1
|
Subramanian S, Thoms JAI, Huang Y, Cornejo-Páramo P, Koch FC, Jacquelin S, Shen S, Song E, Joshi S, Brownlee C, Woll PS, Chacon-Fajardo D, Beck D, Curtis DJ, Yehson K, Antonenas V, O'Brien T, Trickett A, Powell JA, Lewis ID, Pitson SM, Gandhi MK, Lane SW, Vafaee F, Wong ES, Göttgens B, Alinejad-Rokny H, Wong JWH, Pimanda JE. Genome-wide transcription factor-binding maps reveal cell-specific changes in the regulatory architecture of human HSPCs. Blood 2023; 142:1448-1462. [PMID: 37595278 PMCID: PMC10651876 DOI: 10.1182/blood.2023021120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/06/2023] [Accepted: 07/25/2023] [Indexed: 08/20/2023] Open
Abstract
Hematopoietic stem and progenitor cells (HSPCs) rely on a complex interplay among transcription factors (TFs) to regulate differentiation into mature blood cells. A heptad of TFs (FLI1, ERG, GATA2, RUNX1, TAL1, LYL1, LMO2) bind regulatory elements in bulk CD34+ HSPCs. However, whether specific heptad-TF combinations have distinct roles in regulating hematopoietic differentiation remains unknown. We mapped genome-wide chromatin contacts (HiC, H3K27ac, HiChIP), chromatin modifications (H3K4me3, H3K27ac, H3K27me3) and 10 TF binding profiles (heptad, PU.1, CTCF, STAG2) in HSPC subsets (stem/multipotent progenitors plus common myeloid, granulocyte macrophage, and megakaryocyte erythrocyte progenitors) and found TF occupancy and enhancer-promoter interactions varied significantly across cell types and were associated with cell-type-specific gene expression. Distinct regulatory elements were enriched with specific heptad-TF combinations, including stem-cell-specific elements with ERG, and myeloid- and erythroid-specific elements with combinations of FLI1, RUNX1, GATA2, TAL1, LYL1, and LMO2. Furthermore, heptad-occupied regions in HSPCs were subsequently bound by lineage-defining TFs, including PU.1 and GATA1, suggesting that heptad factors may prime regulatory elements for use in mature cell types. We also found that enhancers with cell-type-specific heptad occupancy shared a common grammar with respect to TF binding motifs, suggesting that combinatorial binding of TF complexes was at least partially regulated by features encoded in DNA sequence motifs. Taken together, this study comprehensively characterizes the gene regulatory landscape in rare subpopulations of human HSPCs. The accompanying data sets should serve as a valuable resource for understanding adult hematopoiesis and a framework for analyzing aberrant regulatory networks in leukemic cells.
Collapse
Affiliation(s)
- Shruthi Subramanian
- School of Clinical Medicine, University of New South Wales, Sydney, Australia
| | - Julie A. I. Thoms
- School of Biomedical Sciences, University of New South Wales, Sydney, Australia
| | - Yizhou Huang
- Centre for Health Technologies and the School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
| | | | - Forrest C. Koch
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, Australia
| | | | - Sylvie Shen
- Bone Marrow Transplant Laboratory, NSW Health Pathology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Emma Song
- Bone Marrow Transplant Laboratory, NSW Health Pathology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Swapna Joshi
- School of Clinical Medicine, University of New South Wales, Sydney, Australia
| | - Chris Brownlee
- Mark Wainwright Analytical Centre, University of New South Wales, Sydney, Australia
| | - Petter S. Woll
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Diego Chacon-Fajardo
- Centre for Health Technologies and the School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
| | - Dominik Beck
- Centre for Health Technologies and the School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
| | - David J. Curtis
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia
| | - Kenneth Yehson
- Blood Transplant and Cell Therapies Laboratory, NSW Health Pathology, Westmead, NSW, Australia
| | - Vicki Antonenas
- Blood Transplant and Cell Therapies Laboratory, NSW Health Pathology, Westmead, NSW, Australia
| | | | - Annette Trickett
- Bone Marrow Transplant Laboratory, NSW Health Pathology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Jason A. Powell
- Centre for Cancer Biology, SA Pathology, University of South Australia, Adelaide, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, Australia
| | - Ian D. Lewis
- Centre for Cancer Biology, SA Pathology, University of South Australia, Adelaide, Australia
| | - Stuart M. Pitson
- Centre for Cancer Biology, SA Pathology, University of South Australia, Adelaide, Australia
| | - Maher K. Gandhi
- Blood Cancer Research Group, Mater Research, The University of Queensland, Brisbane, QLD, Australia
| | - Steven W. Lane
- Cancer Program, QIMR Berghofer Medical Research, Brisbane, Australia
| | - Fatemeh Vafaee
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, Australia
- UNSW Data Science Hub, University of New South Wales, Sydney, Australia
| | - Emily S. Wong
- Victor Chang Cardiac Research Institute, Sydney, Australia
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, Australia
| | - Berthold Göttgens
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
| | - Hamid Alinejad-Rokny
- BioMedical Machine Learning Lab, Graduate School of Biomedical Engineering, University of New South Wales, Sydney, Australia
| | - Jason W. H. Wong
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - John E. Pimanda
- School of Clinical Medicine, University of New South Wales, Sydney, Australia
- School of Biomedical Sciences, University of New South Wales, Sydney, Australia
- Haematology Department, Prince of Wales Hospital, Sydney, Australia
| |
Collapse
|
2
|
Sun Z, Fan J, Dang Y, Zhao Y. Enhancer in cancer pathogenesis and treatment. Genet Mol Biol 2023; 46:e20220313. [PMID: 37548349 PMCID: PMC10405138 DOI: 10.1590/1678-4685-gmb-2022-0313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 06/19/2023] [Indexed: 08/08/2023] Open
Abstract
Enhancers are essential cis-acting regulatory elements that determine cell identity and tumor progression. Enhancer function is dependent on the physical interaction between the enhancer and its target promoter inside its local chromatin environment. Enhancer reprogramming is an important mechanism in cancer pathogenesis and can be driven by both cis and trans factors. Super enhancers are acquired at oncogenes in numerous cancer types and represent potential targets for cancer treatment. BET and CDK inhibitors act through mechanisms of enhancer function and have shown promising results in therapy for various types of cancer. Genome editing is another way to reprogram enhancers in cancer treatment. The relationship between enhancers and cancer has been revised by several authors in the past few years, which mainly focuses on the mechanisms by which enhancers can impact cancer. Here, we emphasize SE's role in cancer pathogenesis and the new therapies involving epigenetic regulators (BETi and CDKi). We suggest that understanding mechanisms of activity would aid clinical success for these anti-cancer agents.
Collapse
Affiliation(s)
- Zhuo Sun
- Xi’an Medical University, Xi’an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Weiyang District, Xi’an, Shaanxi, China
- Institute of Basic Medical Sciences, No.1 XinWang Rd, Weiyang District, Shaanxi, China
| | - Jinbo Fan
- Xi’an Medical University, Xi’an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Weiyang District, Xi’an, Shaanxi, China
| | - Yixiong Dang
- Xi’an Medical University, School of Public Health, Weiyang District, Xi’an, 710021 Shaanxi, China
| | - Yufeng Zhao
- Institute of Basic Medical Sciences, No.1 XinWang Rd, Weiyang District, Shaanxi, China
| |
Collapse
|
3
|
Sharma A, Mistriel-Zerbib S, Najar RA, Engal E, Bentata M, Taqatqa N, Dahan S, Cohen K, Jaffe-Herman S, Geminder O, Baker M, Nevo Y, Plaschkes I, Kay G, Drier Y, Berger M, Salton M. Isoforms of the TAL1 transcription factor have different roles in hematopoiesis and cell growth. PLoS Biol 2023; 21:e3002175. [PMID: 37379322 DOI: 10.1371/journal.pbio.3002175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 05/30/2023] [Indexed: 06/30/2023] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) protein 1 (TAL1) is a central transcription factor in hematopoiesis. The timing and level of TAL1 expression orchestrate the differentiation to specialized blood cells and its overexpression is a common cause of T-ALL. Here, we studied the 2 protein isoforms of TAL1, short and long, which are generated by the use of alternative promoters as well as by alternative splicing. We analyzed the expression of each isoform by deleting an enhancer or insulator, or by opening chromatin at the enhancer location. Our results show that each enhancer promotes expression from a specific TAL1 promoter. Expression from a specific promoter gives rise to a unique 5' UTR with differential regulation of translation. Moreover, our study suggests that the enhancers regulate TAL1 exon 3 alternative splicing by inducing changes in the chromatin at the splice site, which we demonstrate is mediated by KMT2B. Furthermore, our results indicate that TAL1-short binds more strongly to TAL1 E-protein partners and functions as a stronger transcription factor than TAL1-long. Specifically TAL1-short has a unique transcription signature promoting apoptosis. Finally, when we expressed both isoforms in mice bone marrow, we found that while overexpression of both isoforms prevents lymphoid differentiation, expression of TAL-short alone leads to hematopoietic stem cell exhaustion. Furthermore, we found that TAL1-short promoted erythropoiesis and reduced cell survival in the CML cell line K562. While TAL1 and its partners are considered promising therapeutic targets in the treatment of T-ALL, our results show that TAL1-short could act as a tumor suppressor and suggest that altering TAL1 isoform's ratio could be a preferred therapeutic approach.
Collapse
Affiliation(s)
- Aveksha Sharma
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shani Mistriel-Zerbib
- Faculty of Medicine, The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Rauf Ahmad Najar
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eden Engal
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mercedes Bentata
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nadeen Taqatqa
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sara Dahan
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Klil Cohen
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shiri Jaffe-Herman
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ophir Geminder
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mai Baker
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yuval Nevo
- Info-CORE, Bioinformatics Unit of the I-CORE Computation Center, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Inbar Plaschkes
- Info-CORE, Bioinformatics Unit of the I-CORE Computation Center, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gillian Kay
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yotam Drier
- Faculty of Medicine, The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Michael Berger
- Faculty of Medicine, The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Maayan Salton
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| |
Collapse
|
4
|
Koh CP, Bahirvani AG, Wang CQ, Yokomizo T, Ng CEL, Du L, Tergaonkar V, Voon DCC, Kitamura H, Hosoi H, Sonoki T, Michelle MMH, Tan LJ, Niibori-Nambu A, Zhang Y, Perkins AS, Hossain Z, Tenen DG, Ito Y, Venkatesh B, Osato M. Highly efficient Runx1 enhancer eR1-mediated genetic engineering for fetal, child and adult hematopoietic stem cells. Gene 2023; 851:147049. [PMID: 36384171 PMCID: PMC10492510 DOI: 10.1016/j.gene.2022.147049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/06/2022] [Accepted: 11/08/2022] [Indexed: 11/15/2022]
Abstract
A cis-regulatory genetic element which targets gene expression to stem cells, termed stem cell enhancer, serves as a molecular handle for stem cell-specific genetic engineering. Here we show the generation and characterization of a tamoxifen-inducible CreERT2 transgenic (Tg) mouse employing previously identified hematopoietic stem cell (HSC) enhancer for Runx1, eR1 (+24 m). Kinetic analysis of labeled cells after tamoxifen injection and transplantation assays revealed that eR1-driven CreERT2 activity marks dormant adult HSCs which slowly but steadily contribute to unperturbed hematopoiesis. Fetal and child HSCs that are uniformly or intermediately active were also efficiently targeted. Notably, a gene ablation at distinct developmental stages, enabled by this system, resulted in different phenotypes. Similarly, an oncogenic Kras induction at distinct ages caused different spectrums of malignant diseases. These results demonstrate that the eR1-CreERT2 Tg mouse serves as a powerful resource for the analyses of both normal and malignant HSCs at all developmental stages.
Collapse
Affiliation(s)
- Cai Ping Koh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117456, Singapore; Department of Biochemistry, Faculty of Medicine, Quest International University, Perak 30250, Malaysia
| | - Avinash Govind Bahirvani
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117456, Singapore
| | - Chelsia Qiuxia Wang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117456, Singapore; Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore
| | - Tomomasa Yokomizo
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117456, Singapore; International Research Center for Medical Sciences, Kumamoto University, Kumamoto 860-0811, Japan
| | - Cherry Ee Lin Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117456, Singapore
| | - Linsen Du
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117456, Singapore
| | - Vinay Tergaonkar
- Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore
| | - Dominic Chih-Cheng Voon
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117456, Singapore; Cancer Research Institute, Kanazawa University, Ishikawa 920-1192, Japan; Institute for Frontier Science Initiative, Kanazawa University, Ishikawa 920-1192, Japan
| | - Hiroaki Kitamura
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117456, Singapore
| | - Hiroki Hosoi
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117456, Singapore; Department of Hematology/Oncology, Wakayama Medical University, Wakayama, Japan
| | - Takashi Sonoki
- Department of Hematology/Oncology, Wakayama Medical University, Wakayama, Japan
| | - Mok Meng Huang Michelle
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117456, Singapore
| | - Lii Jye Tan
- Department of Forensic Medicine, Hospital Raja Permaisuri Bainun, Ipoh, Perak Daruk Ridzuan, Malaysia
| | - Akiko Niibori-Nambu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117456, Singapore; Department of Tumor Genetics and Biology, Graduate School of Medical Sciences, Institute of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Yi Zhang
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY 14642, United States of America
| | - Archibald S Perkins
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY 14642, United States of America
| | - Zakir Hossain
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117456, Singapore
| | - Daniel G Tenen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117456, Singapore
| | - Yoshiaki Ito
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117456, Singapore
| | - Byrappa Venkatesh
- Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore.
| | - Motomi Osato
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117456, Singapore; International Research Center for Medical Sciences, Kumamoto University, Kumamoto 860-0811, Japan; Department of Pediatrics, National University of Singapore, Singapore 119228, Singapore.
| |
Collapse
|
5
|
Gao P, Chen C, Howell ED, Li Y, Tober J, Uzun Y, He B, Gao L, Zhu Q, Siekmann AF, Speck NA, Tan K. Transcriptional regulatory network controlling the ontogeny of hematopoietic stem cells. Genes Dev 2020; 34:950-964. [PMID: 32499402 PMCID: PMC7328518 DOI: 10.1101/gad.338202.120] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 04/28/2020] [Indexed: 12/27/2022]
Abstract
In this study from Gao et al., the authors performed RNA-seq and histone mark ChIP-seq to define the transcriptomes and epigenomes of cells representing key developmental stages of HSC ontogeny in mice. Using a novel computational algorithm, target inference via physical connection (TIPC), they constructed developmental stage-specific transcriptional regulatory networks by linking enhancers and predicted bound transcription factors to their target promoters, thus providing a useful resource for uncovering regulators of HSC formation. Hematopoietic stem cell (HSC) ontogeny is accompanied by dynamic changes in gene regulatory networks. We performed RNA-seq and histone mark ChIP-seq to define the transcriptomes and epigenomes of cells representing key developmental stages of HSC ontogeny in mice. The five populations analyzed were embryonic day 10.5 (E10.5) endothelium and hemogenic endothelium from the major arteries, an enriched population of prehematopoietic stem cells (pre-HSCs), fetal liver HSCs, and adult bone marrow HSCs. Using epigenetic signatures, we identified enhancers for each developmental stage. Only 12% of enhancers are primed, and 78% are active, suggesting the vast majority of enhancers are established de novo without prior priming in earlier stages. We constructed developmental stage-specific transcriptional regulatory networks by linking enhancers and predicted bound transcription factors to their target promoters using a novel computational algorithm, target inference via physical connection (TIPC). TIPC predicted known transcriptional regulators for the endothelial-to-hematopoietic transition, validating our overall approach, and identified putative novel transcription factors, including the broadly expressed transcription factors SP3 and MAZ. Finally, we validated a role for SP3 and MAZ in the formation of hemogenic endothelium. Our data and computational analyses provide a useful resource for uncovering regulators of HSC formation.
Collapse
Affiliation(s)
- Peng Gao
- Division of Oncology, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Changya Chen
- Division of Oncology, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Elizabeth D Howell
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Graduate Group in Cell and Molecular Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Yan Li
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Joanna Tober
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Yasin Uzun
- Division of Oncology, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Bing He
- Division of Oncology, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Long Gao
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Qin Zhu
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Arndt F Siekmann
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Nancy A Speck
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kai Tan
- Division of Oncology, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| |
Collapse
|
6
|
Rothenberg EV. Causal Gene Regulatory Network Modeling and Genomics: Second-Generation Challenges. J Comput Biol 2019; 26:703-718. [PMID: 31063008 DOI: 10.1089/cmb.2019.0098] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Gene regulatory network modeling has played a major role in advancing the understanding of developmental systems, by crystallizing structures of relevant extant information, by formally posing hypothetical functional relationships between network elements, and by offering clear predictive tests to improve understanding of the mechanisms driving developmental progression. Both ordinary differential equation (ODE)-based and Boolean models have also been highly successful in explaining dynamics within subcircuits of more complex processes. In a very small number of cases, gene regulatory network models of much more global scope have been proposed that successfully predict the dynamics of the processes establishing most of an embryonic body plan. Can such successes be expanded to very different developmental systems, including post-embryonic mammalian systems? This perspective discusses several problems that must be solved in more quantitative and predictive theoretical terms, to make this possible. These problems include: the effects of cellular history on chromatin state and how these affect gene accessibility; the dose dependence of activities of many transcription factors (a problem for Boolean models); stochasticity of some transcriptional outputs (a problem for simple ODE models); response timing delays due to epigenetic remodeling requirements; functionally different kinds of repression; and the regulatory syntax that governs responses of genes with multiple enhancers.
Collapse
Affiliation(s)
- Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
| |
Collapse
|
7
|
Essential roles for Cdx in murine primitive hematopoiesis. Dev Biol 2017; 422:115-124. [PMID: 28065741 DOI: 10.1016/j.ydbio.2017.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 01/03/2017] [Accepted: 01/04/2017] [Indexed: 11/24/2022]
Abstract
The Cdx transcription factors play essential roles in primitive hematopoiesis in the zebrafish where they exert their effects, in part, through regulation of hox genes. Defects in hematopoiesis have also been reported in Cdx mutant murine embryonic stem cell models, however, to date no mouse model reflecting the zebrafish Cdx mutant hematopoietic phenotype has been described. This is likely due, in part, to functional redundancy among Cdx members and the early lethality of Cdx2 null mutants. To circumvent these limitations, we used Cre-mediated conditional deletion to assess the impact of concomitant loss of Cdx1 and Cdx2 on murine primitive hematopoiesis. We found that Cdx1/Cdx2 double mutants exhibited defects in primitive hematopoiesis and yolk sac vasculature concomitant with reduced expression of several genes encoding hematopoietic transcription factors including Scl/Tal1. Chromatin immunoprecipitation analysis revealed that Scl was occupied by Cdx2 in vivo, and Cdx mutant hematopoietic yolk sac differentiation defects could be rescued by expression of exogenous Scl. These findings demonstrate critical roles for Cdx members in murine primitive hematopoiesis upstream of Scl.
Collapse
|
8
|
Cañete A, Comaills V, Prados I, Castro AM, Hammad S, Ybot-Gonzalez P, Bockamp E, Hengstler JG, Gottgens B, Sánchez MJ. Characterization of a Fetal Liver Cell Population Endowed with Long-Term Multiorgan Endothelial Reconstitution Potential. Stem Cells 2016; 35:507-521. [PMID: 27615355 PMCID: PMC5298023 DOI: 10.1002/stem.2494] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 07/27/2016] [Accepted: 08/10/2016] [Indexed: 12/26/2022]
Abstract
Stable reconstitution of vascular endothelial beds upon transplantation of progenitor cells represents an important challenge due to the paucity and generally limited integration/expansion potential of most identified vascular related cell subsets. We previously showed that mouse fetal liver (FL) hemato/vascular cells from day 12 of gestation (E12), expressing the Stem Cell Leukaemia (SCL) gene enhancer transgene (SCL‐PLAP+ cells), had robust endothelial engraftment potential when transferred to the blood stream of newborns or adult conditioned recipients, compared to the scarce vascular contribution of adult bone marrow cells. However, the specific SCL‐PLAP+ hematopoietic or endothelial cell subset responsible for the long‐term reconstituting endothelial cell (LTR‐EC) activity and its confinement to FL developmental stages remained unknown. Using a busulfan‐treated newborn transplantation model, we show that LTR‐EC activity is restricted to the SCL‐PLAP+VE‐cadherin+CD45− cell population, devoid of hematopoietic reconstitution activity and largely composed by Lyve1+ endothelial‐committed cells. SCL‐PLAP+ Ve‐cadherin+CD45− cells contributed to the liver sinusoidal endothelium and also to the heart, kidney and lung microvasculature. LTR‐EC activity was detected at different stages of FL development, yet marginal activity was identified in the adult liver, revealing unknown functional differences between fetal and adult liver endothelial/endothelial progenitors. Importantly, the observations that expanding donor‐derived vascular grafts colocalize with proliferating hepatocyte‐like cells and participate in the systemic circulation, support their functional integration into young livers. These findings offer new insights into the engraftment, phonotypical, and developmental characterization of a novel endothelial/endothelial progenitor cell subtype with multiorgan LTR‐EC activity, potentially instrumental for the treatment/genetic correction of vascular diseases. Stem Cells2017;35:507–521
Collapse
Affiliation(s)
- Ana Cañete
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas (CSIC), Junta de Andalucía (JA), Universidad Pablo de Olavide (UPO), Sevilla, Spain
| | - Valentine Comaills
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas (CSIC), Junta de Andalucía (JA), Universidad Pablo de Olavide (UPO), Sevilla, Spain
| | - Isabel Prados
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas (CSIC), Junta de Andalucía (JA), Universidad Pablo de Olavide (UPO), Sevilla, Spain
| | - Ana María Castro
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas (CSIC), Junta de Andalucía (JA), Universidad Pablo de Olavide (UPO), Sevilla, Spain
| | - Seddik Hammad
- Faculty of Veterinary Medicine, Department of Forensic Medicine and Veterinary Toxicology, South Valley University, Qena, Egypt.,Leibniz Research Center for Working Environment and Human Factors (IfADo), TU Dortmund University, Dortmund, Germany
| | - Patricia Ybot-Gonzalez
- Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío, CSIC, Universidad de Sevilla, Seville, Spain
| | - Ernesto Bockamp
- Institute of Translational Immunology, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Jan G Hengstler
- Leibniz Research Center for Working Environment and Human Factors (IfADo), TU Dortmund University, Dortmund, Germany
| | - Bertie Gottgens
- Cambridge Institute for Medical Research & Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge University, United Kingdom
| | - María José Sánchez
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas (CSIC), Junta de Andalucía (JA), Universidad Pablo de Olavide (UPO), Sevilla, Spain
| |
Collapse
|
9
|
Developing HSCs become Notch independent by the end of maturation in the AGM region. Blood 2016; 128:1567-77. [PMID: 27421959 DOI: 10.1182/blood-2016-03-708164] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 07/05/2016] [Indexed: 12/17/2022] Open
Abstract
The first definitive hematopoietic stem cells (dHSCs) in the mouse emerge in the dorsal aorta of the embryonic day (E) 10.5 to 11 aorta-gonad-mesonephros (AGM) region. Notch signaling is essential for early HSC development but is dispensable for the maintenance of adult bone marrow HSCs. How Notch signaling regulates HSC formation in the embryo is poorly understood. We demonstrate here that Notch signaling is active in E10.5 HSC precursors and involves both Notch1 and Notch2 receptors, but is gradually downregulated while they progress toward dHSCs at E11.5. This downregulation is accompanied by gradual functional loss of Notch dependency. Thus, as early as at final steps in the AGM region, HSCs begin acquiring the Notch independency characteristic of adult bone marrow HSCs as part of the maturation program. Our data indicate that fine stage-dependent tuning of Notch signaling may be required for the generation of definitive HSCs from pluripotent cells.
Collapse
|
10
|
The bulk of the hematopoietic stem cell population is dispensable for murine steady-state and stress hematopoiesis. Blood 2016; 128:2285-2296. [PMID: 27357698 DOI: 10.1182/blood-2016-03-706010] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 06/22/2016] [Indexed: 12/12/2022] Open
Abstract
Long-term repopulating (LT) hematopoietic stem cells (HSCs) are the most undifferentiated cells at the top of the hematopoietic hierarchy. The regulation of HSC pool size and its contribution to hematopoiesis are incompletely understood. We depleted hematopoietic stem and progenitor cells (HSPCs) in adult mice in situ and found that LT-HSCs recovered from initially very low levels (<1%) to below 10% of normal numbers but not more, whereas progenitor cells substantially recovered shortly after depletion. In spite of the persistent and massive reduction of LT-HSCs, steady-state hematopoiesis was unaffected and residual HSCs remained quiescent. Hematopoietic stress, although reported to recruit quiescent HSCs into cycle, was well tolerated by HSPC-depleted mice and did not induce expansion of the small LT-HSC compartment. Only upon 5-fluorouracil treatment was HSPC-depleted bone marrow compromised in reconstituting hematopoiesis, demonstrating that HSCs and early progenitors are crucial to compensate myeloablation. Hence, a contracted HSC compartment cannot recover in situ to its original size, and normal steady-state blood cell generation is sustained with <10% of normal LT-HSC numbers without increased contribution of the few residual cells.
Collapse
|
11
|
Stem Cell Leukemia: how a TALented actor can go awry on the hematopoietic stage. Leukemia 2016; 30:1968-1978. [DOI: 10.1038/leu.2016.169] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 05/18/2016] [Accepted: 05/23/2016] [Indexed: 02/06/2023]
|
12
|
Höfer T, Busch K, Klapproth K, Rodewald HR. Fate Mapping and Quantitation of Hematopoiesis In Vivo. Annu Rev Immunol 2016; 34:449-78. [DOI: 10.1146/annurev-immunol-032414-112019] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany;
| | - Katrin Busch
- Division of Cellular Immunology, German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany;
| | - Kay Klapproth
- Division of Cellular Immunology, German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany;
| | - Hans-Reimer Rodewald
- Division of Cellular Immunology, German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany;
| |
Collapse
|
13
|
Schütte J, Wang H, Antoniou S, Jarratt A, Wilson NK, Riepsaame J, Calero-Nieto FJ, Moignard V, Basilico S, Kinston SJ, Hannah RL, Chan MC, Nürnberg ST, Ouwehand WH, Bonzanni N, de Bruijn MF, Göttgens B. An experimentally validated network of nine haematopoietic transcription factors reveals mechanisms of cell state stability. eLife 2016; 5:e11469. [PMID: 26901438 PMCID: PMC4798972 DOI: 10.7554/elife.11469] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 02/12/2016] [Indexed: 12/12/2022] Open
Abstract
Transcription factor (TF) networks determine cell-type identity by establishing and maintaining lineage-specific expression profiles, yet reconstruction of mammalian regulatory network models has been hampered by a lack of comprehensive functional validation of regulatory interactions. Here, we report comprehensive ChIP-Seq, transgenic and reporter gene experimental data that have allowed us to construct an experimentally validated regulatory network model for haematopoietic stem/progenitor cells (HSPCs). Model simulation coupled with subsequent experimental validation using single cell expression profiling revealed potential mechanisms for cell state stabilisation, and also how a leukaemogenic TF fusion protein perturbs key HSPC regulators. The approach presented here should help to improve our understanding of both normal physiological and disease processes.
Collapse
Affiliation(s)
- Judith Schütte
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.,Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Huange Wang
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.,Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Stella Antoniou
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Andrew Jarratt
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Nicola K Wilson
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.,Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Joey Riepsaame
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Fernando J Calero-Nieto
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.,Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Victoria Moignard
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.,Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Silvia Basilico
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.,Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Sarah J Kinston
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.,Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Rebecca L Hannah
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.,Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Mun Chiang Chan
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Sylvia T Nürnberg
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom.,NHS Blood and Transplant, Cambridge, United Kingdom
| | - Willem H Ouwehand
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom.,NHS Blood and Transplant, Cambridge, United Kingdom
| | - Nicola Bonzanni
- IBIVU Centre for Integrative Bioinformatics, VU University Amsterdam, Amsterdam, Netherlands.,Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Marella Ftr de Bruijn
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Berthold Göttgens
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.,Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
14
|
Abstract
Chronic myeloid leukemia (CML) is a myeloproliferative disorder derived from a hematopoietic stem cell (HSC), harboring Philadelphia chromosome (Ph chromosome). Formation of the Ph chromosome is caused by a reciprocal translocation between the chromosomes 9 and 22 t(9;22)(q34;q11), resulting in a fusion protein known as BCR-ABL which has constitutive tyrosine kinase activity and promotes the proliferation of leukemia cells via multiple mechanisms. Studies on CML have led to the identification of the first cancer-associated chromosomal abnormality and the subsequent development of tyrosine kinase inhibitors (TKIs) that inhibit BCR-ABL kinase activity in CML. It has become clear that leukemia stem cells (LSCs) in CML are insensitive to inhibition by TKIs, and eradication of LSCs appears to be difficult. Therefore, some of the major issues in current CML therapy are to understand the biology of LSCs and to investigate why LSCs are insensitive to TKIs for developing curative therapeutic strategies. In this regard, application of mouse models recapitulating human CML disease will be critical. In this chapter, we describe methods for induction of CML in mice with BCR-ABL.
Collapse
Affiliation(s)
- Haojian Zhang
- Medical Research Institute, Wuhan University, No.185, Donghu Road, Wuchang District, Wuhan city, Hubei, 430071, China.
| | - Shaoguang Li
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| |
Collapse
|
15
|
Giotopoulos G, van der Weyden L, Osaki H, Rust AG, Gallipoli P, Meduri E, Horton SJ, Chan WI, Foster D, Prinjha RK, Pimanda JE, Tenen DG, Vassiliou GS, Koschmieder S, Adams DJ, Huntly BJP. A novel mouse model identifies cooperating mutations and therapeutic targets critical for chronic myeloid leukemia progression. J Exp Med 2015; 212:1551-69. [PMID: 26304963 PMCID: PMC4577832 DOI: 10.1084/jem.20141661] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 07/28/2015] [Indexed: 12/14/2022] Open
Abstract
The introduction of highly selective ABL-tyrosine kinase inhibitors (TKIs) has revolutionized therapy for chronic myeloid leukemia (CML). However, TKIs are only efficacious in the chronic phase of the disease and effective therapies for TKI-refractory CML, or after progression to blast crisis (BC), are lacking. Whereas the chronic phase of CML is dependent on BCR-ABL, additional mutations are required for progression to BC. However, the identity of these mutations and the pathways they affect are poorly understood, hampering our ability to identify therapeutic targets and improve outcomes. Here, we describe a novel mouse model that allows identification of mechanisms of BC progression in an unbiased and tractable manner, using transposon-based insertional mutagenesis on the background of chronic phase CML. Our BC model is the first to faithfully recapitulate the phenotype, cellular and molecular biology of human CML progression. We report a heterogeneous and unique pattern of insertions identifying known and novel candidate genes and demonstrate that these pathways drive disease progression and provide potential targets for novel therapeutic strategies. Our model greatly informs the biology of CML progression and provides a potent resource for the development of candidate therapies to improve the dismal outcomes in this highly aggressive disease.
Collapse
MESH Headings
- Animals
- DNA Transposable Elements
- Fusion Proteins, bcr-abl/genetics
- Gene Expression Regulation, Leukemic
- Genes, myb
- Hematopoietic Stem Cells/pathology
- Humans
- Leukemia, Experimental/drug therapy
- Leukemia, Experimental/genetics
- Leukemia, Experimental/mortality
- Leukemia, Experimental/pathology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/mortality
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Mice, Transgenic
- Molecular Targeted Therapy/methods
- Mutagenesis, Insertional
- Mutation
- Tumor Cells, Cultured
- Vascular Endothelial Growth Factor C/genetics
Collapse
Affiliation(s)
- George Giotopoulos
- Department of Haematology, Cambridge Institute for Medical Research and Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 0XY, England, UK Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1TN, England, UK
| | - Louise van der Weyden
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Hikari Osaki
- Department of Haematology, Cambridge Institute for Medical Research and Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 0XY, England, UK Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1TN, England, UK
| | - Alistair G Rust
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK Tumour Profiling Unit, The Institute of Cancer Research, Chester Beatty Laboratories, London SW3 6JB, England, UK
| | - Paolo Gallipoli
- Department of Haematology, Cambridge Institute for Medical Research and Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 0XY, England, UK Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1TN, England, UK
| | - Eshwar Meduri
- Department of Haematology, Cambridge Institute for Medical Research and Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 0XY, England, UK Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1TN, England, UK
| | - Sarah J Horton
- Department of Haematology, Cambridge Institute for Medical Research and Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 0XY, England, UK Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1TN, England, UK
| | - Wai-In Chan
- Department of Haematology, Cambridge Institute for Medical Research and Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 0XY, England, UK Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1TN, England, UK
| | - Donna Foster
- Department of Haematology, Cambridge Institute for Medical Research and Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 0XY, England, UK Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1TN, England, UK
| | - Rab K Prinjha
- Epinova DPU, GlaxoSmithKline, Medicines Research Centre, Stevenage SG1 2NY, England, UK
| | - John E Pimanda
- Lowy Cancer Research Centre and the Prince of Wales Clinical School, University of New South Wales, Sydney, NSW 2052, Australia
| | - Daniel G Tenen
- Cancer Science Institute, National University of Singapore, Singapore 119077 Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115
| | - George S Vassiliou
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, England, UK
| | - Steffen Koschmieder
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, 52062 Aachen, Germany
| | - David J Adams
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Brian J P Huntly
- Department of Haematology, Cambridge Institute for Medical Research and Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 0XY, England, UK Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1TN, England, UK
| |
Collapse
|
16
|
Heinz S, Romanoski CE, Benner C, Glass CK. The selection and function of cell type-specific enhancers. Nat Rev Mol Cell Biol 2015; 16:144-54. [PMID: 25650801 PMCID: PMC4517609 DOI: 10.1038/nrm3949] [Citation(s) in RCA: 670] [Impact Index Per Article: 74.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The human body contains several hundred cell types, all of which share the same genome. In metazoans, much of the regulatory code that drives cell type-specific gene expression is located in distal elements called enhancers. Although mammalian genomes contain millions of potential enhancers, only a small subset of them is active in a given cell type. Cell type-specific enhancer selection involves the binding of lineage-determining transcription factors that prime enhancers. Signal-dependent transcription factors bind to primed enhancers, which enables these broadly expressed factors to regulate gene expression in a cell type-specific manner. The expression of genes that specify cell type identity and function is associated with densely spaced clusters of active enhancers known as super-enhancers. The functions of enhancers and super-enhancers are influenced by, and affect, higher-order genomic organization.
Collapse
Affiliation(s)
| | | | | | - Christopher K. Glass
- Department of Cellular and Molecular Medicine, UC San Diego
- Department of Medicine, UC San Diego
| |
Collapse
|
17
|
Identifying and mapping cell-type-specific chromatin programming of gene expression. Proc Natl Acad Sci U S A 2014; 111:E645-54. [PMID: 24469817 DOI: 10.1073/pnas.1312523111] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A problem of substantial interest is to systematically map variation in chromatin structure to gene-expression regulation across conditions, environments, or differentiated cell types. We developed and applied a quantitative framework for determining the existence, strength, and type of relationship between high-resolution chromatin structure in terms of DNaseI hypersensitivity and genome-wide gene-expression levels in 20 diverse human cell types. We show that ∼25% of genes show cell-type-specific expression explained by alterations in chromatin structure. We find that distal regions of chromatin structure (e.g., ±200 kb) capture more genes with this relationship than local regions (e.g., ±2.5 kb), yet the local regions show a more pronounced effect. By exploiting variation across cell types, we were capable of pinpointing the most likely hypersensitive sites related to cell-type-specific expression, which we show have a range of contextual uses. This quantitative framework is likely applicable to other settings aimed at relating continuous genomic measurements to gene-expression variation.
Collapse
|
18
|
Wilkinson AC, Goode DK, Cheng YH, Dickel DE, Foster S, Sendall T, Tijssen MR, Sanchez MJ, Pennacchio LA, Kirkpatrick AM, Göttgens B. Single site-specific integration targeting coupled with embryonic stem cell differentiation provides a high-throughput alternative to in vivo enhancer analyses. Biol Open 2013; 2:1229-38. [PMID: 24244860 PMCID: PMC3828770 DOI: 10.1242/bio.20136296] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 09/09/2013] [Indexed: 01/05/2023] Open
Abstract
Comprehensive analysis of cis-regulatory elements is key to understanding the dynamic gene regulatory networks that control embryonic development. While transgenic animals represent the gold standard assay, their generation is costly, entails significant animal usage, and in utero development complicates time-course studies. As an alternative, embryonic stem (ES) cells can readily be differentiated in a process that correlates well with developing embryos. Here, we describe a highly effective platform for enhancer assays using an Hsp68/Venus reporter cassette that targets to the Hprt locus in mouse ES cells. This platform combines the flexibility of Gateway® cloning, live cell trackability of a fluorescent reporter, low background and the advantages of single copy insertion into a defined genomic locus. We demonstrate the successful recapitulation of tissue-specific enhancer activity for two cardiac and two haematopoietic enhancers. In addition, we used this assay to dissect the functionality of the highly conserved Ets/Ets/Gata motif in the Scl+19 enhancer, which revealed that the Gata motif is not required for initiation of enhancer activity. We further confirmed that Gata2 is not required for endothelial activity of the Scl+19 enhancer using Gata2−/− Scl+19 transgenic embryos. We have therefore established a valuable toolbox to study gene regulatory networks with broad applicability.
Collapse
Affiliation(s)
- Adam C Wilkinson
- Cambridge Institute for Medical Research and Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge , Hills Road, Cambridge CB2 0XY , UK
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Genome-scale expression and transcription factor binding profiles reveal therapeutic targets in transgenic ERG myeloid leukemia. Blood 2013; 122:2694-703. [PMID: 23974202 DOI: 10.1182/blood-2013-01-477133] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The ETS transcription factor ERG plays a central role in definitive hematopoiesis, and its overexpression in acute myeloid leukemia (AML) is associated with a stem cell signature and poor prognosis. Yet how ERG causes leukemia is unclear. Here we show that pan-hematopoietic ERG expression induces an early progenitor myeloid leukemia in transgenic mice. Integrated genome-scale analysis of gene expression and ERG binding profiles revealed that ERG activates a transcriptional program similar to human AML stem/progenitor cells and to human AML with high ERG expression. This transcriptional program was associated with activation of RAS that was required for leukemia cells growth in vitro and in vivo. We further show that ERG induces expression of the Pim1 kinase oncogene through a novel hematopoietic enhancer validated in transgenic mice and human CD34(+) normal and leukemic cells. Pim1 inhibition disrupts growth and induces apoptosis of ERG-expressing leukemic cells. The importance of the ERG/PIM1 axis is further underscored by the poorer prognosis of AML highly expressing ERG and PIM1. Thus, integrative genomic analysis demonstrates that ERG causes myeloid progenitor leukemia characterized by an induction of leukemia stem cell transcriptional programs. Pim1 and the RAS pathway are potential therapeutic targets of these high-risk leukemias.
Collapse
|
20
|
Sun XJ, Wang Z, Wang L, Jiang Y, Kost N, Soong TD, Chen WY, Tang Z, Nakadai T, Elemento O, Fischle W, Melnick A, Patel DJ, Nimer SD, Roeder RG. A stable transcription factor complex nucleated by oligomeric AML1-ETO controls leukaemogenesis. Nature 2013; 500:93-7. [PMID: 23812588 PMCID: PMC3732535 DOI: 10.1038/nature12287] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 05/13/2013] [Indexed: 12/03/2022]
Abstract
Transcription factors are frequently altered in leukaemia through chromosomal translocation, mutation or aberrant expression1. AML1-ETO, a fusion protein generated by the t(8;21) translocation in acute myeloid leukaemia (AML), is a transcription factor implicated in both gene repression and activation2. AML1-ETO oligomerization, mediated by the NHR2 domain, is critical for leukaemogenesis3–6, making it important to identify coregulatory factors that “read” the NHR2 oligomerization and contribute to leukaemogenesis4. We now show that, in leukaemic cells, AML1-ETO resides in and functions through a stable protein complex (AETFC) that contains several haematopoietic transcription (co)factors. These AETFC components stabilize the complex through multivalent interactions, provide multiple DNA-binding domains for diverse target genes, colocalize genome-wide, cooperatively regulate gene expression, and contribute to leukaemogenesis. Within the AETFC complex, AML1-ETO oligomerization is required for a specific interaction between the oligomerized NHR2 domain and a novel NHR2-binding (N2B) motif in E proteins. Crystallographic analysis of the NHR2-N2B complex reveals a unique interaction pattern in which an N2B peptide makes direct contact with side chains of two NHR2 domains as a dimer, providing a novel model of how dimeric/oligomeric transcription factors create a new protein-binding interface through dimerization/oligomerization. Intriguingly, disruption of this interaction by point mutations abrogates AML1-ETO–induced haematopoietic stem/progenitor cell self-renewal and leukaemogenesis. These results reveal new mechanisms of action of AML1-ETO and a potential therapeutic target in t(8;21)+ AML.
Collapse
Affiliation(s)
- Xiao-Jian Sun
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, New York 10065, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Impaired in vitro erythropoiesis following deletion of the Scl (Tal1) +40 enhancer is largely compensated for in vivo despite a significant reduction in expression. Mol Cell Biol 2013; 33:1254-66. [PMID: 23319051 DOI: 10.1128/mcb.01525-12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The Scl (Tal1) gene encodes a helix-loop-helix transcription factor essential for hematopoietic stem cell and erythroid development. The Scl +40 enhancer is situated downstream of Map17, the 3' flanking gene of Scl, and is active in transgenic mice during primitive and definitive erythropoiesis. To analyze the in vivo function of the Scl +40 enhancer within the Scl/Map17 transcriptional domain, we deleted this element in the germ line. Scl(Δ40/Δ40) mice were viable with reduced numbers of erythroid CFU in both bone marrow and spleen yet displayed a normal response to stress hematopoiesis. Analysis of Scl(Δ40/Δ40) embryonic stem (ES) cells revealed impaired erythroid differentiation, which was accompanied by a failure to upregulate Scl when erythropoiesis was initiated. Map17 expression was also reduced in hematopoietic tissues and differentiating ES cells, and the Scl +40 element was able to enhance activity of the Map17 promoter. However, only Scl but not Map17 could rescue the Scl(Δ40/Δ40) ES phenotype. Together, these data demonstrate that the Scl +40 enhancer is an erythroid cell-specific enhancer that regulates the expression of both Scl and Map17. Moreover, deletion of the +40 enhancer causes a novel erythroid phenotype, which can be rescued by ectopic expression of Scl but not Map17.
Collapse
|
22
|
Smemo S, Campos LC, Moskowitz IP, Krieger JE, Pereira AC, Nobrega MA. Regulatory variation in a TBX5 enhancer leads to isolated congenital heart disease. Hum Mol Genet 2012; 21:3255-63. [PMID: 22543974 PMCID: PMC3384386 DOI: 10.1093/hmg/dds165] [Citation(s) in RCA: 145] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 03/31/2012] [Accepted: 04/20/2012] [Indexed: 12/20/2022] Open
Abstract
Recent studies have identified the genetic underpinnings of a growing number of diseases through targeted exome sequencing. However, this strategy ignores the large component of the genome that does not code for proteins, but is nonetheless biologically functional. To address the possible involvement of regulatory variation in congenital heart diseases (CHDs), we searched for regulatory mutations impacting the activity of TBX5, a dosage-dependent transcription factor with well-defined roles in the heart and limb development that has been associated with the Holt-Oram syndrome (heart-hand syndrome), a condition that affects 1/100 000 newborns. Using a combination of genomics, bioinformatics and mouse genetic engineering, we scanned ∼700 kb of the TBX5 locus in search of cis-regulatory elements. We uncovered three enhancers that collectively recapitulate the endogenous expression pattern of TBX5 in the developing heart. We re-sequenced these enhancer elements in a cohort of non-syndromic patients with isolated atrial and/or ventricular septal defects, the predominant cardiac defects of the Holt-Oram syndrome, and identified a patient with a homozygous mutation in an enhancer ∼90 kb downstream of TBX5. Notably, we demonstrate that this single-base-pair mutation abrogates the ability of the enhancer to drive expression within the heart in vivo using both mouse and zebrafish transgenic models. Given the population-wide frequency of this variant, we estimate that 1/100 000 individuals would be homozygous for this variant, highlighting that a significant number of CHD associated with TBX5 dysfunction might arise from non-coding mutations in TBX5 heart enhancers, effectively decoupling the heart and hand phenotypes of the Holt-Oram syndrome.
Collapse
MESH Headings
- Abnormalities, Multiple/embryology
- Abnormalities, Multiple/genetics
- Abnormalities, Multiple/metabolism
- Animals
- Animals, Genetically Modified
- Base Sequence
- Enhancer Elements, Genetic
- Heart/embryology
- Heart Defects, Congenital/embryology
- Heart Defects, Congenital/genetics
- Heart Defects, Congenital/metabolism
- Heart Septal Defects, Atrial/embryology
- Heart Septal Defects, Atrial/genetics
- Heart Septal Defects, Atrial/metabolism
- Homozygote
- Humans
- Lower Extremity Deformities, Congenital/embryology
- Lower Extremity Deformities, Congenital/genetics
- Lower Extremity Deformities, Congenital/metabolism
- Mice
- Molecular Sequence Data
- Point Mutation
- T-Box Domain Proteins/genetics
- T-Box Domain Proteins/metabolism
- Upper Extremity Deformities, Congenital/embryology
- Upper Extremity Deformities, Congenital/genetics
- Upper Extremity Deformities, Congenital/metabolism
- Zebrafish
Collapse
Affiliation(s)
| | - Luciene C. Campos
- Heart Institute (InCor), University of São Paulo Medical School, São Paulo, Brazil
| | - Ivan P. Moskowitz
- Department of Pediatrics, and
- Department of Pathology, University of Chicago, Chicago, IL, USA, and
| | - José E. Krieger
- Heart Institute (InCor), University of São Paulo Medical School, São Paulo, Brazil
| | - Alexandre C. Pereira
- Heart Institute (InCor), University of São Paulo Medical School, São Paulo, Brazil
| | | |
Collapse
|
23
|
Spensberger D, Kotsopoulou E, Ferreira R, Broccardo C, Scott LM, Fourouclas N, Ottersbach K, Green AR, Göttgens B. Deletion of the Scl +19 enhancer increases the blood stem cell compartment without affecting the formation of mature blood lineages. Exp Hematol 2012; 40:588-598.e1. [PMID: 22401818 PMCID: PMC3387379 DOI: 10.1016/j.exphem.2012.02.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Revised: 02/11/2012] [Accepted: 02/15/2012] [Indexed: 11/29/2022]
Abstract
The stem cell leukemia (Scl)/Tal1 gene is essential for normal blood and endothelial development, and is expressed in hematopoietic stem cells (HSCs), progenitors, erythroid, megakaryocytic, and mast cells. The Scl +19 enhancer is active in HSCs and progenitor cells, megakaryocytes, and mast cells, but not mature erythroid cells. Here we demonstrate that in vivo deletion of the Scl +19 enhancer (Scl(Δ19/Δ19)) results in viable mice with normal Scl expression in mature hematopoietic lineages. By contrast, Scl expression is reduced in the stem/progenitor compartment and flow cytometry analysis revealed that the HSC and megakaryocyte-erythroid progenitor populations are enlarged in Scl(Δ19/Δ19) mice. The increase in HSC numbers contributed to enhanced expansion in bone marrow transplantation assays, but did not affect multilineage repopulation or stress responses. These results affirm that the Scl +19 enhancer plays a key role in the development of hematopoietic stem/progenitor cells, but is not necessary for mature hematopoietic lineages. Moreover, active histone marks across the Scl locus were significantly reduced in Scl(Δ19/Δ19) fetal liver cells without major changes in steady-state messenger RNA levels, suggesting post-transcriptional compensation for loss of a regulatory element, a result that might be widely relevant given the frequent observation of mild phenotypes after deletion of regulatory elements.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Anthony R. Green
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Berthold Göttgens
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| |
Collapse
|
24
|
Baik J, Borges L, Magli A, Thatava T, Perlingeiro RCR. Effect of endoglin overexpression during embryoid body development. Exp Hematol 2012; 40:837-46. [PMID: 22728030 DOI: 10.1016/j.exphem.2012.06.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 05/20/2012] [Accepted: 06/12/2012] [Indexed: 10/28/2022]
Abstract
Increasing evidence points to endoglin (Eng), an accessory receptor for the transforming growth factor-β superfamily commonly associated with the endothelial lineage, as an important regulator of the hematopoietic lineage. We have shown that lack of Eng results in reduced numbers of primitive erythroid colonies as well as downregulation of key hematopoietic genes. To determine the effect of Eng overexpression in hematopoietic development, we generated a doxycycline-inducible embryonic stem cell line. Our results demonstrate that induction of Eng during embryoid body differentiation leads to a significant increase in the frequency of hematopoietic progenitors, in particular, the erythroid lineage, which correlated with upregulation of Scl, Gata1, Runx1, and embryonic globin. Interestingly, activation of the hematopoietic program happened at the expense of endothelial and cardiac cells, as differentiation into these mesoderm lineages was compromised. Eng-induced enhanced erythroid activity was accompanied by high levels of Smad1 phosphorylation. This effect was attenuated by addition of a bone morphogenetic protein (BMP) signaling inhibitor to these cultures. Among the BMPs, BMP4 is well known for its role in hematopoietic specification from mesoderm by promoting expression of several hematopoietic genes, including Scl. Because Scl is considered the master regulator of the hematopoietic program, we investigated whether Scl would be capable of rescuing the defective hematopoietic phenotype observed in Eng(-/-) embryonic stem cells. Scl expression in Eng-deficient embryonic stem cells resulted in increased erythroid colony-forming activity and upregulation of Gata1 and Gata2, positioning Eng upstream of Scl. Taken together, these findings support the premise that Eng modulates the hematopoietic transcriptional network, most likely through regulation of BMP4 signaling.
Collapse
Affiliation(s)
- June Baik
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | | | | | | | | |
Collapse
|
25
|
Curtis DJ, Salmon JM, Pimanda JE. Concise Review: Blood Relatives: Formation and regulation of hematopoietic stem cells by the basic helix-loop-helix transcription factors stem cell leukemia and lymphoblastic leukemia-derived sequence 1. Stem Cells 2012; 30:1053-8. [DOI: 10.1002/stem.1093] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
26
|
Follows GA, Ferreira R, Janes ME, Spensberger D, Cambuli F, Chaney AF, Kinston SJ, Landry JR, Green AR, Göttgens B. Mapping and functional characterisation of a CTCF-dependent insulator element at the 3' border of the murine Scl transcriptional domain. PLoS One 2012; 7:e31484. [PMID: 22396734 PMCID: PMC3291548 DOI: 10.1371/journal.pone.0031484] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 01/09/2012] [Indexed: 11/18/2022] Open
Abstract
The Scl gene encodes a transcription factor essential for haematopoietic development. Scl transcription is regulated by a panel of cis-elements spread over 55 kb with the most distal 3′ element being located downstream of the neighbouring gene Map17, which is co-regulated with Scl in haematopoietic cells. The Scl/Map17 domain is flanked upstream by the ubiquitously expressed Sil gene and downstream by a cluster of Cyp genes active in liver, but the mechanisms responsible for delineating the domain boundaries remain unclear. Here we report identification of a DNaseI hypersensitive site at the 3′ end of the Scl/Map17 domain and 45 kb downstream of the Scl transcription start site. This element is located at the boundary of active and inactive chromatin, does not function as a classical tissue-specific enhancer, binds CTCF and is both necessary and sufficient for insulator function in haematopoietic cells in vitro. Moreover, in a transgenic reporter assay, tissue-specific expression of the Scl promoter in brain was increased by incorporation of 350 bp flanking fragments from the +45 element. Our data suggests that the +45 region functions as a boundary element that separates the Scl/Map17 and Cyp transcriptional domains, and raise the possibility that this element may be useful for improving tissue-specific expression of transgenic constructs.
Collapse
Affiliation(s)
- George A Follows
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Integration of Elf-4 into stem/progenitor and erythroid regulatory networks through locus-wide chromatin studies coupled with in vivo functional validation. Mol Cell Biol 2011; 32:763-73. [PMID: 22158964 DOI: 10.1128/mcb.05745-11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The ETS transcription factor Elf-4 is an important regulator of hematopoietic stem cell (HSC) and T cell homeostasis. To gain insights into the transcriptional circuitry within which Elf-4 operates, we used comparative sequence analysis coupled with chromatin immunoprecipitation (ChIP) with microarray technology (ChIP-chip) assays for specific chromatin marks to identify three promoters and two enhancers active in hematopoietic and endothelial cell lines. Comprehensive functional validation of each of these regulatory regions in transgenic mouse embryos identified a tissue-specific enhancer (-10E) that displayed activity in fetal liver, dorsal aorta, vitelline vessels, yolk sac, and heart. Integration of a ChIP-sequencing (ChIP-Seq) data set for 10 key stem cell transcription factors showed Pu.1, Fli-1, and Erg were bound to the -10E element, and mutation of three highly conserved ETS sites within the enhancer abolished its activity. Finally, the transcriptional repressor Gfi1b was found to bind to and repress one of the Elf-4 promoters (-30P), and we show that this repression of Elf-4 is important for the maturation of primary fetal liver erythroid cells. Taken together, our results provide a comprehensive overview of the transcriptional control of Elf-4 within the hematopoietic system and, thus, integrate Elf-4 into the wider transcriptional regulatory networks that govern hematopoietic development.
Collapse
|
28
|
Czömpöly T, Lábadi A, Kellermayer Z, Olasz K, Arnold HH, Balogh P. Transcription factor Nkx2-3 controls the vascular identity and lymphocyte homing in the spleen. THE JOURNAL OF IMMUNOLOGY 2011; 186:6981-9. [PMID: 21593383 DOI: 10.4049/jimmunol.1003770] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The vasculature in the spleen and peripheral lymph nodes (pLNs) is considerably different, which affects both homing of lymphocytes and antigenic access to these peripheral lymphoid organs. In this paper, we demonstrate that in mice lacking the homeodomain transcription factor Nkx2-3, the spleen develops a pLN-like mRNA expression signature, coupled with the appearance of high endothelial venules (HEVs) that mediate L-selectin-dependent homing of lymphocytes into the mutant spleen. These ectopic HEV-like vessels undergo postnatal maturation and progressively replace MAdCAM-1 by pLN addressin together with the display of CCL21 arrest chemokine in a process that is reminiscent of HEV formation in pLNs. Similarly to pLNs, development of HEV-like vessels in the Nkx2-3-deficient spleen depends on lymphotoxin-β receptor-mediated signaling. The replacement of splenic vessels with a pLN-patterned vasculature impairs the recirculation of adoptively transferred lymphocytes and reduces the uptake of blood-borne pathogens. The Nkx2-3 mutation in BALB/c background causes a particularly disturbed splenic architecture, characterized by the near complete lack of the red pulp, without affecting lymph nodes. Thus, our observations reveal that the organ-specific patterning of splenic vasculature is critically regulated by Nkx2-3, thereby profoundly affecting the lymphocyte homing mechanism and blood filtering capacity of the spleen in a tissue-specific manner.
Collapse
Affiliation(s)
- Tamás Czömpöly
- Department of Immunology and Biotechnology, Faculty of Medicine, University of Pécs, H-7624 Pécs, Hungary
| | | | | | | | | | | |
Collapse
|
29
|
Tijssen M, Cvejic A, Joshi A, Hannah R, Ferreira R, Forrai A, Bellissimo D, Oram S, Smethurst P, Wilson N, Wang X, Ottersbach K, Stemple D, Green A, Ouwehand W, Göttgens B. Genome-wide analysis of simultaneous GATA1/2, RUNX1, FLI1, and SCL binding in megakaryocytes identifies hematopoietic regulators. Dev Cell 2011; 20:597-609. [PMID: 21571218 PMCID: PMC3145975 DOI: 10.1016/j.devcel.2011.04.008] [Citation(s) in RCA: 225] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Revised: 02/28/2011] [Accepted: 04/20/2011] [Indexed: 11/20/2022]
Abstract
Hematopoietic differentiation critically depends on combinations of transcriptional regulators controlling the development of individual lineages. Here, we report the genome-wide binding sites for the five key hematopoietic transcription factors--GATA1, GATA2, RUNX1, FLI1, and TAL1/SCL--in primary human megakaryocytes. Statistical analysis of the 17,263 regions bound by at least one factor demonstrated that simultaneous binding by all five factors was the most enriched pattern and often occurred near known hematopoietic regulators. Eight genes not previously appreciated to function in hematopoiesis that were bound by all five factors were shown to be essential for thrombocyte and/or erythroid development in zebrafish. Moreover, one of these genes encoding the PDZK1IP1 protein shared transcriptional enhancer elements with the blood stem cell regulator TAL1/SCL. Multifactor ChIP-Seq analysis in primary human cells coupled with a high-throughput in vivo perturbation screen therefore offers a powerful strategy to identify essential regulators of complex mammalian differentiation processes.
Collapse
Affiliation(s)
- Marloes R. Tijssen
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
- Department of Haematology, NHS Blood and Transplant Centre, University of Cambridge, Cambridge CB2 0PT, UK
| | - Ana Cvejic
- Department of Haematology, NHS Blood and Transplant Centre, University of Cambridge, Cambridge CB2 0PT, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Anagha Joshi
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Rebecca L. Hannah
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Rita Ferreira
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Ariel Forrai
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Dana C. Bellissimo
- Department of Haematology, NHS Blood and Transplant Centre, University of Cambridge, Cambridge CB2 0PT, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - S. Helen Oram
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Peter A. Smethurst
- Department of Haematology, NHS Blood and Transplant Centre, University of Cambridge, Cambridge CB2 0PT, UK
| | - Nicola K. Wilson
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Xiaonan Wang
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Katrin Ottersbach
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Derek L. Stemple
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Anthony R. Green
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Willem H. Ouwehand
- Department of Haematology, NHS Blood and Transplant Centre, University of Cambridge, Cambridge CB2 0PT, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Berthold Göttgens
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| |
Collapse
|
30
|
Wilson NK, Foster SD, Wang X, Knezevic K, Schütte J, Kaimakis P, Chilarska PM, Kinston S, Ouwehand WH, Dzierzak E, Pimanda JE, de Bruijn MFTR, Göttgens B. Combinatorial transcriptional control in blood stem/progenitor cells: genome-wide analysis of ten major transcriptional regulators. Cell Stem Cell 2011; 7:532-44. [PMID: 20887958 DOI: 10.1016/j.stem.2010.07.016] [Citation(s) in RCA: 535] [Impact Index Per Article: 41.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2010] [Revised: 06/10/2010] [Accepted: 07/21/2010] [Indexed: 11/16/2022]
Abstract
Combinatorial transcription factor (TF) interactions control cellular phenotypes and, therefore, underpin stem cell formation, maintenance, and differentiation. Here, we report the genome-wide binding patterns and combinatorial interactions for ten key regulators of blood stem/progenitor cells (SCL/TAL1, LYL1, LMO2, GATA2, RUNX1, MEIS1, PU.1, ERG, FLI-1, and GFI1B), thus providing the most comprehensive TF data set for any adult stem/progenitor cell type to date. Genome-wide computational analysis of complex binding patterns, followed by functional validation, revealed the following: first, a previously unrecognized combinatorial interaction between a heptad of TFs (SCL, LYL1, LMO2, GATA2, RUNX1, ERG, and FLI-1). Second, we implicate direct protein-protein interactions between four key regulators (RUNX1, GATA2, SCL, and ERG) in stabilizing complex binding to DNA. Third, Runx1(+/-)::Gata2(+/-) compound heterozygous mice are not viable with severe hematopoietic defects at midgestation. Taken together, this study demonstrates the power of genome-wide analysis in generating novel functional insights into the transcriptional control of stem and progenitor cells.
Collapse
Affiliation(s)
- Nicola K Wilson
- University of Cambridge Department of Haematology, Cambridge Institute for Medical Research, Hills Road, Cambridge, CB2 0XY, UK
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Aisagbonhi O, Rai M, Ryzhov S, Atria N, Feoktistov I, Hatzopoulos AK. Experimental myocardial infarction triggers canonical Wnt signaling and endothelial-to-mesenchymal transition. Dis Model Mech 2011; 4:469-83. [PMID: 21324930 PMCID: PMC3124051 DOI: 10.1242/dmm.006510] [Citation(s) in RCA: 218] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Despite available therapies, myocardial infarction (MI) remains a leading cause of death worldwide. Better understanding of the molecular and cellular mechanisms that regulate cardiac repair should help to improve the clinical outcome of MI patients. Using the reporter mouse line TOPGAL, we show that canonical (β-catenin-dependent) Wnt signaling is induced 4 days after experimental MI in subepicardial endothelial cells and perivascular smooth muscle actin (SMA)-positive (SMA+) cells. At 1 week after ischemic injury, a large number of canonical-Wnt-positive cells accumulated in the infarct area during granulation tissue formation. Coincidently with canonical Wnt activation, endothelial-to-mesenchymal transition (EndMT) was also triggered after MI. Using cell lineage tracing, we show that a significant portion of the canonical-Wnt-marked SMA+ mesenchymal cells is derived from endothelial cells. Canonical Wnt signaling induces mesenchymal characteristics in cultured endothelial cells, suggesting a direct role in EndMT. In conclusion, our study demonstrates that canonical Wnt activation and EndMT are molecular and cellular responses to MI and that canonical Wnt signaling activity is a characteristic property of EndMT-derived mesenchymal cells that take part in cardiac tissue repair after MI. These findings could lead to new strategies to improve the course of cardiac repair by temporal and cell-type-specific manipulation of canonical Wnt signaling.
Collapse
Affiliation(s)
- Omonigho Aisagbonhi
- Department of Medicine, Division of Cardiovascular Medicine, Vanderbilt University, 2213 Garland Avenue, Nashville, TN 37232-6300, USA
| | | | | | | | | | | |
Collapse
|
32
|
Wilson NK, Calero-Nieto FJ, Ferreira R, Göttgens B. Transcriptional regulation of haematopoietic transcription factors. Stem Cell Res Ther 2011; 2:6. [PMID: 21345252 PMCID: PMC3092146 DOI: 10.1186/scrt47] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The control of differential gene expression is central to all metazoan biology. Haematopoiesis represents one of the best understood developmental systems where multipotent blood stem cells give rise to a range of phenotypically distinct mature cell types, all characterised by their own distinctive gene expression profiles. Small combinations of lineage-determining transcription factors drive the development of specific mature lineages from multipotent precursors. Given their powerful regulatory nature, it is imperative that the expression of these lineage-determining transcription factors is under tight control, a fact underlined by the observation that their misexpression commonly leads to the development of leukaemia. Here we review recent studies on the transcriptional control of key haematopoietic transcription factors, which demonstrate that gene loci contain multiple modular regulatory regions within which specific regulatory codes can be identified, that some modular elements cooperate to mediate appropriate tissue-specific expression, and that long-range approaches will be necessary to capture all relevant regulatory elements. We also explore how changes in technology will impact on this area of research in the future.
Collapse
Affiliation(s)
- Nicola K Wilson
- University of Cambridge Department of Haematology, Cambridge Institute for Medical Research, Hills Road, Cambridge, CB2 0XY, UK.
| | | | | | | |
Collapse
|
33
|
Abstract
Development progresses through a sequence of cellular identities which are determined by the activities of networks of transcription factor genes. Alterations in cis-regulatory elements of these genes play a major role in evolutionary change, but little is known about the mechanisms responsible for maintaining conserved patterns of gene expression. We have studied the evolution of cis-regulatory mechanisms controlling the SCL gene, which encodes a key transcriptional regulator of blood, vasculature, and brain development and exhibits conserved function and pattern of expression throughout vertebrate evolution. SCL cis-regulatory elements are conserved between frog and chicken but accrued alterations at an accelerated rate between 310 and 200 million years ago, with subsequent fixation of a new cis-regulatory pattern at the beginning of the mammalian radiation. As a consequence, orthologous elements shared by mammals and lower vertebrates exhibit functional differences and binding site turnover between widely separated cis-regulatory modules. However, the net effect of these alterations is constancy of overall regulatory inputs and of expression pattern. Our data demonstrate remarkable cis-regulatory remodelling across the SCL locus and indicate that stable patterns of expression can mask extensive regulatory change. These insights illuminate our understanding of vertebrate evolution.
Collapse
|
34
|
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: 18] [Impact Index Per Article: 1.2] [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.
Collapse
Affiliation(s)
- Katrin Ottersbach
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | | | | | | |
Collapse
|
35
|
Bockamp E, Antunes C, Liebner S, Schmitt S, Cabezas-Wallscheid N, Heck R, Ohnngemach S, Oesch-Bartlomowicz B, Rickert C, Sanchez MJ, Hengstler J, Kaina B, Wilson A, Trumpp A, Eshkind L. In vivo fate mapping with SCL regulatory elements identifies progenitors for primitive and definitive hematopoiesis in mice. Mech Dev 2009; 126:863-72. [DOI: 10.1016/j.mod.2009.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 07/13/2009] [Accepted: 07/17/2009] [Indexed: 12/01/2022]
|
36
|
Speck NA, Iruela-Arispe ML. Conditional Cre/LoxP strategies for the study of hematopoietic stem cell formation. Blood Cells Mol Dis 2009; 43:6-11. [PMID: 19250847 PMCID: PMC2723839 DOI: 10.1016/j.bcmd.2009.01.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2008] [Accepted: 01/05/2009] [Indexed: 11/30/2022]
Abstract
Some of the questions that have intrigued developmental biologists studying blood cell formation are: where do blood cells form, what are their precursors, and what signals are required for their emergence. Elegant embryonic grafting experiments in non-mammalian vertebrates, transplantation assays in mouse, and genetic analyses in zebrafish and mouse have been brought to bear on these problems, with enormous success. More recently investigators have applied conditional gene deletion and replacement strategies to refine our knowledge of this process in mammals. Here we describe several studies that have used the Cre/LoxP system to study blood cell formation, and what has been learned as a result.
Collapse
Affiliation(s)
- Nancy A Speck
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | | |
Collapse
|
37
|
Expression of the leukemia oncogene Lmo2 is controlled by an array of tissue-specific elements dispersed over 100 kb and bound by Tal1/Lmo2, Ets, and Gata factors. Blood 2009; 113:5783-92. [PMID: 19171877 DOI: 10.1182/blood-2008-11-187757] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The Lmo2 gene encodes a transcriptional cofactor critical for the development of hematopoietic stem cells. Ectopic LMO2 expression causes leukemia in T-cell acute lymphoblastic leukemia (T-ALL) patients and severe combined immunodeficiency patients undergoing retroviral gene therapy. Tightly controlled Lmo2 expression is therefore essential, yet no comprehensive analysis of Lmo2 regulation has been published so far. By comparative genomics, we identified 17 highly conserved noncoding elements, 9 of which revealed specific acetylation marks in chromatin-immunoprecipitation and microarray (ChIP-chip) assays performed across 250 kb of the Lmo2 locus in 11 cell types covering different stages of hematopoietic differentiation. All candidate regulatory regions were tested in transgenic mice. An extended LMO2 proximal promoter fragment displayed strong endothelial activity, while the distal promoter showed weak forebrain activity. Eight of the 15 distal candidate elements functioned as enhancers, which together recapitulated the full expression pattern of Lmo2, directing expression to endothelium, hematopoietic cells, tail, and forebrain. Interestingly, distinct combinations of specific distal regulatory elements were required to extend endothelial activity of the LMO2 promoter to yolk sac or fetal liver hematopoietic cells. Finally, Sfpi1/Pu.1, Fli1, Gata2, Tal1/Scl, and Lmo2 were shown to bind to and transactivate Lmo2 hematopoietic enhancers, thus identifying key upstream regulators and positioning Lmo2 within hematopoietic regulatory networks.
Collapse
|
38
|
Garcia-Ortega A, Cañete A, Quintero C, Silberstein L, Gil MP, Alvarez-Dolado M, Dekel B, Gottgens B, Sanchez M. Enhanced Hemato-Vascular Contribution Of SCL-3′Enh Expressing Fetal Liver Cells Uncovers Their Potential To Integrate In Extra-Medullary Adult Niches. Stem Cells 2009; 28:100-12. [DOI: 10.1002/stem.228] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
39
|
Miranda-Saavedra D, Göttgens B. Transcriptional regulatory networks in haematopoiesis. Curr Opin Genet Dev 2008; 18:530-5. [PMID: 18838119 DOI: 10.1016/j.gde.2008.09.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2008] [Revised: 08/29/2008] [Accepted: 09/09/2008] [Indexed: 10/21/2022]
Abstract
The coordinated expression of genes lies at the heart of developmental programmes, with complex regulatory networks controlling the spatial and temporal aspects of gene expression. Haematopoiesis (blood formation) has long served as a model process for studying the specification and subsequent differentiation of stem cells and represents the best characterised adult stem cell system. In this review, we outline how the integration of experimental and computational approaches as applied to haematopoiesis has resulted in some of the most advanced models of transcriptional regulatory networks in mammals.
Collapse
Affiliation(s)
- Diego Miranda-Saavedra
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | | |
Collapse
|
40
|
Endoglin expression in blood and endothelium is differentially regulated by modular assembly of the Ets/Gata hemangioblast code. Blood 2008; 112:4512-22. [PMID: 18805961 DOI: 10.1182/blood-2008-05-157560] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Endoglin is an accessory receptor for TGF-beta signaling and is required for normal hemangioblast, early hematopoietic, and vascular development. We have previously shown that an upstream enhancer, Eng -8, together with the promoter region, mediates robust endothelial expression yet is inactive in blood. To identify hematopoietic regulatory elements, we used array-based methods to determine chromatin accessibility across the entire locus. Subsequent transgenic analysis of candidate elements showed that an endothelial enhancer at Eng +9 when combined with an element at Eng +7 functions as a strong hemato-endothelial enhancer. Chromatin immunoprecipitation (ChIP)-chip analysis demonstrated specific binding of Ets factors to the promoter as well as to the -8, +7+9 enhancers in both blood and endothelial cells. By contrast Pu.1, an Ets factor specific to the blood lineage, and Gata2 binding was only detected in blood. Gata2 was bound only at +7 and GATA motifs were required for hematopoietic activity. This modular assembly of regulators gives blood and endothelial cells the regulatory freedom to independently fine-tune gene expression and emphasizes the role of regulatory divergence in driving functional divergence.
Collapse
|
41
|
Smith AM, Sanchez MJ, Follows GA, Kinston S, Donaldson IJ, Green AR, Göttgens B. A novel mode of enhancer evolution: the Tal1 stem cell enhancer recruited a MIR element to specifically boost its activity. Genome Res 2008; 18:1422-32. [PMID: 18687876 PMCID: PMC2527711 DOI: 10.1101/gr.077008.108] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Altered cis-regulation is thought to underpin much of metazoan evolution, yet the underlying mechanisms remain largely obscure. The stem cell leukemia TAL1 (also known as SCL) transcription factor is essential for the normal development of blood stem cells and we have previously shown that the Tal1 +19 enhancer directs expression to hematopoietic stem cells, hematopoietic progenitors, and to endothelium. Here we demonstrate that an adjacent region 1 kb upstream (+18 element) is in an open chromatin configuration and carries active histone marks but does not function as an enhancer in transgenic mice. Instead, it boosts activity of the +19 enhancer both in stable transfection assays and during differentiation of embryonic stem (ES) cells carrying single-copy reporter constructs targeted to the Hprt locus. The +18 element contains a mammalian interspersed repeat (MIR) which is essential for the +18 function and which was transposed to the Tal1 locus approximately 160 million years ago at the time of the mammalian/marsupial branchpoint. Our data demonstrate a previously unrecognized mechanism whereby enhancer activity is modulated by a transposon exerting a "booster" function which would go undetected by conventional transgenic approaches.
Collapse
Affiliation(s)
- Aileen M Smith
- University of Cambridge Department of Haematology, Cambridge Institute for Medical Research, Cambridge CB2 2XY, United Kingdom
| | | | | | | | | | | | | |
Collapse
|
42
|
Abstract
Transcription factors such as Scl/Tal1, Lmo2, and Runx1 are essential for the development of hematopoietic stem cells (HSCs). However, the precise mechanisms by which these factors interact to form transcriptional networks, as well as the identity of the genes downstream of these regulatory cascades, remain largely unknown. To this end, we generated an Scl(-/-) yolk sac cell line to identify candidate Scl target genes by global expression profiling after reintroduction of a TAT-Scl fusion protein. Bioinformatics analysis resulted in the identification of 9 candidate Scl target transcription factor genes, including Runx1 and Runx3. Chromatin immunoprecipitation confirmed that both Runx genes are direct targets of Scl in the fetal liver and that Runx1 is also occupied by Scl in the yolk sac. Furthermore, binding of an Scl-Lmo2-Gata2 complex was demonstrated to occur on the regions flanking the conserved E-boxes of the Runx1 loci and was shown to transactivate the Runx1 element. Together, our data provide a key component of the transcriptional network of early hematopoiesis by identifying downstream targets of Scl that can explain key aspects of the early Scl(-/-) phenotype.
Collapse
|
43
|
Hochman E, Kinston S, Harmelin A, Göttgens B, Izraeli S. The SCL 3' enhancer responds to Hedgehog signaling during hemangioblast specification. Exp Hematol 2007; 34:1643-50. [PMID: 17157160 DOI: 10.1016/j.exphem.2006.07.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2006] [Revised: 06/27/2006] [Accepted: 07/31/2006] [Indexed: 11/18/2022]
Abstract
OBJECTIVE The Hedgehog family of intercellular proteins has a crucial role in embryonic development. Recent experimental data suggests that the Hedgehog pathway may play a role in early hematopoiesis and angiogenesis. Stem cell leukemia (SCL), a basic helix-loop-helix (bHLH) transcription factor, is essential for the specification and function of the hemangioblast. SCL expression in early hematopoietic precursors and endothelium is directed by a 3' enhancer. We hypothesized that the SCL 3' enhancer is regulated by Hedgehog signaling during specification of mesoderm towards hemangioblastic fate. MATERIALS AND METHODS Whole embryos derived from transgenic mouse lines carrying reporter genes under the regulation of SCL 3' enhancer were cultured in the presence of active Hedgehog peptide. Hedgehog transcriptional regulation of SCL 3' enhancer was studied by in vitro and in vivo binding and reporter assays. RESULTS Hedgehog induced expansion of cells in which the SCL 3' enhancer was transcriptionally activated. A Gli-binding site within the 3' enhancer of SCL was identified and Gli1 was demonstrated to bind and transactivate this enhancer in a sequence-dependent manner. We further demonstrated that the core region of the SCL 3' enhancer is transcriptionally regulated by Hedgehog in-vivo and that the Gli-binding site located in this enhancer is essential for Hedgehog transcriptional regulation in vitro. CONCLUSION These findings suggest that SCL may be a direct target of Hedgehog signaling during hemangioblast specification.
Collapse
Affiliation(s)
- Eldar Hochman
- The Research Section of Pediatric Malignancies, The Sheba Cancer Research Center, Safra Children's Hospital, Sheba Medical Center and Faculty of Medicine, Tel-Aviv University, Tel Hashomer, Israel
| | | | | | | | | |
Collapse
|
44
|
Subbotin VM. Analysis of arterial intimal hyperplasia: review and hypothesis. Theor Biol Med Model 2007; 4:41. [PMID: 17974015 PMCID: PMC2169223 DOI: 10.1186/1742-4682-4-41] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2007] [Accepted: 10/31/2007] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Despite a prodigious investment of funds, we cannot treat or prevent arteriosclerosis and restenosis, particularly its major pathology, arterial intimal hyperplasia. A cornerstone question lies behind all approaches to the disease: what causes the pathology? HYPOTHESIS I argue that the question itself is misplaced because it implies that intimal hyperplasia is a novel pathological phenomenon caused by new mechanisms. A simple inquiry into arterial morphology shows the opposite is true. The normal multi-layer cellular organization of the tunica intima is identical to that of diseased hyperplasia; it is the standard arterial system design in all placentals at least as large as rabbits, including humans. Formed initially as one-layer endothelium lining, this phenotype can either be maintained or differentiate into a normal multi-layer cellular lining, so striking in its resemblance to diseased hyperplasia that we have to name it "benign intimal hyperplasia". However, normal or "benign" intimal hyperplasia, although microscopically identical to pathology, is a controllable phenotype that rarely compromises blood supply. It is remarkable that each human heart has coronary arteries in which a single-layer endothelium differentiates early in life to form a multi-layer intimal hyperplasia and then continues to self-renew in a controlled manner throughout life, relatively rarely compromising the blood supply to the heart, causing complications requiring intervention only in a small fraction of the population, while all humans are carriers of benign hyperplasia. Unfortunately, this fundamental fact has not been widely appreciated in arteriosclerosis research and medical education, which continue to operate on the assumption that the normal arterial intima is always an "ideal" single-layer endothelium. As a result, the disease is perceived and studied as a new pathological event caused by new mechanisms. The discovery that normal coronary arteries are morphologically indistinguishable from deadly coronary arteriosclerosis continues to elicit surprise. CONCLUSION Two questions should inform the priorities of our research: (1) what controls switch the single cell-layer intimal phenotype into normal hyperplasia? (2) how is normal (benign) hyperplasia maintained? We would be hard-pressed to gain practical insights without scrutinizing our premises.
Collapse
|
45
|
Gata2, Fli1, and Scl form a recursively wired gene-regulatory circuit during early hematopoietic development. Proc Natl Acad Sci U S A 2007; 104:17692-7. [PMID: 17962413 DOI: 10.1073/pnas.0707045104] [Citation(s) in RCA: 175] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Conservation of the vertebrate body plan has been attributed to the evolutionary stability of gene-regulatory networks (GRNs). We describe a regulatory circuit made up of Gata2, Fli1, and Scl/Tal1 and their enhancers, Gata2-3, Fli1+12, and Scl+19, that operates during specification of hematopoiesis in the mouse embryo. We show that the Fli1+12 enhancer, like the Gata2-3 and Scl+19 enhancers, targets hematopoietic stem cells (HSCs) and relies on a combination of Ets, Gata, and E-Box motifs. We show that the Gata2-3 enhancer also uses a similar cluster of motifs and that Gata2, Fli1, and Scl are expressed in embryonic day-11.5 dorsal aorta where HSCs originate and in fetal liver where they multiply. The three HSC enhancers in these tissues and in ES cell-derived hemangioblast equivalents are bound by each of these transcription factors (TFs) and form a fully connected triad that constitutes a previously undescribed example of both this network motif in mammalian development and a GRN kernel operating during the specification of a mammalian stem cell.
Collapse
|
46
|
Dekel B, Metsuyanim S, Garcia AM, Quintero C, Sanchez MJ, Izraeli S. Organ-injury-induced reactivation of hemangioblastic precursor cells. Leukemia 2007; 22:103-13. [PMID: 17898790 DOI: 10.1038/sj.leu.2404941] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Early in mammalian development, the stem cell leukemia (SCL/TAL1) gene and its distinct 3' enhancer (SCL 3'En) specify bipotential progenitor cells that give rise to blood and endothelium, thus termed hemangioblasts. We have previously detected a minor population of SCL (+) cells in the postnatal kidney. Here, we demonstrate that cells expressing the SCL 3'En in the adult kidney are comprised of CD45+CD31- hematopoietic cells, CD45-CD31+ endothelial cells and CD45-CD31- interstitial cells. Creation of bone marrow chimeras of SCL 3'En transgenic mice into wild-type hosts shows that all three types of SCL 3'En-expressing cells in the adult kidney can originate from the bone marrow. Ischemia/reperfusion injury to the adult kidney of SCL 3'En transgenic mice results in the intrarenal elevation of SCL and FLK1 mRNA levels and of cells expressing hem-endothelial progenitor markers (CD45, CD34, c-Kit and FLK1). Furthermore, analysis of SCL 3'En in the ischemic kidneys reveals an increase in the abundance of SCL 3'En-expressing cells, predominantly within the CD45 (+) hematopoietic fraction and to a lesser extent in the CD45 (-) fraction. Our results suggest organ-injury-induced reactivation of bone marrow-derived hemangioblasts and possible local angioblastic progenitors expressing SCL and SCL 3'En.
Collapse
Affiliation(s)
- B Dekel
- Department of Pediatrics and Laboratory of Regenerative Nephrology, Edmond and Lili Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.
| | | | | | | | | | | |
Collapse
|
47
|
Ogilvy S, Ferreira R, Piltz SG, Bowen JM, Göttgens B, Green AR. The SCL +40 enhancer targets the midbrain together with primitive and definitive hematopoiesis and is regulated by SCL and GATA proteins. Mol Cell Biol 2007; 27:7206-19. [PMID: 17709394 PMCID: PMC2168913 DOI: 10.1128/mcb.00931-07] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The SCL/Tal-1 gene encodes a basic helix-loop-helix transcription factor with key roles in hematopoietic and neural development. SCL is expressed in, and required for, both primitive and definitive erythropoiesis. Thus far, we have identified only one erythroid SCL enhancer. Located 40 kb downstream of exon 1a, the +40 enhancer displays activity in primitive erythroblasts. We demonstrate here that a 3.7-kb fragment containing this element also targets expression to the midbrain, a known site of endogenous SCL expression. Although the 3.7-kb construct was active in primitive, but not definitive, erythroblasts, a larger 5.0-kb fragment, encompassing the 3.7-kb region, was active in both fetal and adult definitive hematopoietic cells. This included Ter119+ erythroid cells along with fetal liver erythroid and myeloid progenitors. Unlike two other SCL hematopoietic enhancers (+18/19 and -4), +40 enhancer transgenes were inactive in the endothelium. A conserved 400-bp core region, essential for both hematopoietic and midbrain +40 enhancer activity in embryos, relied on two GATA/E-box motifs and was bound in vivo by GATA-1 and SCL in erythroid cells. These results suggest a model in which the SCL +18/19 and/or -4 enhancers initiate SCL expression in early mesodermal derivatives capable of generating blood and endothelium, with subsequent activation of the +40 enhancer via an autoregulatory loop.
Collapse
Affiliation(s)
- S Ogilvy
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
| | | | | | | | | | | |
Collapse
|
48
|
Wu Y, Ferguson JE, Wang H, Kelley R, Ren R, McDonough H, Meeker J, Charles PC, Wang H, Patterson C. PRDM6 is enriched in vascular precursors during development and inhibits endothelial cell proliferation, survival, and differentiation. J Mol Cell Cardiol 2007; 44:47-58. [PMID: 17662997 PMCID: PMC2683064 DOI: 10.1016/j.yjmcc.2007.06.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2007] [Revised: 06/12/2007] [Accepted: 06/14/2007] [Indexed: 01/06/2023]
Abstract
The mechanisms that regulate the differentiation program of multipotential stem cells remain poorly understood. In order to define the cues that delineate endothelial commitment from precursors, we screened for candidate regulatory genes in differentiating mouse embryoid bodies. We found that the PR/SET domain protein, PRDM6, is enriched in flk1(+) hematovascular precursor cells using a microarray-based approach. As determined by 5' RACE, full-length PRDM6 protein contains a PR domain and four Krüppel-like zinc fingers. In situ hybridization in mouse embryos demonstrates staining of the primitive streak, allantois, heart, outflow tract, paraaortic splanchnopleura (P-Sp)/aorto-gonadal-mesonephric (AGM) region and yolk sac, all sites known to be enriched in vascular precursor cells. PRDM6 is also detected in embryonic and adult-derived endothelial cell lines. PRDM6 is co-localized with histone H4 and methylates H4-K20 (but not H3) in vitro and in vivo, which is consistent with the known participation of PR domains in histone methyltransferase activity. Overexpression of PRDM6 in mouse embryonic endothelial cells induces apoptosis by activating caspase-3 and inducing G1 arrest. PRDM6 inhibits cell proliferation as determined by BrdU incorporation in endothelial cells, but not in rat aortic smooth muscle cells. Overexpression of PRDM6 also results in reduced tube formation in cultured endothelial cells grown in Matrigel. Taken together, our data indicate that PRDM6 is expressed by vascular precursors, has differential effects in endothelial cells and smooth muscle cells, and may play a role in vascular precursor differentiation and survival by modulating local chromatin-remodeling activity within hematovascular subpopulations during development.
Collapse
Affiliation(s)
- Yaxu Wu
- Carolina Cardiovascular Biology Center, University of North Carolina, Chapel Hill, NC
| | - James E. Ferguson
- Carolina Cardiovascular Biology Center, University of North Carolina, Chapel Hill, NC
| | - Hong Wang
- Carolina Cardiovascular Biology Center, University of North Carolina, Chapel Hill, NC
| | - Rusty Kelley
- Carolina Cardiovascular Biology Center, University of North Carolina, Chapel Hill, NC
| | - Rongqin Ren
- Carolina Cardiovascular Biology Center, University of North Carolina, Chapel Hill, NC
| | - Holly McDonough
- Carolina Cardiovascular Biology Center, University of North Carolina, Chapel Hill, NC
| | - James Meeker
- Carolina Cardiovascular Biology Center, University of North Carolina, Chapel Hill, NC
| | - Peter C. Charles
- Carolina Cardiovascular Biology Center, University of North Carolina, Chapel Hill, NC
| | - Hengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham
| | - Cam Patterson
- Carolina Cardiovascular Biology Center, University of North Carolina, Chapel Hill, NC
- Departments of Medicine, †Cell and Developmental Biology, and †Pharmacology, University of North Carolina, Chapel Hill, NC
| |
Collapse
|
49
|
Zhang XY, Rodaway ARF. SCL-GFP transgenic zebrafish: in vivo imaging of blood and endothelial development and identification of the initial site of definitive hematopoiesis. Dev Biol 2007; 307:179-94. [PMID: 17559829 DOI: 10.1016/j.ydbio.2007.04.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2006] [Revised: 03/13/2007] [Accepted: 04/03/2007] [Indexed: 11/26/2022]
Abstract
The bHLH transcription factor SCL plays a central role in the generation of hematopoietic cells in vertebrates. We modified a PAC containing the whole zebrafish scl locus, inserting GFP into the first coding exon of scl. In germline-transgenic zebrafish generated using this construct, GFP expression completely recapitulates the endogenous expression of scl in blood, endothelium and CNS. We performed in vivo timelapse imaging of blood and endothelial precursor migration at the single-cell level and show that these cells migrate from the posterior lateral plate mesoderm to their site of differentiation in the intermediate cell mass. The anterior lateral plate domain of GFP expression gives rise to primitive macrophages and the blood vessels of the head. In later embryos, GFP expression identifies clusters of hematopoietic cells that develop between the dorsal aorta and posterior cardinal veins after primitive erythrocytes have entered circulation. Two treatments that block definitive hematopoiesis (treatment with dioxin (TCDD), and injection of an antisense morpholino oligonucleotide targeted to runx1) ablate these hematopoietic clusters. This indicates that these clusters represent the first site of definitive hematopoiesis in zebrafish. This site is anatomically homologous to the proposed source of hematopoietic stem cells in amniotes, the aorta-gonad-mesonephros (AGM) region. A second transgenic line, containing the promoter of scl driving GFP, lacks expression in the definitive clusters.
Collapse
Affiliation(s)
- Xiang Yi Zhang
- King's College London, The Randall Division of Cell and Molecular Biophysics, School of Biomedical Sciences, New Hunt's House, Guy's Campus, London SE1 1UL, UK
| | | |
Collapse
|
50
|
Pimanda JE, Donaldson IJ, de Bruijn MFTR, Kinston S, Knezevic K, Huckle L, Piltz S, Landry JR, Green AR, Tannahill D, Göttgens B. The SCL transcriptional network and BMP signaling pathway interact to regulate RUNX1 activity. Proc Natl Acad Sci U S A 2007; 104:840-5. [PMID: 17213321 PMCID: PMC1783401 DOI: 10.1073/pnas.0607196104] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2006] [Indexed: 11/18/2022] Open
Abstract
Hematopoietic stem cell (HSC) development is regulated by several signaling pathways and a number of key transcription factors, which include Scl/Tal1, Runx1, and members of the Smad family. However, it remains unclear how these various determinants interact. Using a genome-wide computational screen based on the well characterized Scl +19 HSC enhancer, we have identified a related Smad6 enhancer that also targets expression to blood and endothelial cells in transgenic mice. Smad6, Bmp4, and Runx1 transcripts are concentrated along the ventral aspect of the E10.5 dorsal aorta in the aorta-gonad-mesonephros region from which HSCs originate. Moreover, Smad6, an inhibitor of Bmp4 signaling, binds and inhibits Runx1 activity, whereas Smad1, a positive mediator of Bmp4 signaling, transactivates the Runx1 promoter. Taken together, our results integrate three key determinants of HSC development; the Scl transcriptional network, Runx1 activity, and the Bmp4/Smad signaling pathway.
Collapse
Affiliation(s)
- John E. Pimanda
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 2XY, United Kingdom
| | - Ian J. Donaldson
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 2XY, United Kingdom
| | - Marella F. T. R. de Bruijn
- Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom; and
| | - Sarah Kinston
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 2XY, United Kingdom
| | - Kathy Knezevic
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 2XY, United Kingdom
| | - Liz Huckle
- The Wellcome Trust Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | - Sandie Piltz
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 2XY, United Kingdom
| | - Josette-Renée Landry
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 2XY, United Kingdom
| | - Anthony R. Green
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 2XY, United Kingdom
| | - David Tannahill
- The Wellcome Trust Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | - Berthold Göttgens
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 2XY, United Kingdom
| |
Collapse
|