04188-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 04/10/2018] [Indexed: 02/06/2023] Open
Abstract
Hematopoietic stem cells (HSCs) continuously replenish all blood cell types through a series of differentiation steps and repeated cell divisions that involve the generation of lineage-committed progenitors. However, whether cell division in HSCs precedes differentiation is unclear. To this end, we used an HSC cell-tracing approach and Ki67RFP knock-in mice, in a non-conditioned transplantation model, to assess divisional history, cell cycle progression, and differentiation of adult HSCs. Our results reveal that HSCs are able to differentiate into restricted progenitors, especially common myeloid, megakaryocyte-erythroid and pre-megakaryocyte progenitors, without undergoing cell division and even before entering the S phase of the cell cycle. Additionally, the phenotype of the undivided but differentiated progenitors correlated with the expression of lineage-specific genes and loss of multipotency. Thus HSC fate decisions can be uncoupled from physical cell division. These results facilitate a better understanding of the mechanisms that control fate decisions in hematopoietic cells. Dependence of hematopoietic stem cell (HSC) fate on the phase of the cell cycle has not been demonstrated in vivo. Here, the authors find that HSCs can differentiate into a downstream progenitor without physical division, even before progressing into the S phase of the cell cycle.
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Affiliation(s)
- Tatyana Grinenko
- Department of Clinical Pathobiochemistry, Institute for Clinical Chemistry and Laboratory Medicine, Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany.
| | - Anne Eugster
- DFG Research Centre and Cluster of Excellence for Regenerative Therapies Dresden, Technische Universität Dresden, Fetscherstraße 105, 01307, Dresden, Germany
| | - Lars Thielecke
- Institute for Medical Informatics and Biometry (IMB), Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany
| | - Beáta Ramasz
- Department of Clinical Pathobiochemistry, Institute for Clinical Chemistry and Laboratory Medicine, Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany
| | - Anja Krüger
- Department of Clinical Pathobiochemistry, Institute for Clinical Chemistry and Laboratory Medicine, Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany
| | - Sevina Dietz
- DFG Research Centre and Cluster of Excellence for Regenerative Therapies Dresden, Technische Universität Dresden, Fetscherstraße 105, 01307, Dresden, Germany
| | - Ingmar Glauche
- Institute for Medical Informatics and Biometry (IMB), Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany
| | - Alexander Gerbaulet
- Institute for Immunology, Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany
| | - Malte von Bonin
- Medical Clinic and Policlinic I, University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany.,German Cancer Consortium (DKTK), partner site Dresden, Fetscherstraße 74, 01307, Dresden, Germany.,German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Onur Basak
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT, Utrecht, Netherlands.,Cancer Genomics Netherlands, UMC Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, Netherlands.,Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht and Utrecht University, 3584 CG, Utrecht, Netherlands
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT, Utrecht, Netherlands.,Cancer Genomics Netherlands, UMC Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, Netherlands.,Princess Máxima Centre, Lundlaan 6, 3584, EA Utrecht, Netherlands
| | - Triantafyllos Chavakis
- Department of Clinical Pathobiochemistry, Institute for Clinical Chemistry and Laboratory Medicine, Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany.,DFG Research Centre and Cluster of Excellence for Regenerative Therapies Dresden, Technische Universität Dresden, Fetscherstraße 105, 01307, Dresden, Germany
| | - Ben Wielockx
- Department of Clinical Pathobiochemistry, Institute for Clinical Chemistry and Laboratory Medicine, Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany. .,DFG Research Centre and Cluster of Excellence for Regenerative Therapies Dresden, Technische Universität Dresden, Fetscherstraße 105, 01307, Dresden, Germany.
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34
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Kurkewich JL, Boucher A, Klopfenstein N, Baskar R, Kapur R, Dahl R. The mirn23a and mirn23b microrna clusters are necessary for proper hematopoietic progenitor cell production and differentiation. Exp Hematol 2017; 59:14-29. [PMID: 29288704 DOI: 10.1016/j.exphem.2017.12.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 12/17/2017] [Accepted: 12/19/2017] [Indexed: 12/28/2022]
Abstract
Mice deficient for microRNA (miRNA) cluster mirn23a exhibit increased B lymphopoiesis at the expense of myelopoiesis, whereas hematopoietic stem and progenitor cell (HSPC) populations are unchanged. Mammals possess a paralogous mirn23b gene that can give rise to three mature miRNAs (miR-23b, miR-24-1, and miR-27b) that have identical seed/mRNA-targeting sequences to their mirn23a counterparts. To assess whether compound deletion of mirn23a and mirn23b exacerbates the hematopoietic phenotype observed in mirn23a-/- mice, we generated a compound mirn23a-/-mirn23bfl/fl:Mx1-Cre conditional knockout mouse and assayed hematopoietic development after excision of mirn23b. Loss of both genes in adult bone marrow further skewed HSPC differentiation toward B cells at the expense of myeloid cells, demonstrating a dosage-dependent effect on regulating cell differentiation. Strikingly, double-knockout (DKO) mice had decreased bone marrow cellularity with significantly decreased hematopoietic stem cell and HSPC populations, a phenotype not observed in mice deficient for mirn23a alone. Competitive transplantation assays showed decreased contribution of mirn23a-/-mirn23b-/- HSPCs to hematopoietic lineages at 6 and 12 weeks after transplantation. Defects in the proliferation of mirn23a-/-b-/- HSPCs was not observed; however, DKO cells were more apoptotic compared with both wild-type and mirn23a-/- cells. Together, our data show that complete loss of mirn23a/mirn23b miRNAs results in decreased blood production and affects lineage output in a concentration-dependent manner.
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Affiliation(s)
- Jeffrey L Kurkewich
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA; Harper Cancer Research Institute, South Bend, IN, USA
| | - Austin Boucher
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA; Harper Cancer Research Institute, South Bend, IN, USA
| | - Nathan Klopfenstein
- Harper Cancer Research Institute, South Bend, IN, USA; Department of Microbiology and Immunology, Indiana University School of Medicine, South Bend, IN, USA
| | - Ramdas Baskar
- Department of Pediatrics, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Reuben Kapur
- Department of Pediatrics, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Richard Dahl
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA; Harper Cancer Research Institute, South Bend, IN, USA; Department of Microbiology and Immunology, Indiana University School of Medicine, South Bend, IN, USA.
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35
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Wilkinson AC, Nakauchi H, Göttgens B. Mammalian Transcription Factor Networks: Recent Advances in Interrogating Biological Complexity. Cell Syst 2017; 5:319-331. [PMID: 29073372 PMCID: PMC5928788 DOI: 10.1016/j.cels.2017.07.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 06/29/2017] [Accepted: 07/20/2017] [Indexed: 12/11/2022]
Abstract
Transcription factor (TF) networks are a key determinant of cell fate decisions in mammalian development and adult tissue homeostasis and are frequently corrupted in disease. However, our inability to experimentally resolve and interrogate the complexity of mammalian TF networks has hampered the progress in this field. Recent technological advances, in particular large-scale genome-wide approaches, single-cell methodologies, live-cell imaging, and genome editing, are emerging as important technologies in TF network biology. Several recent studies even suggest a need to re-evaluate established models of mammalian TF networks. Here, we provide a brief overview of current and emerging methods to define mammalian TF networks. We also discuss how these emerging technologies facilitate new ways to interrogate complex TF networks, consider the current open questions in the field, and comment on potential future directions and biomedical applications.
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Affiliation(s)
- Adam C Wilkinson
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - Hiromitsu Nakauchi
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA; Division of Stem Cell Therapy, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Berthold Göttgens
- Department of Haematology, Cambridge Institute for Medical Research and Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0XY, UK.
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36
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Abstract
PURPOSE OF REVIEW Hematopoietic stem cells (HSCs) possess two fundamental characteristics, the capacity for self-renewal and the sustained production of all blood cell lineages. The fine balance between HSC expansion and lineage specification is dynamically regulated by the interplay between external and internal stimuli. This review introduces recent advances in the roles played by the stem cell niche, regulatory transcriptional networks, and metabolic pathways in governing HSC self-renewal, commitment, and lineage differentiation. We will further focus on discoveries made by studying hematopoiesis at single-cell resolution. RECENT FINDINGS HSCs require the support of an interactive milieu with their physical position within the perivascular niche dynamically regulating HSC behavior. In these microenvironments, transcription factor networks and nutrient-mediated regulation of energy resources, signaling pathways, and epigenetic status govern HSC quiescence and differentiation. Once HSCs begin their lineage specification, single-cell analyses show that they do not become oligopotent but rather, differentiate directly into committed unipotent progenitors. SUMMARY The diversity of transcriptional networks and metabolic pathways in HSCs and their downstream progeny allows a high level of plasticity in blood differentiation. The intricate interactions between these pathways, within the perivascular niche, broaden the specification of HSCs in pathological and stressed conditions.
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Neto M, Naval-Sánchez M, Potier D, Pereira PS, Geerts D, Aerts S, Casares F. Nuclear receptors connect progenitor transcription factors to cell cycle control. Sci Rep 2017; 7:4845. [PMID: 28687780 PMCID: PMC5501803 DOI: 10.1038/s41598-017-04936-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 05/23/2017] [Indexed: 01/31/2023] Open
Abstract
The specification and growth of organs is controlled simultaneously by networks of transcription factors. While the connection between these transcription factors with fate determinants is increasingly clear, how they establish the link with the cell cycle is far less understood. Here we investigate this link in the developing Drosophila eye, where two transcription factors, the MEIS1 homologue hth and the Zn-finger tsh, synergize to stimulate the proliferation of naïve eye progenitors. Experiments combining transcriptomics, open-chromatin profiling, motif analysis and functional assays indicate that these progenitor transcription factors exert a global regulation of the proliferation program. Rather than directly regulating cell cycle genes, they control proliferation through an intermediary layer of nuclear receptors of the ecdysone/estrogen-signaling pathway. This regulatory subnetwork between hth, tsh and nuclear receptors might be conserved from Drosophila to mammals, as we find a significant co-overexpression of their human homologues in specific cancer types.
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Affiliation(s)
- Marta Neto
- CABD, Andalusian Centre for Developmental Biology, CSIC-UPO-JA, 41013, Seville, Spain.,i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | | | - Delphine Potier
- School of Medicine, University of Leuven, box 602 3000, Leuven, Belgium
| | - Paulo S Pereira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Dirk Geerts
- Department of Medical Biology L2-109, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Stein Aerts
- School of Medicine, University of Leuven, box 602 3000, Leuven, Belgium.
| | - Fernando Casares
- CABD, Andalusian Centre for Developmental Biology, CSIC-UPO-JA, 41013, Seville, Spain.
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Basilico S, Göttgens B. Dysregulation of haematopoietic stem cell regulatory programs in acute myeloid leukaemia. J Mol Med (Berl) 2017; 95:719-727. [PMID: 28429049 PMCID: PMC5487585 DOI: 10.1007/s00109-017-1535-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 03/29/2017] [Accepted: 04/11/2017] [Indexed: 12/28/2022]
Abstract
Haematopoietic stem cells (HSC) are situated at the apex of the haematopoietic differentiation hierarchy, ensuring the life-long supply of mature haematopoietic cells and forming a reservoir to replenish the haematopoietic system in case of emergency such as acute blood loss. To maintain a balanced production of all mature lineages and at the same time secure a stem cell reservoir, intricate regulatory programs have evolved to control multi-lineage differentiation and self-renewal in haematopoietic stem and progenitor cells (HSPCs). Leukaemogenic mutations commonly disrupt these regulatory programs causing a block in differentiation with simultaneous enhancement of proliferation. Here, we briefly summarize key aspects of HSPC regulatory programs, and then focus on their disruption by leukaemogenic fusion genes containing the mixed lineage leukaemia (MLL) gene. Using MLL as an example, we explore important questions of wider significance that are still under debate, including the importance of cell of origin, to what extent leukaemia oncogenes impose specific regulatory programs and the relevance of leukaemia stem cells for disease development and prognosis. Finally, we suggest that disruption of stem cell regulatory programs is likely to play an important role in many other pathologies including ageing-associated regenerative failure.
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Affiliation(s)
- Silvia Basilico
- Department of Haematology, Cambridge Institute for Medical Research and Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Hills Road, Cambridge, CB2 0XY, UK
| | - Berthold Göttgens
- Department of Haematology, Cambridge Institute for Medical Research and Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Hills Road, Cambridge, CB2 0XY, UK.
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Janik S, Nowak U, Łaszkiewicz A, Satyr A, Majkowski M, Marchwicka A, Śnieżewski Ł, Berkowska K, Gabryś M, Cebrat M, Marcinkowska E. Diverse Regulation of Vitamin D Receptor Gene Expression by 1,25-Dihydroxyvitamin D and ATRA in Murine and Human Blood Cells at Early Stages of Their Differentiation. Int J Mol Sci 2017. [PMID: 28635660 PMCID: PMC5486144 DOI: 10.3390/ijms18061323] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Vitamin D receptor (VDR) is present in multiple blood cells, and the hormonal form of vitamin D, 1,25-dihydroxyvitamin D (1,25D) is essential for the proper functioning of the immune system. The role of retinoic acid receptor α (RARα) in hematopoiesis is very important, as the fusion of RARα gene with PML gene initiates acute promyelocytic leukemia where differentiation of the myeloid lineage is blocked, followed by an uncontrolled proliferation of leukemic blasts. RARα takes part in regulation of VDR transcription, and unliganded RARα acts as a transcriptional repressor to VDR gene in acute myeloid leukemia (AML) cells. This is why we decided to examine the effects of the combination of 1,25D and all-trans-retinoic acid (ATRA) on VDR gene expression in normal human and murine blood cells at various steps of their development. We tested the expression of VDR and regulation of this gene in response to 1,25D or ATRA, as well as transcriptional activities of nuclear receptors VDR and RARs in human and murine blood cells. We discovered that regulation of VDR expression in humans is different from in mice. In human blood cells at early stages of their differentiation ATRA, but not 1,25D, upregulates the expression of VDR. In contrast, in murine blood cells 1,25D, but not ATRA, upregulates the expression of VDR. VDR and RAR receptors are present and transcriptionally active in blood cells of both species, especially at early steps of blood development.
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Affiliation(s)
- Sylwia Janik
- Laboratory of Molecular and Cellular Immunology, Department of Tumor Immunology, Institute of Immunology and Experimental Therapy, Polish Academy of Science, Weigla 12, 53-114 Wrocław, Poland.
| | - Urszula Nowak
- Laboratory of Protein Biochemistry, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland.
| | - Agnieszka Łaszkiewicz
- Laboratory of Molecular and Cellular Immunology, Department of Tumor Immunology, Institute of Immunology and Experimental Therapy, Polish Academy of Science, Weigla 12, 53-114 Wrocław, Poland.
| | - Anastasiia Satyr
- Laboratory of Protein Biochemistry, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland.
| | - Michał Majkowski
- Laboratory of Molecular and Cellular Immunology, Department of Tumor Immunology, Institute of Immunology and Experimental Therapy, Polish Academy of Science, Weigla 12, 53-114 Wrocław, Poland.
| | - Aleksandra Marchwicka
- Laboratory of Protein Biochemistry, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland.
| | - Łukasz Śnieżewski
- Laboratory of Molecular and Cellular Immunology, Department of Tumor Immunology, Institute of Immunology and Experimental Therapy, Polish Academy of Science, Weigla 12, 53-114 Wrocław, Poland.
| | - Klaudia Berkowska
- Laboratory of Protein Biochemistry, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland.
| | - Marian Gabryś
- First Department of Obstetrics and Gynecology, Wrocław Medical University, Chałubińskiego 3, 50-368 Wrocław, Poland.
| | - Małgorzata Cebrat
- Laboratory of Molecular and Cellular Immunology, Department of Tumor Immunology, Institute of Immunology and Experimental Therapy, Polish Academy of Science, Weigla 12, 53-114 Wrocław, Poland.
| | - Ewa Marcinkowska
- Laboratory of Protein Biochemistry, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland.
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Vecchiarelli-Federico LM, Liu T, Yao Y, Gao Y, Li Y, Li YJ, Ben-David Y. Fli-1 overexpression in erythroleukemic cells promotes erythroid de-differentiation while Spi-1/PU.1 exerts the opposite effect. Int J Oncol 2017; 51:456-466. [PMID: 28586009 PMCID: PMC5505126 DOI: 10.3892/ijo.2017.4027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 05/23/2017] [Indexed: 01/21/2023] Open
Abstract
The ETS transcription factors play a critical role during hematopoiesis. In F-MuLV-induced erythroleukemia, Fli-1 insertional activation producing high expression of this transcription factor required to promote proliferation. How deregulated Fli-1 expression alters the balance between erythroid differentiation and proliferation is unknown. To address this issue, we exogenously overexpressed Fli-1 in an erythroleukemic cell harboring activation of spi-1/PU.1, another ETS gene involved in erythroleukemogenesis. While the proliferation in culture remains unaffected, Fli-1 overexpression imparts morphological and immunohistochemical characteristics of immature erythroid progenitors. Fli-1 overexpression in erythroleukemic cells increased the numbers of erythroid colonies on methylcellulose and reduced tumorigenicity as evidenced by increase latency of erythroleukemogenesis in mice inoculated with these cells. Although all transplanted mice developed enlargement of the spleen and liver due to leukemic infiltration, Fli-1 overexpression altered the hematopoietic phenotype, significantly increasing the expression of regulatory hematopoietic genes cKIT, SCA-1, CD41 and CD71. In contrast, expression of Spi-1/PU.1 in a Fli-1 producing erythroleukemia cell line in which fli-1 is activated, resulted in increased proliferation through activation of growth promoting proteins MAPK, AKT, cMYC and JAK2. Importantly, these progenitors express high levels of markers such as CD71 and TER119 associated with more mature erythroid cells. Thus, Fli-1 overexpression induces a de-differentiation program by reverting CFU-E to BFU-E erythroid progenitor activity, while Spi-1/PU.1 promoting maturation from BFU-E to CFU-E.
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Affiliation(s)
| | - Tangjingjun Liu
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, Guizhou 550014, P.R. China
| | - Yao Yao
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, Guizhou 550014, P.R. China
| | - Yuanyuan Gao
- Department of Anatomy, College of Basic Medical Sciences, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Yanmei Li
- Molecular and Cellular Biology, Sunnybrook Health Sciences Centre, Toronto, Ontario M4N 3M5, Canada
| | - You-Jun Li
- Department of Anatomy, College of Basic Medical Sciences, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Yaacov Ben-David
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, Guizhou 550014, P.R. China
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41
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Chromatin dynamics during the differentiation of long-term hematopoietic stem cells to multipotent progenitors. Blood Adv 2017; 1:887-898. [PMID: 29296732 DOI: 10.1182/bloodadvances.2016003384] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 05/01/2017] [Indexed: 12/31/2022] Open
Abstract
ATAC-seq provides genome-wide chromatin state in 3 cell types of hematopoietic stem/progenitor cells.Transcription factor cohorts are associated with dynamic changes of open chromatin during the differentiation of LT/ST-HSCs to MPPs.
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42
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Liu Y, Zhang C, Li Z, Wang C, Jia J, Gao T, Hildebrandt G, Zhou D, Bondada S, Ji P, St Clair D, Liu J, Zhan C, Geiger H, Wang S, Liang Y. Latexin Inactivation Enhances Survival and Long-Term Engraftment of Hematopoietic Stem Cells and Expands the Entire Hematopoietic System in Mice. Stem Cell Reports 2017; 8:991-1004. [PMID: 28330618 PMCID: PMC5390104 DOI: 10.1016/j.stemcr.2017.02.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 02/09/2017] [Accepted: 02/10/2017] [Indexed: 12/20/2022] Open
Abstract
Natural genetic diversity offers an important yet largely untapped resource to decipher the molecular mechanisms regulating hematopoietic stem cell (HSC) function. Latexin (Lxn) is a negative stem cell regulatory gene identified on the basis of genetic diversity. By using an Lxn knockout mouse model, we found that Lxn inactivation in vivo led to the physiological expansion of the entire hematopoietic hierarchy. Loss of Lxn enhanced the competitive repopulation capacity and survival of HSCs in a cell-intrinsic manner. Gene profiling of Lxn-null HSCs showed altered expression of genes enriched in cell-matrix and cell-cell interactions. Thrombospondin 1 (Thbs1) was a potential downstream target with a dramatic downregulation in Lxn-null HSCs. Enforced expression of Thbs1 restored the Lxn inactivation-mediated HSC phenotypes. This study reveals that Lxn plays an important role in the maintenance of homeostatic hematopoiesis, and it may lead to development of safe and effective approaches to manipulate HSCs for clinical benefit.
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Affiliation(s)
- Yi Liu
- Department of Physiology, University of Kentucky, Lexington, KY 40536, USA
| | - Cuiping Zhang
- Department of Toxicology and Cancer Biology, University of Kentucky, Health Sciences Research Building Room 340, 1095 V.A. Drive, Lexington, KY 40536, USA
| | - Zhenyu Li
- Department of Internal Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Chi Wang
- Department of Cancer Biostatistics, University of Kentucky, Lexington, KY 40536, USA
| | - Jianhang Jia
- Department of Molecular & Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Tianyan Gao
- Department of Molecular & Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Gerhard Hildebrandt
- Department of Internal Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Daohong Zhou
- Division of Radiation Health, Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Subbarao Bondada
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, Lexington, KY 40536, USA
| | - Peng Ji
- Department of Pathology, Northwestern University, Chicago, IL 60611, USA
| | - Daret St Clair
- Department of Toxicology and Cancer Biology, University of Kentucky, Health Sciences Research Building Room 340, 1095 V.A. Drive, Lexington, KY 40536, USA
| | - Jinze Liu
- Department of Computer Science, University of Kentucky, Lexington, KY 40536, USA
| | - Changguo Zhan
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Hartmut Geiger
- Cincinnati Children's Hospital Medical Center, Experimental Hematology and Cancer Biology, Cincinnati, OH 45229, USA; Institute for Molecular Medicine, University of Ulm, 89081 Ulm, Germany
| | - Shuxia Wang
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Ying Liang
- Department of Toxicology and Cancer Biology, University of Kentucky, Health Sciences Research Building Room 340, 1095 V.A. Drive, Lexington, KY 40536, USA.
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43
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Guitart AV, Panagopoulou TI, Villacreces A, Vukovic M, Sepulveda C, Allen L, Carter RN, van de Lagemaat LN, Morgan M, Giles P, Sas Z, Gonzalez MV, Lawson H, Paris J, Edwards-Hicks J, Schaak K, Subramani C, Gezer D, Armesilla-Diaz A, Wills J, Easterbrook A, Coman D, So CWE, O'Carroll D, Vernimmen D, Rodrigues NP, Pollard PJ, Morton NM, Finch A, Kranc KR. Fumarate hydratase is a critical metabolic regulator of hematopoietic stem cell functions. J Exp Med 2017; 214:719-735. [PMID: 28202494 PMCID: PMC5339674 DOI: 10.1084/jem.20161087] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 11/29/2016] [Accepted: 01/20/2017] [Indexed: 11/04/2022] Open
Abstract
Strict regulation of stem cell metabolism is essential for tissue functions and tumor suppression. In this study, we investigated the role of fumarate hydratase (Fh1), a key component of the mitochondrial tricarboxylic acid (TCA) cycle and cytosolic fumarate metabolism, in normal and leukemic hematopoiesis. Hematopoiesis-specific Fh1 deletion (resulting in endogenous fumarate accumulation and a genetic TCA cycle block reflected by decreased maximal mitochondrial respiration) caused lethal fetal liver hematopoietic defects and hematopoietic stem cell (HSC) failure. Reexpression of extramitochondrial Fh1 (which normalized fumarate levels but not maximal mitochondrial respiration) rescued these phenotypes, indicating the causal role of cellular fumarate accumulation. However, HSCs lacking mitochondrial Fh1 (which had normal fumarate levels but defective maximal mitochondrial respiration) failed to self-renew and displayed lymphoid differentiation defects. In contrast, leukemia-initiating cells lacking mitochondrial Fh1 efficiently propagated Meis1/Hoxa9-driven leukemia. Thus, we identify novel roles for fumarate metabolism in HSC maintenance and hematopoietic differentiation and reveal a differential requirement for mitochondrial Fh1 in normal hematopoiesis and leukemia propagation.
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Affiliation(s)
- Amelie V Guitart
- Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH8 9YL, Scotland, UK
| | - Theano I Panagopoulou
- Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH8 9YL, Scotland, UK
| | - Arnaud Villacreces
- Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH8 9YL, Scotland, UK
| | - Milica Vukovic
- Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH8 9YL, Scotland, UK
| | - Catarina Sepulveda
- Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH8 9YL, Scotland, UK
| | - Lewis Allen
- Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH8 9YL, Scotland, UK
| | - Roderick N Carter
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH8 9YL, Scotland, UK
| | - Louie N van de Lagemaat
- Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH8 9YL, Scotland, UK
- The Roslin Institute, University of Edinburgh, Edinburgh EH8 9YL, Scotland, UK
| | - Marcos Morgan
- Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH8 9YL, Scotland, UK
| | - Peter Giles
- Wales Gene Park and Wales Cancer Research Centre, Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF10 3XQ, Wales, UK
| | - Zuzanna Sas
- Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH8 9YL, Scotland, UK
| | - Marta Vila Gonzalez
- Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH8 9YL, Scotland, UK
| | - Hannah Lawson
- Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH8 9YL, Scotland, UK
| | - Jasmin Paris
- Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH8 9YL, Scotland, UK
| | - Joy Edwards-Hicks
- Edinburgh Cancer Research UK Centre, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH8 9YL, Scotland, UK
| | - Katrin Schaak
- Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH8 9YL, Scotland, UK
| | - Chithra Subramani
- Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH8 9YL, Scotland, UK
| | - Deniz Gezer
- Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH8 9YL, Scotland, UK
| | - Alejandro Armesilla-Diaz
- Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH8 9YL, Scotland, UK
| | - Jimi Wills
- Edinburgh Cancer Research UK Centre, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH8 9YL, Scotland, UK
| | - Aaron Easterbrook
- Mater Children's Private Hospital Brisbane, South Brisbane, Queensland 4101, Australia
| | - David Coman
- Department of Metabolic Medicine, The Lady Cilento Children's Hospital, South Brisbane, Queensland 4101, Australia
| | - Chi Wai Eric So
- Department of Haematological Medicine, Division of Cancer Studies, King's College London, London WC2R 2LS, England, UK
| | - Donal O'Carroll
- Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH8 9YL, Scotland, UK
| | - Douglas Vernimmen
- The Roslin Institute, University of Edinburgh, Edinburgh EH8 9YL, Scotland, UK
| | - Neil P Rodrigues
- The European Cancer Stem Cell Research Institute, School of Biosciences, Cardiff University, Cardiff CF10 3XQ, Wales, UK
| | - Patrick J Pollard
- Edinburgh Cancer Research UK Centre, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH8 9YL, Scotland, UK
| | - Nicholas M Morton
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH8 9YL, Scotland, UK
| | - Andrew Finch
- Edinburgh Cancer Research UK Centre, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH8 9YL, Scotland, UK
| | - Kamil R Kranc
- Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH8 9YL, Scotland, UK
- Edinburgh Cancer Research UK Centre, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH8 9YL, Scotland, UK
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44
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PUMILIO/FOXP1 signaling drives expansion of hematopoietic stem/progenitor and leukemia cells. Blood 2017; 129:2493-2506. [PMID: 28232582 DOI: 10.1182/blood-2016-10-747436] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 02/20/2017] [Indexed: 12/13/2022] Open
Abstract
RNA-binding proteins (RBPs) have emerged as important regulators of invertebrate adult stem cells, but their activities remain poorly appreciated in mammals. Using a short hairpin RNA strategy, we demonstrate here that the 2 mammalian RBPs, PUMILIO (PUM)1 and PUM2, members of the PUF family of posttranscriptional regulators, are essential for hematopoietic stem/progenitor cell (HSPC) proliferation and survival in vitro and in vivo upon reconstitution assays. Moreover, we found that PUM1/2 sustain myeloid leukemic cell growth. Through a proteomic approach, we identified the FOXP1 transcription factor as a new target of PUM1/2. Contrary to its canonical repressive activity, PUM1/2 rather promote FOXP1 expression by a direct binding to 2 canonical PUM responsive elements present in the FOXP1-3' untranslated region (UTR). Expression of FOXP1 strongly correlates with PUM1 and PUM2 levels in primary HSPCs and myeloid leukemia cells. We demonstrate that FOXP1 by itself supports HSPC and leukemic cell growth, thus mimicking PUM activities. Mechanistically, FOXP1 represses the expression of the p21-CIP1 and p27-KIP1 cell cycle inhibitors. Enforced FOXP1 expression reverses shPUM antiproliferative and proapoptotic activities. Altogether, our results reveal a novel regulatory pathway, underscoring a previously unknown and interconnected key role of PUM1/2 and FOXP1 in regulating normal HSPC and leukemic cell growth.
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45
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Sontag S, Förster M, Qin J, Wanek P, Mitzka S, Schüler HM, Koschmieder S, Rose-John S, Seré K, Zenke M. Modelling IRF8 Deficient Human Hematopoiesis and Dendritic Cell Development with Engineered iPS Cells. Stem Cells 2017; 35:898-908. [DOI: 10.1002/stem.2565] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 12/20/2016] [Indexed: 12/11/2022]
Affiliation(s)
- Stephanie Sontag
- Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School; Aachen Germany
- Helmholtz Institute for Biomedical Engineering; RWTH Aachen University; Aachen Germany
| | - Malrun Förster
- Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School; Aachen Germany
- Helmholtz Institute for Biomedical Engineering; RWTH Aachen University; Aachen Germany
| | - Jie Qin
- Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School; Aachen Germany
- Helmholtz Institute for Biomedical Engineering; RWTH Aachen University; Aachen Germany
| | - Paul Wanek
- Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School; Aachen Germany
- Helmholtz Institute for Biomedical Engineering; RWTH Aachen University; Aachen Germany
| | - Saskia Mitzka
- Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School; Aachen Germany
- Helmholtz Institute for Biomedical Engineering; RWTH Aachen University; Aachen Germany
| | - Herdit M. Schüler
- Department of Human Genetics, RWTH Aachen University Medical School; Aachen Germany
| | - Steffen Koschmieder
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation; RWTH Aachen University Medical School; Aachen Germany
| | - Stefan Rose-John
- Medical Faculty, Institute of Biochemistry, Christian-Albrechts-University; Kiel Germany
| | - Kristin Seré
- Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School; Aachen Germany
- Helmholtz Institute for Biomedical Engineering; RWTH Aachen University; Aachen Germany
| | - Martin Zenke
- Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School; Aachen Germany
- Helmholtz Institute for Biomedical Engineering; RWTH Aachen University; Aachen Germany
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46
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Clapes T, Lefkopoulos S, Trompouki E. Stress and Non-Stress Roles of Inflammatory Signals during HSC Emergence and Maintenance. Front Immunol 2016; 7:487. [PMID: 27872627 PMCID: PMC5098161 DOI: 10.3389/fimmu.2016.00487] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 10/21/2016] [Indexed: 12/22/2022] Open
Abstract
Hematopoietic stem cells (HSCs) are a rare population that gives rise to almost all cells of the hematopoietic system, including immune cells. Until recently, it was thought that immune cells sense inflammatory signaling and HSCs respond only secondarily to these signals. However, it was later shown that adult HSCs could directly sense and respond to inflammatory signals, resulting in a higher output of immune cells. Recent studies demonstrated that inflammatory signaling is also vital for HSC ontogeny. These signals are thought to arise in the absence of pathogens, are active during development, and indispensable for HSC formation. In contrast, during times of stress and disease, inflammatory responses can be activated and can have devastating effects on HSCs. In this review, we summarize the current knowledge about inflammatory signaling in HSC development and maintenance, as well as the endogenous molecular cues that can trigger inflammatory pathway activation. Finally, we comment of the role of inflammatory signaling in hematopoietic diseases.
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Affiliation(s)
- Thomas Clapes
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics , Freiburg , Germany
| | - Stylianos Lefkopoulos
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics , Freiburg , Germany
| | - Eirini Trompouki
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics , Freiburg , Germany
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47
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Cico A, Andrieu-Soler C, Soler E. Enhancers and their dynamics during hematopoietic differentiation and emerging strategies for therapeutic action. FEBS Lett 2016; 590:4084-4104. [DOI: 10.1002/1873-3468.12424] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 09/08/2016] [Accepted: 09/12/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Alba Cico
- Inserm UMR967, CEA/DRF/iRCM; Fontenay-aux-Roses France
| | - Charlotte Andrieu-Soler
- Inserm UMR967, CEA/DRF/iRCM; Fontenay-aux-Roses France
- CNRS; Institute of Molecular Genetics (IGMM); Montpellier France
| | - Eric Soler
- Inserm UMR967, CEA/DRF/iRCM; Fontenay-aux-Roses France
- CNRS; Institute of Molecular Genetics (IGMM); Montpellier France
- Laboratory of Excellence GR-Ex; Paris France
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48
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Cellular Engineering for the Production of New Blood Components. Transfus Med 2016. [DOI: 10.1002/9781119236504.ch18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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49
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Hamey FK, Nestorowa S, Wilson NK, Göttgens B. Advancing haematopoietic stem and progenitor cell biology through single-cell profiling. FEBS Lett 2016; 590:4052-4067. [PMID: 27259698 DOI: 10.1002/1873-3468.12231] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 05/27/2016] [Accepted: 05/31/2016] [Indexed: 12/25/2022]
Abstract
Haematopoietic stem and progenitor cells (HSPCs) sit at the top of the haematopoietic hierarchy, and their fate choices need to be carefully controlled to ensure balanced production of all mature blood cell types. As cell fate decisions are made at the level of the individual cells, recent technological advances in measuring gene and protein expression in increasingly large numbers of single cells have been rapidly adopted to study both normal and pathological HSPC function. In this review we emphasise the importance of combining the correct computational models with single-cell experimental techniques, and illustrate how such integrated approaches have been used to resolve heterogeneities in populations, reconstruct lineage differentiation, identify regulatory relationships and link molecular profiling to cellular function.
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Affiliation(s)
- Fiona K Hamey
- Department of Haematology and Wellcome Trust - MRC Cambridge Stem Cell Institute, University of Cambridge, UK
| | - Sonia Nestorowa
- Department of Haematology and Wellcome Trust - MRC Cambridge Stem Cell Institute, University of Cambridge, UK
| | - Nicola K Wilson
- Department of Haematology and Wellcome Trust - MRC Cambridge Stem Cell Institute, University of Cambridge, UK
| | - Berthold Göttgens
- Department of Haematology and Wellcome Trust - MRC Cambridge Stem Cell Institute, University of Cambridge, UK
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50
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Chasman D, Fotuhi Siahpirani A, Roy S. Network-based approaches for analysis of complex biological systems. Curr Opin Biotechnol 2016; 39:157-166. [PMID: 27115495 DOI: 10.1016/j.copbio.2016.04.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Revised: 04/04/2016] [Accepted: 04/05/2016] [Indexed: 12/22/2022]
Abstract
Cells function and respond to changes in their environment by the coordinated activity of their molecular components, including mRNAs, proteins and metabolites. At the heart of proper cellular function are molecular networks connecting these components to process extra-cellular environmental signals and drive dynamic, context-specific cellular responses. Network-based computational approaches aim to systematically integrate measurements from high-throughput experiments to gain a global understanding of cellular function under changing environmental conditions. We provide an overview of recent methodological developments toward solving two major computational problems within this field in the past two years (2013-2015): network reconstruction and network-based interpretation. Looking forward, we envision development of methods that can predict phenotypes with high accuracy as well as provide biologically plausible mechanistic hypotheses.
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Affiliation(s)
- Deborah Chasman
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, United States
| | - Alireza Fotuhi Siahpirani
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI 53706, United States; Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, United States; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53792, United States
| | - Sushmita Roy
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, United States; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53792, United States; Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI 53706, United States.
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