1
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Heller V, Wang L, Schneider E, Gerstner M, Bajer L, Decker R, Boenig H, Lausen J. ID3 promotes erythroid differentiation and is repressed by a TAL1-PRMT6 complex. J Biol Chem 2025; 301:108119. [PMID: 39716491 PMCID: PMC11847539 DOI: 10.1016/j.jbc.2024.108119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 12/03/2024] [Accepted: 12/17/2024] [Indexed: 12/25/2024] Open
Abstract
Erythropoiesis is controlled by transcription factors that recruit epigenetic cofactors to establish and maintain erythrocyte-specific gene expression patterns while repressing alternative lineage commitment. The transcription factor TAL1 (T-cell acute lymphocytic leukemia 1) is critical for establishing erythroid gene expression. It acts as an activator or repressor of genes, depending on associated epigenetic cofactors. Understanding the epigenetic function of TAL1 during erythropoiesis is key to improving in vitro erythroid differentiation and understanding pathological erythropoiesis. Therefore, the regulatory mechanisms that control the function of TAL1 during erythropoiesis are under intense investigation. Here, we show that TAL1 interacts with protein-arginine-methyltransferase-6 (PRMT6) on the ID3 (inhibitor-of-DNA-binding-3) gene in K562 and hCD34+ cells. The ID protein family is a critical transcriptional regulator of hematopoietic cell differentiation. We show that TAL1 and PRMT6 are present at the ID3 promoter, and that TAL1 is involved in the recruitment of PRMT6. Here, PRMT6 epigenetically regulates ID3 expression by mediating dimethylation of histone 3 at arginine 2. Thus, TAL1-PRMT6 epigenetically represses ID3 expression in progenitors, which is relieved upon erythroid differentiation, leading to increased expression. Overexpression of ID3 in primary hCD34+ cells enhances erythropoiesis. Our results show that a TAL1-PRMT6 complex regulates genes important for erythropoiesis, such as ID3. Manipulation of ID3 expression may be a way to promote in vitro differentiation of hCD34+ cells into erythrocytes.
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Affiliation(s)
- Vivien Heller
- Department of Eukaryotic Genetics, Institute of Biomedical Genetics, University of Stuttgart, Stuttgart, Germany
| | - Lei Wang
- Department of Eukaryotic Genetics, Institute of Biomedical Genetics, University of Stuttgart, Stuttgart, Germany
| | - Edith Schneider
- Department of Eukaryotic Genetics, Institute of Biomedical Genetics, University of Stuttgart, Stuttgart, Germany
| | - Mirjam Gerstner
- Department of Eukaryotic Genetics, Institute of Biomedical Genetics, University of Stuttgart, Stuttgart, Germany
| | - Luana Bajer
- Department of Eukaryotic Genetics, Institute of Biomedical Genetics, University of Stuttgart, Stuttgart, Germany
| | - Robin Decker
- Department of Eukaryotic Genetics, Institute of Biomedical Genetics, University of Stuttgart, Stuttgart, Germany
| | - Halvard Boenig
- Institute for Transfusion Medicine and Immunohematology and German Red Cross Blood Service BaWüHe, Institute Frankfurt, Faculty of Medicine, Goethe University, Frankfurt, Germany
| | - Joern Lausen
- Department of Eukaryotic Genetics, Institute of Biomedical Genetics, University of Stuttgart, Stuttgart, Germany.
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2
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Handzlik JE. Data-driven modeling predicts gene regulatory network dynamics during the differentiation of multipotential hematopoietic progenitors. PLoS Comput Biol 2022; 18:e1009779. [PMID: 35030198 PMCID: PMC8794271 DOI: 10.1371/journal.pcbi.1009779] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 01/27/2022] [Accepted: 12/21/2021] [Indexed: 01/05/2023] Open
Abstract
Cellular differentiation during hematopoiesis is guided by gene regulatory networks (GRNs) comprising transcription factors (TFs) and the effectors of cytokine signaling. Based largely on analyses conducted at steady state, these GRNs are thought to be organized as a hierarchy of bistable switches, with antagonism between Gata1 and PU.1 driving red- and white-blood cell differentiation. Here, we utilize transient gene expression patterns to infer the genetic architecture—the type and strength of regulatory interconnections—and dynamics of a twelve-gene GRN including key TFs and cytokine receptors. We trained gene circuits, dynamical models that learn genetic architecture, on high temporal-resolution gene-expression data from the differentiation of an inducible cell line into erythrocytes and neutrophils. The model is able to predict the consequences of gene knockout, knockdown, and overexpression experiments and the inferred interconnections are largely consistent with prior empirical evidence. The inferred genetic architecture is densely interconnected rather than hierarchical, featuring extensive cross-antagonism between genes from alternative lineages and positive feedback from cytokine receptors. The analysis of the dynamics of gene regulation in the model reveals that PU.1 is one of the last genes to be upregulated in neutrophil conditions and that the upregulation of PU.1 and other neutrophil genes is driven by Cebpa and Gfi1 instead. This model inference is confirmed in an independent single-cell RNA-Seq dataset from mouse bone marrow in which Cebpa and Gfi1 expression precedes the neutrophil-specific upregulation of PU.1 during differentiation. These results demonstrate that full PU.1 upregulation during neutrophil development involves regulatory influences extrinsic to the Gata1-PU.1 bistable switch. Furthermore, although there is extensive cross-antagonism between erythroid and neutrophil genes, it does not have a hierarchical structure. More generally, we show that the combination of high-resolution time series data and data-driven dynamical modeling can uncover the dynamics and causality of developmental events that might otherwise be obscured. The supply of blood cells is replenished by the maturation of hematopoietic progenitor cells into different cell types. Which cell type a progenitor cell develops into is determined by a complex network of genes whose protein products directly or indirectly regulate each others’ expression and that of downstream genes characteristic of the cell type. We inferred the nature and causality of the regulatory connections in a 12-gene network known to affect the decision between erythrocyte and neutrophil cell fates using a predictive machine-learning approach. Our analysis showed that the overall architecture of the network is densely interconnected and not hierarchical. Furthermore, the model inferred that PU.1, considered a master regulator of all white-blood cell lineages, is upregulated during neutrophil development by two other proteins, Cebpa and Gfi1. We validated this prediction by showing that Cebpa and Gfi1 expression precedes that of PU.1 in single-cell gene expression data from mouse bone marrow. These results revise the architecture of the gene network and the causality of regulatory events guiding hematopoiesis. The results also show that combining machine learning approaches with time course data can help resolve causality during development.
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Affiliation(s)
- Joanna E Handzlik
- Department of Biology, University of North Dakota, Grand Forks, North Dakota, United States of America
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3
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Loughran SJ, Haas S, Wilkinson AC, Klein AM, Brand M. Lineage commitment of hematopoietic stem cells and progenitors: insights from recent single cell and lineage tracing technologies. Exp Hematol 2020; 88:1-6. [PMID: 32653531 DOI: 10.1016/j.exphem.2020.07.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 12/31/2022]
Abstract
Blood production is essential to maintain human health, and even small perturbations in hematopoiesis can cause disease. Hematopoiesis has therefore been the focus of much research for many years. Experiments determining the lineage potentials of hematopoietic stem and progenitor cells (HSPCs) in vitro and after transplantation revealed a hierarchy of progenitor cell states, where differentiating cells undergo lineage commitment-a series of irreversible changes that progressively restrict their potential. New technologies have recently been developed that allow for a more detailed analysis of the molecular states and fates of differentiating HSPCs. Proteomic and lineage-tracing approaches, alongside single-cell transcriptomic analyses, have recently helped to reveal the biological complexity underlying lineage commitment during hematopoiesis. Recent insights from these new technologies were presented by Dr. Marjorie Brand and Dr. Allon Klein in the Summer 2019 ISEH Webinar, and are discussed in this Perspective.
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Affiliation(s)
- Stephen J Loughran
- Wellcome-MRC Cambridge Stem Cell Institute and Department of Haematology, University of Cambridge, Cambridge, United Kingdom.
| | - Simon Haas
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine and Division of Stem Cells and Cancer, DKFZ German Cancer Research Centre, Heidelberg, Germany
| | - Adam C Wilkinson
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA; Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Allon M Klein
- Department of Systems Biology, Harvard Medical School, Boston, MA
| | - Marjorie Brand
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada
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4
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Repele A, Krueger S, Bhattacharyya T, Tuineau MY. The regulatory control of Cebpa enhancers and silencers in the myeloid and red-blood cell lineages. PLoS One 2019; 14:e0217580. [PMID: 31181110 PMCID: PMC6557489 DOI: 10.1371/journal.pone.0217580] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/14/2019] [Indexed: 12/31/2022] Open
Abstract
Cebpa encodes a transcription factor (TF) that plays an instructive role in the development of multiple myeloid lineages. The expression of Cebpa itself is finely modulated, as Cebpa is expressed at high and intermediate levels in neutrophils and macrophages respectively and downregulated in non-myeloid lineages. The cis-regulatory logic underlying the lineage-specific modulation of Cebpa's expression level is yet to be fully characterized. Previously, we had identified 6 new cis-regulatory modules (CRMs) in a 78kb region surrounding Cebpa. We had also inferred the TFs that regulate each CRM by fitting a sequence-based thermodynamic model to a comprehensive reporter activity dataset. Here, we report the cis-regulatory logic of Cebpa CRMs at the resolution of individual binding sites. We tested the binding sites and functional roles of inferred TFs by designing and constructing mutated CRMs and comparing theoretical predictions of their activity against empirical measurements in a myeloid cell line. The enhancers were confirmed to be activated by combinations of PU.1, C/EBP family TFs, Egr1, and Gfi1 as predicted by the model. We show that silencers repress the activity of the proximal promoter in a dominant manner in G1ME cells, which are derived from the red-blood cell lineage. Dominant repression in G1ME cells can be traced to binding sites for GATA and Myb, a motif shared by all of the silencers. Finally, we demonstrate that GATA and Myb act redundantly to silence the proximal promoter. These results indicate that dominant repression is a novel mechanism for resolving hematopoietic lineages. Furthermore, Cebpa has a fail-safe cis-regulatory architecture, featuring several functionally similar CRMs, each of which contains redundant binding sites for multiple TFs. Lastly, by experimentally demonstrating the predictive ability of our sequence-based thermodynamic model, this work highlights the utility of this computational approach for understanding mammalian gene regulation.
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Affiliation(s)
- Andrea Repele
- Department of Biology, University of North Dakota, Grand Forks, ND, United States of America
| | - Shawn Krueger
- Department of Biology, University of North Dakota, Grand Forks, ND, United States of America
| | - Tapas Bhattacharyya
- Department of Biology, University of North Dakota, Grand Forks, ND, United States of America
| | - Michelle Y Tuineau
- Department of Biology, University of North Dakota, Grand Forks, ND, United States of America
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5
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Bokes P, King JR. Limit-cycle oscillatory coexpression of cross-inhibitory transcription factors: a model mechanism for lineage promiscuity. MATHEMATICAL MEDICINE AND BIOLOGY-A JOURNAL OF THE IMA 2019; 36:113-137. [PMID: 30869799 DOI: 10.1093/imammb/dqy003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Accepted: 01/29/2018] [Indexed: 12/12/2022]
Abstract
Lineage switches are genetic regulatory motifs that govern and maintain the commitment of a developing cell to a particular cell fate. A canonical example of a lineage switch is the pair of transcription factors PU.1 and GATA-1, of which the former is affiliated with the myeloid and the latter with the erythroid lineage within the haematopoietic system. On a molecular level, PU.1 and GATA-1 positively regulate themselves and antagonize each other via direct protein-protein interactions. Here we use mathematical modelling to identify a novel type of dynamic behaviour that can be supported by such a regulatory architecture. Guided by the specifics of the PU.1-GATA-1 interaction, we formulate, using the law of mass action, a system of differential equations for the key molecular concentrations. After a series of systematic approximations, the system is reduced to a simpler one, which is tractable to phase-plane and linearization methods. The reduced system formally resembles, and generalizes, a well-known model for competitive species from mathematical ecology. However, in addition to the qualitative regimes exhibited by a pair of competitive species (exclusivity, bistable exclusivity, stable-node coexpression) it also allows for oscillatory limit-cycle coexpression. A key outcome of the model is that, in the context of cell-fate choice, such oscillations could be harnessed by a differentiating cell to prime alternately for opposite outcomes; a bifurcation-theory approach is adopted to characterize this possibility.
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Affiliation(s)
- Pavol Bokes
- Department of Applied Mathematics and Statistics, Comenius University, Bratislava, Slovakia
| | - John R King
- School of Mathematical Sciences and SBRC Nottingham, University of Nottingham, Nottingham, United Kingdom
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6
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Zhang YW, Cabezas-Wallscheid N. Assessment of Young and Aged Hematopoietic Stem Cell Activity by Competitive Serial Transplantation Assays. Methods Mol Biol 2019; 2017:193-203. [PMID: 31197778 DOI: 10.1007/978-1-4939-9574-5_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Healthy hematopoietic stem cells (HSCs) are capable to self-renew and reconstitute the complete hematopoietic system. Upon aging, there is an increased incidence of blood-related diseases. Age-related phenotypes have been widely studied by bone marrow transplantation experiments, where reconstitution of the transplanted cells is a direct measure of HSC activity. In this protocol we describe a competitive bone marrow transplantation assay to functionally test young and old HSCs.
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Affiliation(s)
- Yu Wei Zhang
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.,International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Freiburg, Germany
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7
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A novel role of CKIP-1 in promoting megakaryocytic differentiation. Oncotarget 2018; 8:30138-30150. [PMID: 28404913 PMCID: PMC5444732 DOI: 10.18632/oncotarget.15619] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 01/27/2017] [Indexed: 11/30/2022] Open
Abstract
Casein kinase 2-interacting protein-1 (CKIP-1) is a known regulator of cardiomyocytes and macrophage proliferation. In this study, we showed that CKIP-1 was involved in the process of megakaryocytic differentiation. During megakaryocytic differentiation of K562 cells, CKIP-1 was dramatically upregulated and this upregulation induced by PMA was mediated through downregulation of transcription factor GATA-1. By transient transfection, oligonucleotide-directed mutagenesis and chromatin immunoprecipitation assays, we identified the transcriptional regulation of CKIP-1 by GATA-1. Overexpression of CKIP-1 initiated events of spontaneous megakaryocytic differentiation in K562 cells. Conversely, knockdown of CKIP-1 in cell lines suppressed megakaryocytic differentiation. Mechanistically, overexpression of CKIP-1 changed the expression levels of transcription factors that have been shown to be critical in erythro-megakaryocytic differentiation such as Fli-1, c-Myb and c-Myc. In vivo analysis confirmed that CKIP-1−/− mice had decreased number of CD41+ cells harvested from bone marrow, and lower platelet levels when compared to wild-type littermates. This is the first direct evidence suggesting that CKIP-1 is a novel regulator of megakaryocytic differentiation.
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8
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Lin J, Liu W, Luan T, Yuan L, Jiang W, Cai H, Yuan W, Wang Y, Zhang Q, Wang L. High expression of PU.1 is associated with Her-2 and shorter survival in patients with breast cancer. Oncol Lett 2017; 14:8220-8226. [PMID: 29344265 DOI: 10.3892/ol.2017.7204] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 08/23/2017] [Indexed: 12/27/2022] Open
Abstract
The transcription factor PU.1 was previously identified as an oncogene or a tumor suppressor in different types of leukemia. The aim of the present study was to investigate the expression of PU.1 in breast cancer and to analyze its association with clinical features and prognosis. Immunohistochemistry was used to determine PU.1 expression in breast cancer tissue microarrays and paraffin-embedded sections. The association between PU.1 expression and clinicopathological factors was assessed by using chi-square test. The survival analysis of patients was conducted by using Kaplan-Meier analysis and log-rank tests. Cox regression was utilized for univariate and multivariate analyses of prognostic factors. The results indicated that the expression level of PU.1 protein in breast cancer samples was significantly higher compared with normal breast tissues (P=2.63×10-8). Furthermore, the level of PU.1 expression was detected to be positively associated with androgen receptor (P=0.027) and human epidermal growth factor receptor 2 status (P=2.03×10-21) as well as molecular subtype (P=3.51×10-11). Furthermore, patients with negative PU.1 expression had longer OR compared with those with positive PU.1 expression (P=3.67×10-4). Multivariate Cox regression analysis revealed that PU.1 expression level and tumor-node-metastasis stage were independent prognostic factors for overall survival (P=0.034 and P=0.018, respectively). Therefore, PU.1 protein expression may contribute to breast cancer progression and may be a valuable molecular marker to predict the prognosis of patients with breast cancer.
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Affiliation(s)
- Jing Lin
- Department of Cytobiology, Institute of Cancer Prevention and Treatment, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China.,Department of Cytobiology, Heilongjiang Academy of Medical Sciences, Harbin, Heilongjiang 150081, P.R. China
| | - Wei Liu
- Department of Pathology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Tian Luan
- Department of Cytobiology, Institute of Cancer Prevention and Treatment, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China.,Department of Cytobiology, Heilongjiang Academy of Medical Sciences, Harbin, Heilongjiang 150081, P.R. China
| | - Lili Yuan
- Department of Cytobiology, Institute of Cancer Prevention and Treatment, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China.,Department of Cytobiology, Heilongjiang Academy of Medical Sciences, Harbin, Heilongjiang 150081, P.R. China
| | - Wei Jiang
- Department of Biomedical Mathematics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Huilong Cai
- Department of Cytobiology, Institute of Cancer Prevention and Treatment, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China.,Department of Cytobiology, Heilongjiang Academy of Medical Sciences, Harbin, Heilongjiang 150081, P.R. China
| | - Weiguang Yuan
- Department of Cytobiology, Institute of Cancer Prevention and Treatment, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China.,Department of Cytobiology, Heilongjiang Academy of Medical Sciences, Harbin, Heilongjiang 150081, P.R. China
| | - Yuwen Wang
- Department of Laboratory Diagnostics, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Qingyuan Zhang
- Department of Cytobiology, Institute of Cancer Prevention and Treatment, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China.,Department of Cytobiology, Heilongjiang Academy of Medical Sciences, Harbin, Heilongjiang 150081, P.R. China.,Department of Internal Medicine, The Third Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Lihong Wang
- Department of Cytobiology, Institute of Cancer Prevention and Treatment, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China.,Department of Cytobiology, Heilongjiang Academy of Medical Sciences, Harbin, Heilongjiang 150081, P.R. China.,Department of Pathophysiology, Medical School of Southeast University, Nanjing, Jiangsu 210009, P.R. China
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9
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Herkt SC, Kuvardina ON, Herglotz J, Schneider L, Meyer A, Pommerenke C, Salinas-Riester G, Seifried E, Bonig H, Lausen J. Protein arginine methyltransferase 6 controls erythroid gene expression and differentiation of human CD34 + progenitor cells. Haematologica 2017; 103:18-29. [PMID: 29025910 PMCID: PMC5777187 DOI: 10.3324/haematol.2017.174516] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 10/06/2017] [Indexed: 01/22/2023] Open
Abstract
Hematopoietic differentiation is driven by transcription factors, which orchestrate a finely tuned transcriptional network. At bipotential branching points lineage decisions are made, where key transcription factors initiate cell type-specific gene expression programs. These programs are stabilized by the epigenetic activity of recruited chromatin-modifying cofactors. An example is the association of the transcription factor RUNX1 with protein arginine methyltransferase 6 (PRMT6) at the megakaryocytic/erythroid bifurcation. However, little is known about the specific influence of PRMT6 on this important branching point. Here, we show that PRMT6 inhibits erythroid gene expression during megakaryopoiesis of primary human CD34+ progenitor cells. PRMT6 is recruited to erythroid genes, such as glycophorin A. Consequently, a repressive histone modification pattern with high H3R2me2a and low H3K4me3 is established. Importantly, inhibition of PRMT6 by shRNA or small molecule inhibitors leads to upregulation of erythroid genes and promotes erythropoiesis. Our data reveal that PRMT6 plays a role in the control of erythroid/megakaryocytic differentiation and open up the possibility that manipulation of PRMT6 activity could facilitate enhanced erythropoiesis for therapeutic use.
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Affiliation(s)
- Stefanie C Herkt
- Institute for Transfusion Medicine and Immunohematology, Goethe-University and German Red Cross Blood Service, Frankfurt am Main
| | - Olga N Kuvardina
- Institute for Transfusion Medicine and Immunohematology, Goethe-University and German Red Cross Blood Service, Frankfurt am Main
| | - Julia Herglotz
- Institute for Transfusion Medicine and Immunohematology, Goethe-University and German Red Cross Blood Service, Frankfurt am Main
| | - Lucas Schneider
- Institute for Transfusion Medicine and Immunohematology, Goethe-University and German Red Cross Blood Service, Frankfurt am Main
| | - Annekarin Meyer
- Institute for Transfusion Medicine and Immunohematology, Goethe-University and German Red Cross Blood Service, Frankfurt am Main
| | | | | | - Erhard Seifried
- Institute for Transfusion Medicine and Immunohematology, Goethe-University and German Red Cross Blood Service, Frankfurt am Main
| | - Halvard Bonig
- Institute for Transfusion Medicine and Immunohematology, Goethe-University and German Red Cross Blood Service, Frankfurt am Main
| | - Jörn Lausen
- Institute for Transfusion Medicine and Immunohematology, Goethe-University and German Red Cross Blood Service, Frankfurt am Main
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10
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Structure of Nascent Chromatin Is Essential for Hematopoietic Lineage Specification. Cell Rep 2017; 19:295-306. [PMID: 28402853 DOI: 10.1016/j.celrep.2017.03.035] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 12/28/2016] [Accepted: 03/09/2017] [Indexed: 12/12/2022] Open
Abstract
The role of chromatin structure in lineage commitment of multipotent hematopoietic progenitors (HPCs) is presently unclear. We show here that CD34+ HPCs possess a post-replicative chromatin globally devoid of the repressive histone mark H3K27me3. This H3K27-unmodified chromatin is required for recruitment of lineage-determining transcription factors (TFs) C/EBPα, PU.1, and GATA-1 to DNA just after DNA replication upon cytokine-induced myeloid or erythroid commitment. Blocking DNA replication or increasing H3K27me3 levels prevents recruitment of these TFs to DNA and suppresses cytokine-induced erythroid or myeloid differentiation. However, H3K27me3 is rapidly associated with nascent DNA in more primitive human and murine HPCs. Treatment of these cells with instructive cytokines leads to a significant delay in accumulation of H3K27me3 in nascent chromatin due to activity of the H3K27me3 demethylase UTX. Thus, HPCs utilize special mechanisms of chromatin modification for recruitment of specific TFs to DNA during early stages of lineage specification.
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11
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Priam P, Krasteva V, Rousseau P, D'Angelo G, Gaboury L, Sauvageau G, Lessard JA. SMARCD2 subunit of SWI/SNF chromatin-remodeling complexes mediates granulopoiesis through a CEBPɛ dependent mechanism. Nat Genet 2017; 49:753-764. [PMID: 28369034 DOI: 10.1038/ng.3812] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 02/14/2017] [Indexed: 12/15/2022]
Abstract
Recent studies suggest that individual subunits of chromatin-remodeling complexes produce biologically specific meaning in different cell types through combinatorial assembly. Here we show that granulocyte development requires SMARCD2, a subunit of ATP-dependent SWI/SNF (BAF) chromatin-remodeling complexes. Smarcd2-deficient mice fail to generate functionally mature neutrophils and eosinophils, a phenotype reminiscent of neutrophil-specific granule deficiency (SGD) in humans, for which loss-of-function mutations in CEBPE (encoding CEBPɛ) have been reported. SMARCD2-containing SWI/SNF complexes are necessary for CEBPɛ transcription factor recruitment to the promoter of neutrophilic secondary granule genes and for granulocyte differentiation. The homologous SMARCD1 protein (63% identical at the amino acid level) cannot replace the role of SMARCD2 in granulocyte development. We find that SMARCD2 functional specificity is conferred by its divergent coiled-coil 1 and SWIB domains. Strikingly, both CEBPE and SMARCD2 loss-of-function mutations identified in patients with SGD abolish the interaction with SWI/SNF and thereby secondary granule gene expression, thus providing a molecular basis for this disease.
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Affiliation(s)
- Pierre Priam
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, Quebec, Canada.,Department of Pathology and Cellular Biology, Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Veneta Krasteva
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, Quebec, Canada.,Department of Pathology and Cellular Biology, Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Philippe Rousseau
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, Quebec, Canada
| | - Giovanni D'Angelo
- Division of Hematology-Oncology, Maisonneuve-Rosemont Hospital, Montreal, Quebec, Canada
| | - Louis Gaboury
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, Quebec, Canada.,Department of Pathology and Cellular Biology, Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Guy Sauvageau
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, Quebec, Canada.,Division of Hematology-Oncology, Maisonneuve-Rosemont Hospital, Montreal, Quebec, Canada.,Leukemia Cell Bank of Quebec, Maisonneuve-Rosemont Hospital, Montreal, Quebec, Canada.,Department of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Julie A Lessard
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, Quebec, Canada.,Department of Pathology and Cellular Biology, Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
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12
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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: 0.8] [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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13
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Bertolino E, Reinitz J, Manu. The analysis of novel distal Cebpa enhancers and silencers using a transcriptional model reveals the complex regulatory logic of hematopoietic lineage specification. Dev Biol 2016; 413:128-44. [PMID: 26945717 DOI: 10.1016/j.ydbio.2016.02.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 01/13/2016] [Accepted: 02/15/2016] [Indexed: 11/25/2022]
Abstract
C/EBPα plays an instructive role in the macrophage-neutrophil cell-fate decision and its expression is necessary for neutrophil development. How Cebpa itself is regulated in the myeloid lineage is not known. We decoded the cis-regulatory logic of Cebpa, and two other myeloid transcription factors, Egr1 and Egr2, using a combined experimental-computational approach. With a reporter design capable of detecting both distal enhancers and silencers, we analyzed 46 putative cis-regulatory modules (CRMs) in cells representing myeloid progenitors, and derived early macrophages or neutrophils. In addition to novel enhancers, this analysis revealed a surprisingly large number of silencers. We determined the regulatory roles of 15 potential transcriptional regulators by testing 32,768 alternative sequence-based transcriptional models against CRM activity data. This comprehensive analysis allowed us to infer the cis-regulatory logic for most of the CRMs. Silencer-mediated repression of Cebpa was found to be effected mainly by TFs expressed in non-myeloid lineages, highlighting a previously unappreciated contribution of long-distance silencing to hematopoietic lineage resolution. The repression of Cebpa by multiple factors expressed in alternative lineages suggests that hematopoietic genes are organized into densely interconnected repressive networks instead of hierarchies of mutually repressive pairs of pivotal TFs. More generally, our results demonstrate that de novo cis-regulatory dissection is feasible on a large scale with the aid of transcriptional modeling. Current address: Department of Biology, University of North Dakota, 10 Cornell Street, Stop 9019, Grand Forks, ND 58202-9019, USA.
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Affiliation(s)
- Eric Bertolino
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA.
| | - John Reinitz
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA; Department of Statistics, The University of Chicago, Chicago, IL 60637, USA; Department of Ecology and Evolution and Institute of Genomics and Systems Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Manu
- Department of Ecology and Evolution and Institute of Genomics and Systems Biology, The University of Chicago, Chicago, IL 60637, USA; Department of Biology, University of North Dakota, 10 Cornell Street, Stop 9019, Grand Forks, ND 58202-9019, USA.
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14
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E2A Antagonizes PU.1 Activity through Inhibition of DNA Binding. BIOMED RESEARCH INTERNATIONAL 2016; 2016:3983686. [PMID: 26942192 PMCID: PMC4749766 DOI: 10.1155/2016/3983686] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 01/06/2016] [Indexed: 11/18/2022]
Abstract
Antagonistic interactions between transcription factors contribute to cell fate decisions made by multipotent hematopoietic progenitor cells. Concentration of the transcription factor PU.1 affects myeloid/lymphoid development with high levels of PU.1 directing myeloid cell fate acquisition at the expense of B cell differentiation. High levels of PU.1 may be required for myelopoiesis in order to overcome inhibition of its activity by transcription factors that promote B cell development. The B cell transcription factors, E2A and EBF, are necessary for commitment of multipotential progenitors and lymphoid primed multipotential progenitors to lymphocytes. In this report we hypothesized that factors required for early B cell commitment would bind to PU.1 and antagonize its ability to induce myeloid differentiation. We investigated whether E2A and/or EBF associate with PU.1. We observed that the E2A component, E47, but not EBF, directly binds to PU.1. Additionally E47 represses PU.1-dependent transactivation of the MCSFR promoter through antagonizing PU.1's ability to bind to DNA. Exogenous E47 expression in hematopoietic cells inhibits myeloid differentiation. Our data suggest that E2A antagonism of PU.1 activity contributes to its ability to commit multipotential hematopoietic progenitors to the lymphoid lineages.
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15
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Bartels M, Murphy K, Rieter E, Bruin M. Understanding chronic neutropenia: life is short. Br J Haematol 2015; 172:157-69. [PMID: 26456767 DOI: 10.1111/bjh.13798] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The pathophysiological mechanisms underlying chronic neutropenia are extensive, varying from haematopoietic stem cell disorders resulting in defective neutrophil production, to accelerated apoptosis of neutrophil progenitors or circulating mature neutrophils. While the knowledge concerning genetic defects associated with congenital neutropenia or bone marrow failure is increasing rapidly, the functional role and consequences of these genetic alterations is often not well understood. In addition, there is a large group of diseases, including primary immunodeficiencies and metabolic diseases, in which chronic neutropenia is one of the symptoms, while there is no clear bone marrow pathology or haematopoietic stem cell dysfunction. Altogether, these disease entities illustrate the complexity of normal neutrophil development, the functional role of the (bone marrow) microenvironment and the increased propensity to undergo apoptosis, which is typical for neutrophils. The large variety of disorders associated with chronic neutropenia makes classification almost impossible and possibly not desirable, based on the clinical phenotypes. However, a better understanding of the regulation of normal myeloid differentiation and neutrophil development is of great importance in the diagnostic evaluation of unexplained chronic neutropenia. In this review we propose insights in the pathophysiology of chronic neutropenia in the context of the functional role of key players during normal neutrophil development, neutrophil release and neutrophil survival.
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Affiliation(s)
- Marije Bartels
- Department of Paediatric Haematology and Stem Cell Transplantation, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Kate Murphy
- Department of Paediatric Haematology and Stem Cell Transplantation, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Ester Rieter
- Department of Paediatric Haematology and Stem Cell Transplantation, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Marrie Bruin
- Department of Paediatric Haematology and Stem Cell Transplantation, University Medical Centre Utrecht, Utrecht, the Netherlands
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16
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Qian F, Deng J, Lee YG, Zhu J, Karpurapu M, Chung S, Zheng JN, Xiao L, Park GY, Christman JW. The transcription factor PU.1 promotes alternative macrophage polarization and asthmatic airway inflammation. J Mol Cell Biol 2015; 7:557-67. [PMID: 26101328 DOI: 10.1093/jmcb/mjv042] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 02/10/2015] [Indexed: 12/25/2022] Open
Abstract
The transcription factor PU.1 is involved in regulation of macrophage differentiation and maturation. However, the role of PU.1 in alternatively activated macrophage (AAM) and asthmatic inflammation has yet been investigated. Here we report that PU.1 serves as a critical regulator of AAM polarization and promotes the pathological progress of asthmatic airway inflammation. In response to the challenge of DRA (dust mite, ragweed, and Aspergillus) allergens, conditional PU.1-deficient (PU/ER(T)(+/-)) mice displayed attenuated allergic airway inflammation, including decreased alveolar eosinophil infiltration and reduced production of IgE, which were associated with decreased mucous glands and goblet cell hyperplasia. The reduced asthmatic inflammation in PU/ER(T)(+/-) mice was restored by adoptive transfer of IL-4-induced wild-type (WT) macrophages. Moreover, after treating PU/ER(T)(+/-) mice with tamoxifen to rescue PU.1 function, the allergic asthmatic inflammation was significantly restored. In vitro studies demonstrate that treatment of PU.1-deficient macrophages with IL-4 attenuated the expression of chitinase 3-like 3 (Ym-1) and resistin-like molecule alpha 1 (Fizz-1), two specific markers of AAM polarization. In addition, PU.1 expression in macrophages was inducible in response to IL-4 challenge, which was associated with phosphorylation of signal transducer and activator of transcription 6 (STAT6). Furthermore, DRA challenge in sensitized mice almost abrogated gene expression of Ym-1 and Fizz-1 in lung tissues of PU/ER(T)(+/-) mice compared with WT mice. These data, all together, indicate that PU.1 plays a critical role in AAM polarization and asthmatic inflammation.
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Affiliation(s)
- Feng Qian
- School of Pharmacy, Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China Department of Internal Medicine, Section of Pulmonary, Allergy, Critical Care, and Sleep Medicine, The Ohio State University, Columbus, USA
| | - Jing Deng
- Department of Internal Medicine, Section of Pulmonary, Allergy, Critical Care, and Sleep Medicine, The Ohio State University, Columbus, USA
| | - Yong Gyu Lee
- Department of Internal Medicine, Section of Pulmonary, Allergy, Critical Care, and Sleep Medicine, The Ohio State University, Columbus, USA
| | - Jimmy Zhu
- Department of Physiology and Biophysics, College of Medicine, University of Illinois at Chicago, Chicago, USA
| | - Manjula Karpurapu
- Department of Internal Medicine, Section of Pulmonary, Allergy, Critical Care, and Sleep Medicine, The Ohio State University, Columbus, USA
| | - Sangwoon Chung
- Department of Internal Medicine, Section of Pulmonary, Allergy, Critical Care, and Sleep Medicine, The Ohio State University, Columbus, USA
| | - Jun-Nian Zheng
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical College, Xuzhou, China
| | - Lei Xiao
- Department of Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, University of Illinois at Chicago, Chicago, USA
| | - Gye Young Park
- Department of Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, University of Illinois at Chicago, Chicago, USA
| | - John W Christman
- Department of Internal Medicine, Section of Pulmonary, Allergy, Critical Care, and Sleep Medicine, The Ohio State University, Columbus, USA
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17
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Abstract
C/EBPε, a member of the CCAAT/enhancer binding protein (C/EBP) family of transcription factors, is exclusively expressed in myeloid cells and regulates transition from the promyelocytic stage to the myelocytic stage of neutrophil development, being indispensable for secondary and tertiary granule formation. Knowledge concerning the functional role of C/EBPε posttranslational modifications is limited to studies concerning phosphorylation and sumoylation. In the current study, using ectopic expression and ex vivo differentiation of CD34(+) hematopoietic progenitor cells, we demonstrate that C/EBPε is acetylated, which was confirmed by mass spectrometry analysis, identifying 4 acetylated lysines in 3 distinct functional domains. Regulation of C/EBPε acetylation levels by the p300 acetyltransferase and the sirtuin 1 deacetylase controls transcriptional activity, which can at least in part be explained by modulation of DNA binding. During neutrophil development, acetylation of lysines 121 and 198 were found to be crucial for terminal neutrophil differentiation and the expression of neutrophil-specific granule proteins, including lactoferrin and collagenase. Taken together, our data illustrate a critical role for acetylation in the functional regulation of C/EBPε activity during terminal neutrophil development.
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18
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Gutknecht MF, Bouton AH. Functional significance of mononuclear phagocyte populations generated through adult hematopoiesis. J Leukoc Biol 2014; 96:969-80. [PMID: 25225678 PMCID: PMC4226790 DOI: 10.1189/jlb.1ri0414-195r] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 08/14/2014] [Accepted: 08/15/2014] [Indexed: 12/23/2022] Open
Abstract
Tissue homeostasis requires a complete repertoire of functional macrophages in peripheral tissues. Recent evidence indicates that many resident tissue macrophages are seeded during embryonic development and persist through adulthood as a consequence of localized proliferation. Mononuclear phagocytes are also produced during adult hematopoiesis; these cells are then recruited to sites throughout the body, where they function in tissue repair and remodeling, resolution of inflammation, maintenance of homeostasis, and disease progression. The focus of this review is on mononuclear phagocytes that comprise the nonresident monocyte/macrophage populations in the body. Key features of monocyte differentiation are presented, focusing primarily on the developmental hierarchy that is established through this process, the markers used to identify discrete cell populations, and novel, functional attributes of these cells. These features are then explored in the context of the tumor microenvironment, where mononuclear phagocytes exhibit extensive plasticity in phenotype and function.
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Affiliation(s)
- Michael F Gutknecht
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Amy H Bouton
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
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19
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Schnöder TM, Arreba-Tutusaus P, Griehl I, Bullinger L, Buschbeck M, Lane SW, Döhner K, Plass C, Lipka DB, Heidel FH, Fischer T. Epo-induced erythroid maturation is dependent on Plcγ1 signaling. Cell Death Differ 2014; 22:974-85. [PMID: 25394487 DOI: 10.1038/cdd.2014.186] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 09/18/2014] [Accepted: 10/06/2014] [Indexed: 12/22/2022] Open
Abstract
Erythropoiesis is a tightly regulated process. Development of red blood cells occurs through differentiation of hematopoietic stem cells (HSCs) into more committed progenitors and finally into erythrocytes. Binding of erythropoietin (Epo) to its receptor (EpoR) is required for erythropoiesis as it promotes survival and late maturation of erythroid progenitors. In vivo and in vitro studies have highlighted the requirement of EpoR signaling through Janus kinase 2 (Jak2) tyrosine kinase and Stat5a/b as a central pathway. Here, we demonstrate that phospholipase C gamma 1 (Plcγ1) is activated downstream of EpoR-Jak2 independently of Stat5. Plcγ1-deficient pro-erythroblasts and erythroid progenitors exhibited strong impairment in differentiation and colony-forming potential. In vivo, suppression of Plcγ1 in immunophenotypically defined HSCs (Lin(-)Sca1(+)KIT(+)CD48(-)CD150(+)) severely reduced erythroid development. To identify Plcγ1 effector molecules involved in regulation of erythroid differentiation, we assessed changes occurring at the global transcriptional and DNA methylation level after inactivation of Plcγ1. The top common downstream effector was H2afy2, which encodes for the histone variant macroH2A2 (mH2A2). Inactivation of mH2A2 expression recapitulated the effects of Plcγ1 depletion on erythroid maturation. Taken together, our findings identify Plcγ1 and its downstream target mH2A2, as a 'non-canonical' Epo signaling pathway essential for erythroid differentiation.
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Affiliation(s)
- T M Schnöder
- Department of Hematology and Oncology, Center for Internal Medicine, Otto-von-Guericke University Medical Center, Magdeburg, Germany
| | - P Arreba-Tutusaus
- Department of Hematology and Oncology, Center for Internal Medicine, Otto-von-Guericke University Medical Center, Magdeburg, Germany
| | - I Griehl
- Department of Hematology and Oncology, Center for Internal Medicine, Otto-von-Guericke University Medical Center, Magdeburg, Germany
| | - L Bullinger
- Internal Medicine III, Department of Hematology/Oncology, University Hospital Ulm, Ulm, Germany
| | - M Buschbeck
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Campus Can Ruti, Badalona, Spain
| | - S W Lane
- Division of Immunology, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Australia
| | - K Döhner
- Internal Medicine III, Department of Hematology/Oncology, University Hospital Ulm, Ulm, Germany
| | - C Plass
- Division of Epigenomics and Cancer Risk Factors (C010), German Cancer Research Center, Heidelberg, Germany
| | - D B Lipka
- 1] Department of Hematology and Oncology, Center for Internal Medicine, Otto-von-Guericke University Medical Center, Magdeburg, Germany [2] Division of Epigenomics and Cancer Risk Factors (C010), German Cancer Research Center, Heidelberg, Germany
| | - F H Heidel
- Department of Hematology and Oncology, Center for Internal Medicine, Otto-von-Guericke University Medical Center, Magdeburg, Germany
| | - T Fischer
- Department of Hematology and Oncology, Center for Internal Medicine, Otto-von-Guericke University Medical Center, Magdeburg, Germany
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20
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Crespo I, Del Sol A. A general strategy for cellular reprogramming: the importance of transcription factor cross-repression. Stem Cells 2014; 31:2127-35. [PMID: 23873656 DOI: 10.1002/stem.1473] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 06/01/2013] [Accepted: 06/08/2013] [Indexed: 02/06/2023]
Abstract
Transcription factor cross-repression is an important concept in cellular differentiation. A bistable toggle switch constitutes a molecular mechanism that determines cellular commitment and provides stability to transcriptional programs of binary cell fate choices. Experiments support that perturbations of these toggle switches can interconvert these binary cell fate choices, suggesting potential reprogramming strategies. However, more complex types of cellular transitions could involve perturbations of combinations of different types of multistable motifs. Here, we introduce a method that generalizes the concept of transcription factor cross-repression to systematically predict sets of genes, whose perturbations induce cellular transitions between any given pair of cell types. Furthermore, to our knowledge, this is the first method that systematically makes these predictions without prior knowledge of potential candidate genes and pathways involved, providing guidance on systems where little is known. Given the increasing interest of cellular reprogramming in medicine and basic research, our method represents a useful computational methodology to assist researchers in the field in designing experimental strategies.
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Affiliation(s)
- Isaac Crespo
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362 Esch-Belval, University of Luxembourg, L-1511, Luxembourg, Luxembourg
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21
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Prange KHM, Singh AA, Martens JHA. The genome-wide molecular signature of transcription factors in leukemia. Exp Hematol 2014; 42:637-50. [PMID: 24814246 DOI: 10.1016/j.exphem.2014.04.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 04/22/2014] [Accepted: 04/23/2014] [Indexed: 01/08/2023]
Abstract
Transcription factors control expression of genes essential for the normal functioning of the hematopoietic system and regulate development of distinct blood cell types. During leukemogenesis, aberrant regulation of transcription factors such as RUNX1, CBFβ, MLL, C/EBPα, SPI1, GATA, and TAL1 is central to the disease. Here, we will discuss the mechanisms of transcription factor deregulation in leukemia and how in recent years next-generation sequencing approaches have helped to elucidate the molecular role of many of these aberrantly expressed transcription factors. We will focus on the complexes in which these factors reside, the role of posttranslational modification of these factors, their involvement in setting up higher order chromatin structures, and their influence on the local epigenetic environment. We suggest that only comprehensive knowledge on all these aspects will increase our understanding of aberrant gene expression in leukemia as well as open new entry points for therapeutic intervention.
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Affiliation(s)
- Koen H M Prange
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Abhishek A Singh
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Joost H A Martens
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands.
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22
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Kong XZ, Yin RH, Ning HM, Zheng WW, Dong XM, Yang Y, Xu FF, Li JJ, Zhan YQ, Yu M, Ge CH, Zhang JH, Chen H, Li CY, Yang XM. Effects of THAP11 on erythroid differentiation and megakaryocytic differentiation of K562 cells. PLoS One 2014; 9:e91557. [PMID: 24637716 PMCID: PMC3956667 DOI: 10.1371/journal.pone.0091557] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 02/13/2014] [Indexed: 12/16/2022] Open
Abstract
Hematopoiesis is a complex process regulated by sets of transcription factors in a stage-specific and context-dependent manner. THAP11 is a transcription factor involved in cell growth, ES cell pluripotency, and embryogenesis. Here we showed that THAP11 was down-regulated during erythroid differentiation but up-regulated during megakaryocytic differentiation of cord blood CD34+ cells. Overexpression of THAP11 in K562 cells inhibited the erythroid differentiation induced by hemin with decreased numbers of benzidine-positive cells and decreased mRNA levels of α-globin (HBA) and glycophorin A (GPA), and knockdown of THAP11 enhanced the erythroid differentiation. Conversely, THAP11 overexpression accelerated the megakaryocytic differentiation induced by phorbol myristate acetate (PMA) with increased percentage of CD41+ cells, increased numbers of 4N cells, and elevated CD61 mRNA levels, and THAP11 knockdown attenuated the megakaryocytic differentiation. The expression levels of transcription factors such as c-Myc, c-Myb, GATA-2, and Fli1 were changed by THAP11 overexpression. In this way, our results suggested that THAP11 reversibly regulated erythroid and megakaryocytic differentiation.
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Affiliation(s)
- Xiang-Zhen Kong
- Department of Pharmaceutical Engineering, Tianjin University, Tianjin, China
- Department of Biochemistry and Molecular Biology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Rong-Hua Yin
- Department of Biochemistry and Molecular Biology, Beijing Institute of Radiation Medicine, Beijing, China
- State Key Laboratory of Proteomics, Beijing, China
| | - Hong-Mei Ning
- Department of Hematopoietic Stem Cell Transplantation, Affiliated Hospital to Academy of Military Medical Sciences, Beijing, China
| | - Wei-Wei Zheng
- Department of Biochemistry and Molecular Biology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Xiao-Ming Dong
- Department of Pharmaceutical Engineering, Tianjin University, Tianjin, China
| | - Yang Yang
- Department of Chemistry, Purdue University, West Lafayette, Indiana, United States of America
| | - Fei-Fei Xu
- Department of Biochemistry and Molecular Biology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Jian-Jie Li
- Department of Pulmonary Neoplasms Internal Medicine, Affiliated Hospital to Academy of Military Medicine Sciences, Beijing, China
| | - Yi-Qun Zhan
- Department of Biochemistry and Molecular Biology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Miao Yu
- Department of Biochemistry and Molecular Biology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Chang-Hui Ge
- Department of Biochemistry and Molecular Biology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Jian-Hong Zhang
- Department of Biochemistry and Molecular Biology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Hui Chen
- Department of Biochemistry and Molecular Biology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Chang-Yan Li
- Department of Biochemistry and Molecular Biology, Beijing Institute of Radiation Medicine, Beijing, China
- State Key Laboratory of Proteomics, Beijing, China
- * E-mail: (XMY); (CYL)
| | - Xiao-Ming Yang
- Department of Pharmaceutical Engineering, Tianjin University, Tianjin, China
- Department of Biochemistry and Molecular Biology, Beijing Institute of Radiation Medicine, Beijing, China
- State Key Laboratory of Proteomics, Beijing, China
- * E-mail: (XMY); (CYL)
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23
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Bartels M, Calgarotto AK, Martens AC, Maso V, da Silva SL, Bierings MB, de Souza Queiroz ML, Coffer PJ. Differential effects of nitrostyrene derivatives on myelopoiesis involve regulation of C/EBPα and p38MAPK activity. PLoS One 2014; 9:e90586. [PMID: 24614182 PMCID: PMC3948686 DOI: 10.1371/journal.pone.0090586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 02/03/2014] [Indexed: 11/18/2022] Open
Abstract
Bone marrow failure syndromes and MDS represent a heterogenous group of diseases, characterized by ineffective myelopoiesis, the risk of clonal evolution and a generally poor response to chemotherapy-based treatment regimen. Nitrostyrene derivatives have been studied as protein phosphatase inhibitors in various tumor models. Pharmacological studies have identified nitrostyrene as the structural core underlying a pro-apoptotic effect in tumor cells, yet their effects on normal cells, including those of the hematopoietic system, are largely unknown. In this study, utilizing umbilical cord blood-derived myeloid progenitor cells, patient-derived bone marrow cells, and a (BALB/c) mouse model; we investigated the effects of treatment with two nitrostyrene derivatives (NTS1 and NTS2) on myeloid development. We demonstrate that these compounds stimulate the expansion and differentiation of myeloid progenitors in vitro and improve myeloid reconstitution after chemotherapy-induced bone marrow depletion in vitro and in vivo. These effects were accompanied by increased C/EBPα expression and activity and inhibition of the p38MAPK signalling pathway. Together, our data suggest that nitrostyrenes improve myelopoiesis and represent potential new treatment strategies for patients suffering from bone marrow failure syndromes, hypocellular myelodysplastic syndrome and chemotherapy-induced aplasia.
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Affiliation(s)
- Marije Bartels
- Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands; Division of Pediatrics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Andrana K Calgarotto
- Departamento de Farmacologica, Universidade Estadual de Campinas, Campinas/SP, Brazil
| | - Anton C Martens
- Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands; Department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Victor Maso
- Departamento de Farmacologica, Universidade Estadual de Campinas, Campinas/SP, Brazil
| | - Saulo L da Silva
- Departamento de Química, Universidade Federal de São João Del-Rei, Ouro Branco/MG, Brazil
| | - Marc B Bierings
- Division of Pediatrics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Paul J Coffer
- Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands; Division of Pediatrics, University Medical Center Utrecht, Utrecht, The Netherlands
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24
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Calvi LM, Link DC. Cellular complexity of the bone marrow hematopoietic stem cell niche. Calcif Tissue Int 2014; 94:112-24. [PMID: 24101231 PMCID: PMC3936515 DOI: 10.1007/s00223-013-9805-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 09/15/2013] [Indexed: 12/17/2022]
Abstract
The skeleton serves as the principal site for hematopoiesis in adult terrestrial vertebrates. The function of the hematopoietic system is to maintain homeostatic levels of all circulating blood cells, including myeloid cells, lymphoid cells, red blood cells, and platelets. This action requires the daily production of more than 500 billion blood cells. The vast majority of these cells are synthesized in the bone marrow, where they arise from a limited number of hematopoietic stem cells (HSCs) that are multipotent and capable of extensive self-renewal. These attributes of HSCs are best demonstrated by marrow transplantation, where even a single HSC can repopulate the entire hematopoietic system. HSCs are therefore adult stem cells capable of multilineage repopulation, poised between cell fate choices which include quiescence, self-renewal, differentiation, and apoptosis. While HSC fate choices are in part determined by multiple stochastic fluctuations of cell autonomous processes, according to the niche hypothesis, signals from the microenvironment are also likely to determine stem cell fate. While it had long been postulated that signals within the bone marrow could provide regulation of hematopoietic cells, it is only in the past decade that advances in flow cytometry and genetic models have allowed for a deeper understanding of the microenvironmental regulation of HSCs. In this review, we will highlight the cellular regulatory components of the HSC niche.
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Affiliation(s)
- Laura M Calvi
- Division of Endocrinology and Metabolism, Department of Medicine, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA,
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25
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Schuster MB, Frank AK, Bagger FO, Rapin N, Vikesaa J, Porse BT. Lack of the p42 form of C/EBPα leads to spontaneous immortalization and lineage infidelity of committed myeloid progenitors. Exp Hematol 2013; 41:882-893.e16. [PMID: 23831605 DOI: 10.1016/j.exphem.2013.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 06/06/2013] [Indexed: 01/10/2023]
Abstract
Acute myeloid leukemia (AML) develops via a multistep process involving several genetic and epigenetic events, which ultimately leads to the formation of a heterogeneous population of malignant cells, of which only a small subpopulation termed the leukemia initiating cell (LIC) is able to sustain the leukemia. The identity of the LIC is highly diverse and ranges from populations resembling hematopoietic stem cells or multipotent progenitors (MPPs) to more committed myeloid progenitors, and the question still remains whether this is a direct consequence of which cells are targets of the final transforming events. In this study, we use premalignant cells from a Cebpa mutant AML model, in which the LIC population resembles granulocyte-macrophage progenitors (GMPs), to show that premalignant GMPs undergo spontaneous immortalization with a high clonal frequency when cultured in vitro, suggesting that these cells constitute the target of the final transforming events. Furthermore, we show that premalignant GMPs are characterized by a distinct T cell gene expression signature correlating with an increased potential for differentiation toward the T cell lineage. These findings have implications for our understanding of the transcriptional wiring in premalignant myeloid progenitors and how this contributes to the development of AML.
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Affiliation(s)
- Mikkel B Schuster
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Denmark; Biotech Research and Innovation Center, University of Copenhagen, Copenhagen, Denmark; Danish Stem Cell Center, Faculty of Health Sciences, University of Copenhagen, Denmark
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26
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Antebi YE, Reich-Zeliger S, Hart Y, Mayo A, Eizenberg I, Rimer J, Putheti P, Pe'er D, Friedman N. Mapping differentiation under mixed culture conditions reveals a tunable continuum of T cell fates. PLoS Biol 2013; 11:e1001616. [PMID: 23935451 PMCID: PMC3728017 DOI: 10.1371/journal.pbio.1001616] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 06/14/2013] [Indexed: 12/17/2022] Open
Abstract
An experimental and theoretical study of T cell differentiation in response to mixed-input conditions reveals that cells can tune between Th1 and Th2 states through a continuum of mixed phenotypes. Cell differentiation is typically directed by external signals that drive opposing regulatory pathways. Studying differentiation under polarizing conditions, with only one input signal provided, is limited in its ability to resolve the logic of interactions between opposing pathways. Dissection of this logic can be facilitated by mapping the system's response to mixtures of input signals, which are expected to occur in vivo, where cells are simultaneously exposed to various signals with potentially opposing effects. Here, we systematically map the response of naïve T cells to mixtures of signals driving differentiation into the Th1 and Th2 lineages. We characterize cell state at the single cell level by measuring levels of the two lineage-specific transcription factors (T-bet and GATA3) and two lineage characteristic cytokines (IFN-γ and IL-4) that are driven by these transcription regulators. We find a continuum of mixed phenotypes in which individual cells co-express the two lineage-specific master regulators at levels that gradually depend on levels of the two input signals. Using mathematical modeling we show that such tunable mixed phenotype arises if autoregulatory positive feedback loops in the gene network regulating this process are gradual and dominant over cross-pathway inhibition. We also find that expression of the lineage-specific cytokines follows two independent stochastic processes that are biased by expression levels of the master regulators. Thus, cytokine expression is highly heterogeneous under mixed conditions, with subpopulations of cells expressing only IFN-γ, only IL-4, both cytokines, or neither. The fraction of cells in each of these subpopulations changes gradually with input conditions, reproducing the continuous internal state at the cell population level. These results suggest a differentiation scheme in which cells reflect uncertainty through a continuously tuneable mixed phenotype combined with a biased stochastic decision rather than a binary phenotype with a deterministic decision. During cell differentiation, progenitor cells respond to external signals that drive the expression of genes that are characteristic of the differentiated cell states. This process is controlled by gene regulatory networks that typically involve positive autoregulation and cross-inhibition between master regulators of the two differentiated states. Mapping the system's response to mixtures of external signals can help us to understand the operational logic of these binary cell fate decisions. Here, we study differentiation of CD4+ T cells into Th1 and Th2 lineages under mixed-input conditions, at the single cell level. We reveal that cell state is not restricted to a small number of well-defined phenotypes, but rather tunes through a continuum of mixed-phenotype states in which levels of lineage-specifying transcription factors gradually change with the levels of the two inputs. Using mathematical modeling we establish the conditions under which the system has one stable steady state that continuously tunes in response to changes in levels of the inputs. Results of this model qualitatively explain our experimental observations. We further characterize expression patterns of downstream lineage-specific genes—cytokines that are driven by the two master regulators upon cell re-stimulation. We find a highly heterogeneous population with cells expressing either one of the cytokines, both cytokines, or neither. Of note, the fraction of cells in these subpopulations continuously tunes with input levels, thus reproducing a tunable state at the cell population level. Our results can be explained by a two-stage scheme in which the gene regulatory network is responsible for a continuously tunable cell state, which is translated into a heterogeneous cytokine expression pattern through uncorrelated and biased stochastic processes.
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Affiliation(s)
- Yaron E. Antebi
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Yuval Hart
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Avi Mayo
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Inbal Eizenberg
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Jacob Rimer
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Prabhakar Putheti
- Transplantation Institute and Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Dana Pe'er
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Nir Friedman
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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27
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Panning data for gold: the search for master regulators of cell fate. Nat Methods 2013; 10:476-7. [PMID: 23722206 DOI: 10.1038/nmeth.2491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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28
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Mossadegh-Keller N, Sarrazin S, Kandalla PK, Espinosa L, Stanley ER, Nutt SL, Moore J, Sieweke MH. M-CSF instructs myeloid lineage fate in single haematopoietic stem cells. Nature 2013; 497:239-43. [PMID: 23575636 DOI: 10.1038/nature12026] [Citation(s) in RCA: 280] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 02/20/2013] [Indexed: 02/08/2023]
Abstract
Under stress conditions such as infection or inflammation the body rapidly needs to generate new blood cells that are adapted to the challenge. Haematopoietic cytokines are known to increase output of specific mature cells by affecting survival, expansion and differentiation of lineage-committed progenitors, but it has been debated whether long-term haematopoietic stem cells (HSCs) are susceptible to direct lineage-specifying effects of cytokines. Although genetic changes in transcription factor balance can sensitize HSCs to cytokine instruction, the initiation of HSC commitment is generally thought to be triggered by stochastic fluctuation in cell-intrinsic regulators such as lineage-specific transcription factors, leaving cytokines to ensure survival and proliferation of the progeny cells. Here we show that macrophage colony-stimulating factor (M-CSF, also called CSF1), a myeloid cytokine released during infection and inflammation, can directly induce the myeloid master regulator PU.1 and instruct myeloid cell-fate change in mouse HSCs, independently of selective survival or proliferation. Video imaging and single-cell gene expression analysis revealed that stimulation of highly purified HSCs with M-CSF in culture resulted in activation of the PU.1 promoter and an increased number of PU.1(+) cells with myeloid gene signature and differentiation potential. In vivo, high systemic levels of M-CSF directly stimulated M-CSF-receptor-dependent activation of endogenous PU.1 protein in single HSCs and induced a PU.1-dependent myeloid differentiation preference. Our data demonstrate that lineage-specific cytokines can act directly on HSCs in vitro and in vivo to instruct a change of cell identity. This fundamentally changes the current view of how HSCs respond to environmental challenge and implicates stress-induced cytokines as direct instructors of HSC fate.
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Affiliation(s)
- Noushine Mossadegh-Keller
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université, UM2, Campus de Luminy, Case 906, 13288 Marseille Cedex 09, France
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29
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Catacchio I, Berardi S, Reale A, De Luisi A, Racanelli V, Vacca A, Ria R. Evidence for bone marrow adult stem cell plasticity: properties, molecular mechanisms, negative aspects, and clinical applications of hematopoietic and mesenchymal stem cells transdifferentiation. Stem Cells Int 2013; 2013:589139. [PMID: 23606860 PMCID: PMC3625599 DOI: 10.1155/2013/589139] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 02/22/2013] [Indexed: 12/24/2022] Open
Abstract
In contrast to the pluripotent embryonic stem cells (ESCs) which are able to give rise to all cell types of the body, mammalian adult stem cells (ASCs) appeared to be more limited in their differentiation potential and to be committed to their tissue of origin. Recently, surprising new findings have contradicted central dogmas of commitment of ASCs by showing their plasticity to differentiate across tissue lineage boundaries, irrespective of classical germ layer designations. The present paper supports the plasticity of the bone marrow stem cells (BMSCs), bringing the most striking and the latest evidences of the transdifferentiation properties of the bone marrow hematopoietic and mesenchymal stem cells (BMHSCs, and BMMSCs), the two BM populations of ASCs better characterized. In addition, we report the possible mechanisms that may explain these events, outlining the clinical importance of these phenomena and the relative problems.
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Affiliation(s)
- Ivana Catacchio
- Department of Biomedical Sciences and Human Oncology, Section of Internal Medicine and Clinical Oncology, University of Bari Medical School, Policlinico, Piazza Giulio Cesare 11, I-70124 Bari, Italy
| | - Simona Berardi
- Department of Biomedical Sciences and Human Oncology, Section of Internal Medicine and Clinical Oncology, University of Bari Medical School, Policlinico, Piazza Giulio Cesare 11, I-70124 Bari, Italy
| | - Antonia Reale
- Department of Biomedical Sciences and Human Oncology, Section of Internal Medicine and Clinical Oncology, University of Bari Medical School, Policlinico, Piazza Giulio Cesare 11, I-70124 Bari, Italy
| | - Annunziata De Luisi
- Department of Biomedical Sciences and Human Oncology, Section of Internal Medicine and Clinical Oncology, University of Bari Medical School, Policlinico, Piazza Giulio Cesare 11, I-70124 Bari, Italy
| | - Vito Racanelli
- Department of Biomedical Sciences and Human Oncology, Section of Internal Medicine and Clinical Oncology, University of Bari Medical School, Policlinico, Piazza Giulio Cesare 11, I-70124 Bari, Italy
| | - Angelo Vacca
- Department of Biomedical Sciences and Human Oncology, Section of Internal Medicine and Clinical Oncology, University of Bari Medical School, Policlinico, Piazza Giulio Cesare 11, I-70124 Bari, Italy
| | - Roberto Ria
- Department of Biomedical Sciences and Human Oncology, Section of Internal Medicine and Clinical Oncology, University of Bari Medical School, Policlinico, Piazza Giulio Cesare 11, I-70124 Bari, Italy
- Department of Biomedical Sciences and Human Oncology, Section of Internal Medicine, University of Bari Medical School, Policlinico, Piazza Giulio Cesare 11, I-70124 Bari, Italy
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30
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Tanaka H, Naito T, Muroi S, Seo W, Chihara R, Miyamoto C, Kominami R, Taniuchi I. Epigenetic Thpok silencing limits the time window to choose CD4(+) helper-lineage fate in the thymus. EMBO J 2013; 32:1183-94. [PMID: 23481257 DOI: 10.1038/emboj.2013.47] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 02/06/2013] [Indexed: 12/17/2022] Open
Abstract
CD4(+) helper and CD8(+) cytotoxic T cells differentiate from common precursors in the thymus after T-cell receptor (TCR)-mediated selection. Commitment to the helper lineage depends on persistent TCR signals and expression of the ThPOK transcription factor, whereas a ThPOK cis-regulatory element, ThPOK silencer, represses Thpok gene expression during commitment to the cytotoxic lineage. Here, we show that silencer-mediated alterations of chromatin structures in cytotoxic-lineage thymocytes establish a repressive state that is epigenetically inherited in peripheral CD8(+) T cells even after removal of the silencer. When silencer activity is enhanced in helper-lineage cells, by increasing its copy number, a similar heritable Thpok silencing occurs. Epigenetic locking of the Thpok locus may therefore be an independent event from commitment to the cytotoxic lineage. These findings imply that long-lasting TCR signals are needed to establish stable Thpok expression activity to commit to helper T-cell fate and that full commitment to the helper lineage requires persistent reversal of silencer activity during a particular time window.
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Affiliation(s)
- Hirokazu Tanaka
- Laboratory for Transcriptional Regulation, RIKEN Research Center for Allergy and Immunology, Yokohama, Kanagawa 230-0045, Japan
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31
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Abstract
Enormous numbers of adult blood cells are constantly regenerated throughout life from hematopoietic stem cells through a series of progenitor stages. Accessibility, robust functional assays, well-established prospective isolation, and successful clinical application made hematopoiesis the classical mammalian stem cell system. Most of the basic concepts of stem cell biology have been defined in this system. At the same time, many long-standing disputes in hematopoiesis research illustrate our still limited understanding. Here we discuss the embryonic development and lifelong maintenance of the hematopoietic system, its cellular components, and some of the hypotheses about the molecular mechanisms involved in controlling hematopoietic cell fates.
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Affiliation(s)
- Michael A Rieger
- Georg-Speyer-Haus, Institute for Biomedical Research, Frankfurt (Main), Germany
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32
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Nizzardo M, Simone C, Falcone M, Riboldi G, Comi GP, Bresolin N, Corti S. Direct reprogramming of adult somatic cells into other lineages: past evidence and future perspectives. Cell Transplant 2012; 22:921-44. [PMID: 23044010 DOI: 10.3727/096368912x657477] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Direct reprogramming of an adult cell into another differentiated lineage-such as fibroblasts into neurons, cardiomyocytes, or blood cells-without passage through an undifferentiated pluripotent stage is a new area of research that has recently emerged alongside stem cell technology and induced pluripotent stem cell reprogramming; indeed, this avenue of investigation has begun to play a central role in basic biological research and regenerative medicine. Even though the field seems new, its origins go back to the 1980s when it was demonstrated that differentiated adult cells can be converted into another cell lineage through the overexpression of transcription factors, establishing mature cell plasticity. Here, we retrace transdifferentiation experiments from the discovery of master control genes to recent in vivo reprogramming of one somatic cell into another from the perspective of possible applications for the development of new therapeutic approaches for human diseases.
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Affiliation(s)
- Monica Nizzardo
- Department of Neurological Sciences, Dino Ferrari Centre, University of Milan, IRCCS Foundation Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
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33
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Halley JD, Smith-Miles K, Winkler DA, Kalkan T, Huang S, Smith A. Self-organizing circuitry and emergent computation in mouse embryonic stem cells. Stem Cell Res 2012; 8:324-33. [PMID: 22169460 DOI: 10.1016/j.scr.2011.11.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 10/13/2011] [Accepted: 11/02/2011] [Indexed: 01/28/2023] Open
Abstract
Pluripotency is a cellular state of multiple options. Here, we highlight the potential for self-organization to contribute to stem cell fate computation. A new way of considering regulatory circuitry is presented that describes the expression of each transcription factor (TF) as a branching process that propagates through time, interacting and competing with others. In a single cell, the interactions between multiple branching processes generate a collective process called 'critical-like self-organization'. We explain how this phenomenon provides a valid description of whole genome regulatory circuit dynamics. The hypothesis of exploratory stem cell decision-making proposes that critical-like self-organization (also called rapid self-organized criticality) provides the backbone for cell fate computation in regulative embryos and pluripotent stem cells. Unspecific amplification of TF expression is predicted to initiate this self-organizing circuitry, where cascades of gene expression propagate and may interact either synergistically or antagonistically. The emergent and highly dynamic circuitry is affected by various sources of selection pressure, such as the expression of TFs with disproportionate influence over other genes, and extrinsic biological and physical stimuli that differentially modulate particular gene expression cascades. Extrinsic conditions continuously trigger waves of transcription that ripple throughout regulatory networks on multiple spatiotemporal scales, providing the context within which circuitry self-organizes. In this framework, a distinction between instructive and selective mechanisms of fate determination is misleading because it is the 'interference pattern', rather than any single instructing or selecting factor, that is ultimately responsible for computing and directing cell fate. Using this framework, we consider whether the idea of a naïve ground state of pluripotency and that of a fluctuating transcriptome are compatible, and whether a ground state like that captured in vitro could exist in vivo.
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Affiliation(s)
- J D Halley
- Wellcome Trust Centre for Stem Cell Research, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK.
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34
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Rhee JM, Iannaccone PM. Mapping mouse hemangioblast maturation from headfold stages. Dev Biol 2012; 365:1-13. [PMID: 22426104 DOI: 10.1016/j.ydbio.2012.02.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Revised: 02/14/2012] [Accepted: 02/15/2012] [Indexed: 11/18/2022]
Abstract
The mouse posterior primitive streak at neural plate/headfold stages (NP/HF, ~7.5 dpc-8 dpc) represents an optimal window from which hemangioblasts can be isolated. We performed immunohistochemistry on this domain using established monoclonal antibodies for proteins that affect blood and endothelial fates. We demonstrate that HoxB4 and GATA1 are the first set of markers that segregate independently to endothelial or blood populations during NP/HF stages of mouse embryonic development. In a subset of cells, both proteins are co-expressed and immunoreactivities appear mutually excluded within nuclear spaces. We searched for this particular state at later sites of hematopoietic stem cell emergence, viz., the aorta-gonad-mesonephros (AGM) and the fetal liver at 10.5-11.5 dpc, and found that only a rare number of cells displayed this character. Based on this spatial-temporal argument, we propose that the earliest blood progenitors emerge either directly from the epiblast or through segregation within the allantoic core domain (ACD) through reduction of cell adhesion and pSmad1/5 nuclear signaling, followed by a stochastic decision toward a blood or endothelial fate that involves GATA1 and HoxB4, respectively. A third form in which binding distributions are balanced may represent a common condition shared by hemangioblasts and HSCs. We developed a heuristic model of hemangioblast maturation, in part, to be explicit about our assumptions.
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Affiliation(s)
- Jerry M Rhee
- Children's Memorial Research Center, Department of Pediatrics, Developmental Biology Program, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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35
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Ding X, Lin Q, Ensenat-Waser R, Rose-John S, Zenke M. Polycomb Group Protein Bmi1 Promotes Hematopoietic Cell Development from Embryonic Stem Cells. Stem Cells Dev 2012; 21:121-32. [DOI: 10.1089/scd.2010.0539] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Xiaolei Ding
- 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
| | - Qiong Lin
- 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
| | - Roberto Ensenat-Waser
- Joint Research Centre, Institute for Health and Consumer Protection, In Vitro Methods Unit, European Commission, Ispra, Italy
| | - Stefan Rose-John
- Institute of Biochemistry, Christian-Albrechts-University, Kiel, 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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36
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Kang K, Jung H, Nam S, Lim JS. NDRG2 Promotes GATA-1 Expression through Regulation of the JAK2/STAT Pathway in PMA-stimulated U937 Cells. Immune Netw 2011; 11:348-57. [PMID: 22346774 PMCID: PMC3275703 DOI: 10.4110/in.2011.11.6.348] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2011] [Revised: 10/18/2011] [Accepted: 10/29/2011] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND N-myc downstream-regulated gene 2 (NDRG2), a member of a newly described family of differentiation-related genes, has been characterized as a regulator of dendritic cells. However, the role of NDRG2 on the expression and activation of transcription factors in blood cells remains poorly understood. In this study, we investigated the effects of NDRG2 overexpression on GATA-1 expression in PMA-stimulated U937 cells. METHODS We generated NDRG2-overexpressing U937 cell line (U937-NDRG2) and treated the cells with PMA to investigate the role of NDRG2 on GATA-1 expression. RESULTS NDRG2 overexpression in U937 cells significantly induced GATA-1 expression in response to PMA stimulation. Interestingly, JAK2/STAT and BMP-4/Smad pathways associated with the induction of GATA-1 were activated in PMA-stimulated U937-NDRG2 cells. We found that the inhibition of JAK2 activation, but not of BMP-4/Smad signaling, can elicit a decrease of PMA-induced GATA-1 expression in U937-NDRG2 cells. CONCLUSION The results reveal that NDRG2 promotes the expression of GATA-1 through activation of the JAK2/STAT pathway, but not through the regulation of the BMP-4/Smad pathway in U937 cells. Our findings further suggest that NDRG2 may play a role as a regulator of erythrocyte and megakaryocyte differentiation during hematopoiesis.
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Affiliation(s)
- Kyeongah Kang
- Department of Biological Science and the Research Center for Women's Disease, Sookmyung Women's University, Seoul 140-742, Korea
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37
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Dynamic long-range chromatin interactions control Myb proto-oncogene transcription during erythroid development. EMBO J 2011; 31:986-99. [PMID: 22157820 PMCID: PMC3280550 DOI: 10.1038/emboj.2011.450] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Accepted: 11/16/2011] [Indexed: 12/31/2022] Open
Abstract
The key haematopoietic regulator Myb is essential for coordinating proliferation and differentiation. ChIP-Sequencing and Chromosome Conformation Capture (3C)-Sequencing were used to characterize the structural and protein-binding dynamics of the Myb locus during erythroid differentiation. In proliferating cells expressing Myb, enhancers within the Myb-Hbs1l intergenic region were shown to form an active chromatin hub (ACH) containing the Myb promoter and first intron. This first intron was found to harbour the transition site from transcription initiation to elongation, which takes place around a conserved CTCF site. Upon erythroid differentiation, Myb expression is downregulated and the ACH destabilized. We propose a model for Myb activation by distal enhancers dynamically bound by KLF1 and the GATA1/TAL1/LDB1 complex, which primarily function as a transcription elongation element through chromatin looping.
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38
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Sarrazin S, Sieweke M. Integration of cytokine and transcription factor signals in hematopoietic stem cell commitment. Semin Immunol 2011; 23:326-34. [DOI: 10.1016/j.smim.2011.08.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 08/19/2011] [Indexed: 02/03/2023]
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39
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Pluripotency factors in embryonic stem cells regulate differentiation into germ layers. Cell 2011; 145:875-89. [PMID: 21663792 DOI: 10.1016/j.cell.2011.05.017] [Citation(s) in RCA: 419] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 03/03/2011] [Accepted: 05/16/2011] [Indexed: 02/06/2023]
Abstract
Cell fate decisions are fundamental for development, but we do not know how transcriptional networks reorganize during the transition from a pluripotent to a differentiated cell state. Here, we asked how mouse embryonic stem cells (ESCs) leave the pluripotent state and choose between germ layer fates. By analyzing the dynamics of the transcriptional circuit that maintains pluripotency, we found that Oct4 and Sox2, proteins that maintain ESC identity, also orchestrate germ layer fate selection. Oct4 suppresses neural ectodermal differentiation and promotes mesendodermal differentiation; Sox2 inhibits mesendodermal differentiation and promotes neural ectodermal differentiation. Differentiation signals continuously and asymmetrically modulate Oct4 and Sox2 protein levels, altering their binding pattern in the genome, and leading to cell fate choice. The same factors that maintain pluripotency thus also integrate external signals and control lineage selection. Our study provides a framework for understanding how complex transcription factor networks control cell fate decisions in progenitor cells.
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40
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Krumsiek J, Marr C, Schroeder T, Theis FJ. Hierarchical differentiation of myeloid progenitors is encoded in the transcription factor network. PLoS One 2011; 6:e22649. [PMID: 21853041 PMCID: PMC3154193 DOI: 10.1371/journal.pone.0022649] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Accepted: 06/27/2011] [Indexed: 11/29/2022] Open
Abstract
Hematopoiesis is an ideal model system for stem cell biology with advanced experimental access. A systems view on the interactions of core transcription factors is important for understanding differentiation mechanisms and dynamics. In this manuscript, we construct a Boolean network to model myeloid differentiation, specifically from common myeloid progenitors to megakaryocytes, erythrocytes, granulocytes and monocytes. By interpreting the hematopoietic literature and translating experimental evidence into Boolean rules, we implement binary dynamics on the resulting 11-factor regulatory network. Our network contains interesting functional modules and a concatenation of mutual antagonistic pairs. The state space of our model is a hierarchical, acyclic graph, typifying the principles of myeloid differentiation. We observe excellent agreement between the steady states of our model and microarray expression profiles of two different studies. Moreover, perturbations of the network topology correctly reproduce reported knockout phenotypes in silico. We predict previously uncharacterized regulatory interactions and alterations of the differentiation process, and line out reprogramming strategies.
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Affiliation(s)
- Jan Krumsiek
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, München, Germany
| | - Carsten Marr
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, München, Germany
| | - Timm Schroeder
- Institute of Stem Cell Research, Helmholtz Zentrum München, München, Germany
| | - Fabian J. Theis
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, München, Germany
- Department of Mathematics, Technische Universität München, München, Germany
- * E-mail:
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41
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Capron C, Lacout C, Lécluse Y, Wagner-Ballon O, Kaushik AL, Cramer-Bordé E, Sablitzky F, Duménil D, Vainchenker W. LYL-1 deficiency induces a stress erythropoiesis. Exp Hematol 2011; 39:629-42. [PMID: 21420467 DOI: 10.1016/j.exphem.2011.02.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Revised: 02/02/2011] [Accepted: 02/26/2011] [Indexed: 11/19/2022]
Abstract
OBJECTIVE LYL-1 is a transcription factor containing a basic helix-loop-helix motif closely related to SCL/TAL-1, a regulator of erythroid differentiation. Because LYL-1 is expressed in erythroid cell populations, we addressed its role in erythropoiesis using knockin mice. MATERIALS AND METHODS Erythropoiesis of LYL-1(-/-) mice was studied by progenitor assays, flow cytometry, reconstitution assays, and functional tests. Expression of LYL-1, SCL, and GATA-1 was assessed at messenger RNA level by quantitative reverse transcription polymerase chain reaction. RESULTS LYL-1(-/-) mice displayed decreased erythropoiesis with a partial arrest in differentiation, and enhanced apoptosis associated with decreased Bcl-x(L) expression in the bone marrow (BM). In addition, LYL-1(-/-) BM cells were severely impaired in their abilities to reconstitute the erythroid lineage in competitive assays, suggesting a cell autonomous abnormality of erythropoiesis. In parallel, erythroid progenitor and precursor cells were significantly increased in the spleen of LYL-1(-/-) mice. Expression of LYL-1 was differentially regulated during maturation of erythroblasts and strikingly different between spleen- and BM-derived erythroblasts. Expression of LYL-1 decreased during erythroid differentiation in the spleen whereas it increased in the BM to reach the same level in mature erythroblasts as in the soleen. Loss of Lyl-1 expression was accompanied with an increase of SCL/TAL-1 and GATA-1 transcripts in spleen but not in BM-derived erythroblasts. Furthermore, phenylhydrazine-induced stress erythropoiesis was elevated in LYL-1(-/-) mice and mutant BM and spleen erythroid progenitors were hypersensitive to erythropoietin. CONCLUSIONS Taken together, these results suggest that LYL-1 plays a definite role in erythropoiesis, albeit with different effects in BM specifically regulating basal erythropoiesis, and spleen, controlling stress-induced erythropoiesis.
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Affiliation(s)
- Claude Capron
- INSERM U1009, IFR 54, Institut Gustave Roussy, Villejuif, France
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Bakshi R, Hassan MQ, Pratap J, Lian JB, Montecino MA, van Wijnen AJ, Stein JL, Imbalzano AN, Stein GS. The human SWI/SNF complex associates with RUNX1 to control transcription of hematopoietic target genes. J Cell Physiol 2010; 225:569-76. [PMID: 20506188 DOI: 10.1002/jcp.22240] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The acute myeloid leukemia 1 (AML1, RUNX1) transcription factor is a key regulator of hematopoietic differentiation that forms multi-protein complexes with co-regulatory proteins. These complexes are assembled at target gene promoters in nuclear microenvironments to mediate phenotypic gene expression and chromatin-related epigenetic modifications. Here, immunofluorescence microscopy and biochemical assays are used to show that RUNX1 associates with the human ATP-dependent SWI/SNF chromatin remodeling complex. The SWI/SNF subunits BRG1 and INI1 bind in vivo to RUNX1 target gene promoters (e.g., GMCSF, IL3, MCSF-R, MIP, and p21). These interactions correlate with histone modifications characteristic of active chromatin, including acetylated H4 and dimethylated H3 lysine 4. Downregulation of RUNX1 by RNA interference diminishes the binding of BRG1 and INI1 at selected target genes. Taken together, our findings indicate that RUNX1 interacts with the human SWI/SNF complex to control hematopoietic-specific gene expression.
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Affiliation(s)
- Rachit Bakshi
- Department of Cell Biology and Cancer Center, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
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Dumitriu B, Bhattaram P, Dy P, Huang Y, Quayum N, Jensen J, Lefebvre V. Sox6 is necessary for efficient erythropoiesis in adult mice under physiological and anemia-induced stress conditions. PLoS One 2010; 5:e12088. [PMID: 20711497 PMCID: PMC2918505 DOI: 10.1371/journal.pone.0012088] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2010] [Accepted: 07/15/2010] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Definitive erythropoiesis is a vital process throughout life. Both its basal activity under physiological conditions and its increased activity under anemia-induced stress conditions are highly stimulated by the hormone erythropoietin. The transcription factor Sox6 was previously shown to enhance fetal erythropoiesis together and beyond erythropoietin signaling, but its importance in adulthood and mechanisms of action remain unknown. We used here Sox6 conditional null mice and molecular assays to address these questions. METHODOLOGY/PRINCIPAL FINDINGS Sox6fl/flErGFPCre adult mice, which lacked Sox6 in erythroid cells, exhibited compensated anemia, erythroid cell developmental defects, and anisocytotic, short-lived red cells under physiological conditions, proving that Sox6 promotes basal erythropoiesis. Tamoxifen treatment of Sox6fl/flCaggCreER mice induced widespread inactivation of Sox6 in a timely controlled manner and resulted in erythroblast defects before reticulocytosis, demonstrating that impaired erythropoiesis is a primary cause rather than consequence of anemia in the absence of Sox6. Twenty five percent of Sox6fl/flErGFPCre mice died 4 or 5 days after induction of acute anemia with phenylhydrazine. The others recovered slowly. They promptly increased their erythropoietin level and amplified their erythroid progenitor pool, but then exhibited severe erythroblast and reticulocyte defects. Sox6 is thus essential in the maturation phase of stress erythropoiesis that follows the erythropoietin-dependent amplification phase. Sox6 inactivation resulted in upregulation of embryonic globin genes, but embryonic globin chains remained scarce and apparently inconsequential. Sox6 inactivation also resulted in downregulation of erythroid terminal markers, including the Bcl2l1 gene for the anti-apoptotic factor Bcl-xL, and in vitro assays indicated that Sox6 directly upregulates Bcl2l1 downstream of and beyond erythropoietin signaling. CONCLUSIONS/SIGNIFICANCE This study demonstrates that Sox6 is necessary for efficient erythropoiesis in adult mice under both basal and stress conditions. It is primarily involved in enhancing the survival rate and maturation process of erythroid cells and acts at least in part by upregulating Bcl2l1.
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Affiliation(s)
- Bogdan Dumitriu
- Department of Cell Biology and Orthopaedic Research Center, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, United States of America
- Department of Internal Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, United States of America
| | - Pallavi Bhattaram
- Department of Cell Biology and Orthopaedic Research Center, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, United States of America
| | - Peter Dy
- Department of Cell Biology and Orthopaedic Research Center, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, United States of America
| | - Yuanshuai Huang
- Department of Cell Biology and Orthopaedic Research Center, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, United States of America
| | - Nayeem Quayum
- Department of Stem Cell Biology and Regenerative Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, United States of America
| | - Jan Jensen
- Department of Stem Cell Biology and Regenerative Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, United States of America
| | - Véronique Lefebvre
- Department of Cell Biology and Orthopaedic Research Center, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, United States of America
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Krumsiek J, Pölsterl S, Wittmann DM, Theis FJ. Odefy--from discrete to continuous models. BMC Bioinformatics 2010; 11:233. [PMID: 20459647 PMCID: PMC2873544 DOI: 10.1186/1471-2105-11-233] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Accepted: 05/07/2010] [Indexed: 01/17/2023] Open
Abstract
Background Phenomenological information about regulatory interactions is frequently available and can be readily converted to Boolean models. Fully quantitative models, on the other hand, provide detailed insights into the precise dynamics of the underlying system. In order to connect discrete and continuous modeling approaches, methods for the conversion of Boolean systems into systems of ordinary differential equations have been developed recently. As biological interaction networks have steadily grown in size and complexity, a fully automated framework for the conversion process is desirable. Results We present Odefy, a MATLAB- and Octave-compatible toolbox for the automated transformation of Boolean models into systems of ordinary differential equations. Models can be created from sets of Boolean equations or graph representations of Boolean networks. Alternatively, the user can import Boolean models from the CellNetAnalyzer toolbox, GINSim and the PBN toolbox. The Boolean models are transformed to systems of ordinary differential equations by multivariate polynomial interpolation and optional application of sigmoidal Hill functions. Our toolbox contains basic simulation and visualization functionalities for both, the Boolean as well as the continuous models. For further analyses, models can be exported to SQUAD, GNA, MATLAB script files, the SB toolbox, SBML and R script files. Odefy contains a user-friendly graphical user interface for convenient access to the simulation and exporting functionalities. We illustrate the validity of our transformation approach as well as the usage and benefit of the Odefy toolbox for two biological systems: a mutual inhibitory switch known from stem cell differentiation and a regulatory network giving rise to a specific spatial expression pattern at the mid-hindbrain boundary. Conclusions Odefy provides an easy-to-use toolbox for the automatic conversion of Boolean models to systems of ordinary differential equations. It can be efficiently connected to a variety of input and output formats for further analysis and investigations. The toolbox is open-source and can be downloaded at http://cmb.helmholtz-muenchen.de/odefy.
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Affiliation(s)
- Jan Krumsiek
- Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Munich-Neuherberg, Germany
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Soler E, Andrieu-Soler C, de Boer E, Bryne JC, Thongjuea S, Stadhouders R, Palstra RJ, Stevens M, Kockx C, van Ijcken W, Hou J, Steinhoff C, Rijkers E, Lenhard B, Grosveld F. The genome-wide dynamics of the binding of Ldb1 complexes during erythroid differentiation. Genes Dev 2010; 24:277-89. [PMID: 20123907 DOI: 10.1101/gad.551810] [Citation(s) in RCA: 203] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
One of the complexes formed by the hematopoietic transcription factor Gata1 is a complex with the Ldb1 (LIM domain-binding protein 1) and Tal1 proteins. It is known to be important for the development and differentiation of the erythroid cell lineage and is thought to be implicated in long-range interactions. Here, the dynamics of the composition of the complex-in particular, the binding of the negative regulators Eto2 and Mtgr1-are studied, in the context of their genome-wide targets. This shows that the complex acts almost exclusively as an activator, binding a very specific combination of sequences, with a positioning relative to transcription start site, depending on the type of the core promoter. The activation is accompanied by a net decrease in the relative binding of Eto2 and Mtgr1. A Chromosome Conformation Capture sequencing (3C-seq) assay also shows that the binding of the Ldb1 complex marks genomic interaction sites in vivo. This establishes the Ldb1 complex as a positive regulator of the final steps of erythroid differentiation that acts through the shedding of negative regulators and the active interaction between regulatory sequences.
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Affiliation(s)
- Eric Soler
- Department of Cell Biology, Erasmus Medical Center, 3015GE Rotterdam, The Netherlands.
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Abstract
The ability to produce stem cells by induced pluripotency (iPS reprogramming) has rekindled an interest in earlier studies showing that transcription factors can directly convert specialized cells from one lineage to another. Lineage reprogramming has become a powerful tool to study cell fate choice during differentiation, akin to inducing mutations for the discovery of gene functions. The lessons learnt provide a rubric for how cells may be manipulated for therapeutic purposes.
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Yu M, Riva L, Xie H, Schindler Y, Moran TB, Cheng Y, Yu D, Hardison R, Weiss MJ, Orkin SH, Bernstein BE, Fraenkel E, Cantor AB. Insights into GATA-1-mediated gene activation versus repression via genome-wide chromatin occupancy analysis. Mol Cell 2009; 36:682-95. [PMID: 19941827 PMCID: PMC2800995 DOI: 10.1016/j.molcel.2009.11.002] [Citation(s) in RCA: 257] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Revised: 09/05/2009] [Accepted: 10/30/2009] [Indexed: 01/29/2023]
Abstract
The transcription factor GATA-1 is required for terminal erythroid maturation and functions as an activator or repressor depending on gene context. Yet its in vivo site selectivity and ability to distinguish between activated versus repressed genes remain incompletely understood. In this study, we performed GATA-1 ChIP-seq in erythroid cells and compared it to GATA-1-induced gene expression changes. Bound and differentially expressed genes contain a greater number of GATA-binding motifs, a higher frequency of palindromic GATA sites, and closer occupancy to the transcriptional start site versus nondifferentially expressed genes. Moreover, we show that the transcription factor Zbtb7a occupies GATA-1-bound regions of some direct GATA-1 target genes, that the presence of SCL/TAL1 helps distinguish transcriptional activation versus repression, and that polycomb repressive complex 2 (PRC2) is involved in epigenetic silencing of a subset of GATA-1-repressed genes. These data provide insights into GATA-1-mediated gene regulation in vivo.
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Affiliation(s)
- Ming Yu
- Department of Pediatric Hematology-Oncology, Children's Hospital Boston and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Laura Riva
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Huafeng Xie
- Department of Pediatric Hematology-Oncology, Children's Hospital Boston and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Yocheved Schindler
- Department of Pediatric Hematology-Oncology, Children's Hospital Boston and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Tyler B. Moran
- Department of Pediatric Hematology-Oncology, Children's Hospital Boston and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Yong Cheng
- Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Duonan Yu
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ross Hardison
- Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Mitchell J Weiss
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Stuart H. Orkin
- Department of Pediatric Hematology-Oncology, Children's Hospital Boston and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Bradley E. Bernstein
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School and the Broad Institute, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ernest Fraenkel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA, USA
| | - Alan B. Cantor
- Department of Pediatric Hematology-Oncology, Children's Hospital Boston and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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Loizou JI, Oser G, Shukla V, Sawan C, Murr R, Wang ZQ, Trumpp A, Herceg Z. Histone acetyltransferase cofactor Trrap is essential for maintaining the hematopoietic stem/progenitor cell pool. THE JOURNAL OF IMMUNOLOGY 2009; 183:6422-31. [PMID: 19880447 DOI: 10.4049/jimmunol.0901969] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The pool of hematopoietic stem/progenitor cells, which provide life-long reconstitution of all hematopoietic lineages, is tightly controlled and regulated by self-renewal and apoptosis. Histone modifiers and chromatin states are believed to govern establishment, maintenance, and propagation of distinct patterns of gene expression in stem cells, however the underlying mechanism remains poorly understood. In this study, we identified a role for the histone acetytransferase cofactor Trrap in the maintenance of hematopietic stem/progenitor cells. Conditional deletion of the Trrap gene in mice resulted in ablation of bone marrow and increased lethality. This was due to the depletion of early hematopoietic progenitors, including hematopoietic stem cells, via a cell-autonomous mechanism. Analysis of purified bone marrow progenitors revealed that these defects are associated with induction of p53-independent apoptosis and deregulation of Myc transcription factors. Together, this study has identified a critical role for Trrap in the mechanism that maintains hematopoietic stem cells and hematopoietic system, and underscores the importance of Trrap and histone modifications in tissue homeostasis.
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Affiliation(s)
- Joanna I Loizou
- International Agency for Research on Cancer (IARC), Lyon, France
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Ottersbach K, Smith A, Wood A, Göttgens B. Ontogeny of haematopoiesis: recent advances and open questions. Br J Haematol 2009; 148:343-55. [PMID: 19863543 DOI: 10.1111/j.1365-2141.2009.07953.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Unravelling the embryonic origins of the haematopoietic system has been the subject of sustained research for more than a century. Nevertheless, many important questions are still either unanswered or remain a matter of intense debate. Recent progress in mouse and embryonic stem cell model systems as well as imaging and post-genomic technologies has provided new insights into many of these open questions. Here we place into context recent reports on the anatomical site of blood stem cell emergence and, using red blood cells as an example, illustrate how the development of stem cells and the other blood lineages is both temporally and spatially decoupled. In addition, we outline how embryonic stem cell assays are increasingly used as a powerful surrogate for studying lineage relationships and developmental potential of early embryonic blood progenitors. Finally, we review how recent progress in the reconstruction of transcriptional regulatory networks is beginning to define the connectivity between key regulators that control early blood development. In light of these rapid recent advances, research into the embryonic origins of the haematopoietic system should remain one of the most vibrant disciplines within the wider field of haematology for the foreseeable future.
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Affiliation(s)
- Katrin Ottersbach
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
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Integrating extrinsic and intrinsic cues into a minimal model of lineage commitment for hematopoietic progenitors. PLoS Comput Biol 2009; 5:e1000518. [PMID: 19911036 PMCID: PMC2736398 DOI: 10.1371/journal.pcbi.1000518] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2009] [Accepted: 08/25/2009] [Indexed: 02/08/2023] Open
Abstract
Autoregulation of transcription factors and cross-antagonism between lineage-specific transcription factors are a recurrent theme in cell differentiation. An equally prevalent event that is frequently overlooked in lineage commitment models is the upregulation of lineage-specific receptors, often through lineage-specific transcription factors. Here, we use a minimal model that combines cell-extrinsic and cell-intrinsic elements of regulation in order to understand how both instructive and stochastic events can inform cell commitment decisions in hematopoiesis. Our results suggest that cytokine-mediated positive receptor feedback can induce a “switch-like” response to external stimuli during multilineage differentiation by providing robustness to both bipotent and committed states while protecting progenitors from noise-induced differentiation or decommitment. Our model provides support to both the instructive and stochastic theories of commitment: cell fates are ultimately driven by lineage-specific transcription factors, but cytokine signaling can strongly bias lineage commitment by regulating these inherently noisy cell-fate decisions with complex, pertinent behaviors such as ligand-mediated ultrasensitivity and robust multistability. The simulations further suggest that the kinetics of differentiation to a mature cell state can depend on the starting progenitor state as well as on the route of commitment that is chosen. Lastly, our model shows good agreement with lineage-specific receptor expression kinetics from microarray experiments and provides a computational framework that can integrate both classical and alternative commitment paths in hematopoiesis that have been observed experimentally. Complex biomolecular interaction pathways in signaling networks can lead to non-intuitive behaviors that can prove critical for the regulation and robustness of biological processes. In this work, we present a signaling topology that can generate dynamic responses that are particularly pertinent to cell commitment in hematopoiesis. Our minimal model explores fundamental questions of instructive signaling that have persisted in cell-fate decisions. We show that even when lineage commitment decisions are inherently noisy, external cytokine signals, amplified by receptor upregulation, can bias the lineage choices of a progenitor cell. The multipotent progenitor, based on its differentiation potential, can exhibit several layers of memory to provide stability to both intermediate and mature states and can potentially bypass canonical intermediate states in generating mature cell types. Thus, our model provides a computational framework that can accommodate both classical and non-classical commitment paths in hematopoiesis.
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