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Imaz-Rosshandler I, Rode C, Guibentif C, Harland LTG, Ton MLN, Dhapola P, Keitley D, Argelaguet R, Calero-Nieto FJ, Nichols J, Marioni JC, de Bruijn MFTR, Göttgens B. Tracking early mammalian organogenesis - prediction and validation of differentiation trajectories at whole organism scale. Development 2024; 151:dev201867. [PMID: 37982461 PMCID: PMC10906099 DOI: 10.1242/dev.201867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 10/30/2023] [Indexed: 11/21/2023]
Abstract
Early organogenesis represents a key step in animal development, during which pluripotent cells diversify to initiate organ formation. Here, we sampled 300,000 single-cell transcriptomes from mouse embryos between E8.5 and E9.5 in 6-h intervals and combined this new dataset with our previous atlas (E6.5-E8.5) to produce a densely sampled timecourse of >400,000 cells from early gastrulation to organogenesis. Computational lineage reconstruction identified complex waves of blood and endothelial development, including a new programme for somite-derived endothelium. We also dissected the E7.5 primitive streak into four adjacent regions, performed scRNA-seq and predicted cell fates computationally. Finally, we defined developmental state/fate relationships by combining orthotopic grafting, microscopic analysis and scRNA-seq to transcriptionally determine cell fates of grafted primitive streak regions after 24 h of in vitro embryo culture. Experimentally determined fate outcomes were in good agreement with computationally predicted fates, demonstrating how classical grafting experiments can be revisited to establish high-resolution cell state/fate relationships. Such interdisciplinary approaches will benefit future studies in developmental biology and guide the in vitro production of cells for organ regeneration and repair.
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Affiliation(s)
- Ivan Imaz-Rosshandler
- Department of Haematology, University of Cambridge, Cambridge CB2 0RE, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Christina Rode
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Carolina Guibentif
- Department of Microbiology and Immunology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Luke T. G. Harland
- Department of Haematology, University of Cambridge, Cambridge CB2 0RE, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Mai-Linh N. Ton
- Department of Haematology, University of Cambridge, Cambridge CB2 0RE, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Parashar Dhapola
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, 221 00 Lund, Sweden
| | - Daniel Keitley
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Ricard Argelaguet
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
- Altos Labs Cambridge Institute, Granta Park, Cambridge CB21 6GP, UK
| | - Fernando J. Calero-Nieto
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Jennifer Nichols
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - John C. Marioni
- Wellcome Sanger Institute, Wellcome Genome Campus, Saffron Walden CB10 1SA, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Saffron Walden CB10 1SA, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Marella F. T. R. de Bruijn
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Berthold Göttgens
- Department of Haematology, University of Cambridge, Cambridge CB2 0RE, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
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2
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Silvério-Alves R, Kurochkin I, Rydström A, Vazquez Echegaray C, Haider J, Nicholls M, Rode C, Thelaus L, Lindgren AY, Ferreira AG, Brandão R, Larsson J, de Bruijn MFTR, Martin-Gonzalez J, Pereira CF. GATA2 mitotic bookmarking is required for definitive haematopoiesis. Nat Commun 2023; 14:4645. [PMID: 37580379 PMCID: PMC10425459 DOI: 10.1038/s41467-023-40391-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 07/26/2023] [Indexed: 08/16/2023] Open
Abstract
In mitosis, most transcription factors detach from chromatin, but some are retained and bookmark genomic sites. Mitotic bookmarking has been implicated in lineage inheritance, pluripotency and reprogramming. However, the biological significance of this mechanism in vivo remains unclear. Here, we address mitotic retention of the hemogenic factors GATA2, GFI1B and FOS during haematopoietic specification. We show that GATA2 remains bound to chromatin throughout mitosis, in contrast to GFI1B and FOS, via C-terminal zinc finger-mediated DNA binding. GATA2 bookmarks a subset of its interphase targets that are co-enriched for RUNX1 and other regulators of definitive haematopoiesis. Remarkably, homozygous mice harbouring the cyclin B1 mitosis degradation domain upstream Gata2 partially phenocopy knockout mice. Degradation of GATA2 at mitotic exit abolishes definitive haematopoiesis at aorta-gonad-mesonephros, placenta and foetal liver, but does not impair yolk sac haematopoiesis. Our findings implicate GATA2-mediated mitotic bookmarking as critical for definitive haematopoiesis and highlight a dependency on bookmarkers for lineage commitment.
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Affiliation(s)
- Rita Silvério-Alves
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84, Lund, Sweden
- CNC - Centre for Neuroscience and Cell Biology, University of Coimbra, Largo Marquês do Pombal, 3004-517, Coimbra, Portugal
- Doctoral Programme in Experimental Biology and Biomedicine, University of Coimbra, Largo Marquês do Pombal, 3004-517, Coimbra, Portugal
| | - Ilia Kurochkin
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84, Lund, Sweden
| | - Anna Rydström
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
| | - Camila Vazquez Echegaray
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84, Lund, Sweden
| | - Jakob Haider
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84, Lund, Sweden
| | - Matthew Nicholls
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
| | - Christina Rode
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
| | - Louise Thelaus
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84, Lund, Sweden
| | - Aida Yifter Lindgren
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84, Lund, Sweden
| | - Alexandra Gabriela Ferreira
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84, Lund, Sweden
- CNC - Centre for Neuroscience and Cell Biology, University of Coimbra, Largo Marquês do Pombal, 3004-517, Coimbra, Portugal
- Doctoral Programme in Experimental Biology and Biomedicine, University of Coimbra, Largo Marquês do Pombal, 3004-517, Coimbra, Portugal
| | - Rafael Brandão
- Core Facility for Transgenic Mice, Department of Experimental Medicine, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Jonas Larsson
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84, Lund, Sweden
| | - Marella F T R de Bruijn
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
| | - Javier Martin-Gonzalez
- Core Facility for Transgenic Mice, Department of Experimental Medicine, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Carlos-Filipe Pereira
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden.
- Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84, Lund, Sweden.
- CNC - Centre for Neuroscience and Cell Biology, University of Coimbra, Largo Marquês do Pombal, 3004-517, Coimbra, Portugal.
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3
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Owens DDG, Anselmi G, Oudelaar AM, Downes DJ, Cavallo A, Harman JR, Schwessinger R, Bucakci A, Greder L, de Ornellas S, Jeziorska D, Telenius J, Hughes JR, de Bruijn MFTR. Dynamic Runx1 chromatin boundaries affect gene expression in hematopoietic development. Nat Commun 2022; 13:773. [PMID: 35140205 PMCID: PMC8828719 DOI: 10.1038/s41467-022-28376-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 01/12/2022] [Indexed: 01/22/2023] Open
Abstract
The transcription factor RUNX1 is a critical regulator of developmental hematopoiesis and is frequently disrupted in leukemia. Runx1 is a large, complex gene that is expressed from two alternative promoters under the spatiotemporal control of multiple hematopoietic enhancers. To dissect the dynamic regulation of Runx1 in hematopoietic development, we analyzed its three-dimensional chromatin conformation in mouse embryonic stem cell (ESC) differentiation cultures. Runx1 resides in a 1.1 Mb topologically associating domain (TAD) demarcated by convergent CTCF motifs. As ESCs differentiate to mesoderm, chromatin accessibility, Runx1 enhancer-promoter (E-P) interactions, and CTCF-CTCF interactions increase in the TAD, along with initiation of Runx1 expression from the P2 promoter. Differentiation to hematopoietic progenitor cells is associated with the formation of tissue-specific sub-TADs over Runx1, a shift in E-P interactions, P1 promoter demethylation, and robust expression from both Runx1 promoters. Deletion of promoter-proximal CTCF sites at the sub-TAD boundaries has no obvious effects on E-P interactions but leads to partial loss of domain structure, mildly affects gene expression, and delays hematopoietic development. Together, our analysis of gene regulation at a large multi-promoter developmental gene reveals that dynamic sub-TAD chromatin boundaries play a role in establishing TAD structure and coordinated gene expression.
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Affiliation(s)
- Dominic D G Owens
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Giorgio Anselmi
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - A Marieke Oudelaar
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Damien J Downes
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Alessandro Cavallo
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Joe R Harman
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Ron Schwessinger
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Akin Bucakci
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Lucas Greder
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Sara de Ornellas
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Physical and Theoretical Chemistry Building, Department of Chemistry, University of Oxford, Oxford, UK
| | - Danuta Jeziorska
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jelena Telenius
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jim R Hughes
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
| | - Marella F T R de Bruijn
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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4
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Azzoni E, Frontera V, Anselmi G, Rode C, James C, Deltcheva EM, Demian AS, Brown J, Barone C, Patelli A, Harman JR, Nicholls M, Conway SJ, Morrissey E, Jacobsen SEW, Sparrow DB, Harris AL, Enver T, de Bruijn MFTR. The onset of circulation triggers a metabolic switch required for endothelial to hematopoietic transition. Cell Rep 2021; 37:110103. [PMID: 34910918 PMCID: PMC8692754 DOI: 10.1016/j.celrep.2021.110103] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 10/11/2021] [Accepted: 11/15/2021] [Indexed: 12/14/2022] Open
Abstract
Hematopoietic stem cells (HSCs) emerge during development from the vascular wall of the main embryonic arteries. The onset of circulation triggers several processes that provide critical external factors for HSC generation. Nevertheless, it is not fully understood how and when the onset of circulation affects HSC emergence. Here we show that in Ncx1-/- mouse embryos devoid of circulation the HSC lineage develops until the phenotypic pro-HSC stage. However, these cells reside in an abnormal microenvironment, fail to activate the hematopoietic program downstream of Runx1, and are functionally impaired. Single-cell transcriptomics shows that during the endothelial-to-hematopoietic transition, Ncx1-/- cells fail to undergo a glycolysis to oxidative phosphorylation metabolic switch present in wild-type cells. Interestingly, experimental activation of glycolysis results in decreased intraembryonic hematopoiesis. Our results suggest that the onset of circulation triggers metabolic changes that allow HSC generation to proceed.
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Affiliation(s)
- Emanuele Azzoni
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK.
| | - Vincent Frontera
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Giorgio Anselmi
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Christina Rode
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Chela James
- Department of Cancer Biology, UCL Cancer Institute, University College London, London, WC1E 6DD, UK
| | - Elitza M Deltcheva
- Department of Cancer Biology, UCL Cancer Institute, University College London, London, WC1E 6DD, UK
| | - Atanasiu S Demian
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - John Brown
- Department of Cancer Biology, UCL Cancer Institute, University College London, London, WC1E 6DD, UK
| | - Cristiana Barone
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, 20900, Italy
| | - Arianna Patelli
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, 20900, Italy
| | - Joe R Harman
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Matthew Nicholls
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Simon J Conway
- HB Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, IN 46033, USA
| | - Edward Morrissey
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Sten Eirik W Jacobsen
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK; Hematopoietic Stem Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK; Department of Cell and Molecular Biology, Wallenberg Institute for Regenerative Medicine and Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet and Karolinska University Hospital, 171 77 Stockholm, Sweden
| | - Duncan B Sparrow
- Department of Physiology, Anatomy and Genetics, BHF Centre of Research Excellence, University of Oxford, Oxford, OX1 3PT, UK
| | - Adrian L Harris
- Department of Oncology, Molecular Oncology Laboratories, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Tariq Enver
- Department of Cancer Biology, UCL Cancer Institute, University College London, London, WC1E 6DD, UK; Division of Molecular Medicine and Gene Therapy, Lund University, Lund, 22184, Sweden
| | - Marella F T R de Bruijn
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK.
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5
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Neo WH, Meng Y, Rodriguez-Meira A, Fadlullah MZH, Booth CAG, Azzoni E, Thongjuea S, de Bruijn MFTR, Jacobsen SEW, Mead AJ, Lacaud G. Ezh2 is essential for the generation of functional yolk sac derived erythro-myeloid progenitors. Nat Commun 2021; 12:7019. [PMID: 34857757 PMCID: PMC8640066 DOI: 10.1038/s41467-021-27140-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 10/27/2021] [Indexed: 01/01/2023] Open
Abstract
Yolk sac (YS) hematopoiesis is critical for the survival of the embryo and a major source of tissue-resident macrophages that persist into adulthood. Yet, the transcriptional and epigenetic regulation of YS hematopoiesis remains poorly characterized. Here we report that the epigenetic regulator Ezh2 is essential for YS hematopoiesis but dispensable for subsequent aorta-gonad-mesonephros (AGM) blood development. Loss of EZH2 activity in hemogenic endothelium (HE) leads to the generation of phenotypically intact but functionally deficient erythro-myeloid progenitors (EMPs), while the generation of primitive erythroid cells is not affected. EZH2 activity is critical for the generation of functional EMPs at the onset of the endothelial-to-hematopoietic transition but subsequently dispensable. We identify a lack of Wnt signaling downregulation as the primary reason for the production of non-functional EMPs. Together, our findings demonstrate a critical and stage-specific role of Ezh2 in modulating Wnt signaling during the generation of EMPs from YS HE.
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Affiliation(s)
- Wen Hao Neo
- Haematopoietic Stem Cell Biology Laboratory, MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK.
- Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Macclesfield, SK10 4TG, UK.
| | - Yiran Meng
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Alba Rodriguez-Meira
- Haematopoietic Stem Cell Biology Laboratory, MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Muhammad Z H Fadlullah
- Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Macclesfield, SK10 4TG, UK
| | - Christopher A G Booth
- Haematopoietic Stem Cell Biology Laboratory, MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Emanuele Azzoni
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Supat Thongjuea
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Marella F T R de Bruijn
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Sten Eirik W Jacobsen
- Haematopoietic Stem Cell Biology Laboratory, MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine and Department of Cell and Molecular Biology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Adam J Mead
- Haematopoietic Stem Cell Biology Laboratory, MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK.
| | - Georges Lacaud
- Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Macclesfield, SK10 4TG, UK.
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6
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Harman JR, Thorne R, Jamilly M, Tapia M, Crump NT, Rice S, Beveridge R, Morrissey E, de Bruijn MFTR, Roberts I, Roy A, Fulga TA, Milne TA. A KMT2A-AFF1 gene regulatory network highlights the role of core transcription factors and reveals the regulatory logic of key downstream target genes. Genome Res 2021; 31:1159-1173. [PMID: 34088716 PMCID: PMC8256865 DOI: 10.1101/gr.268490.120] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 06/02/2021] [Indexed: 12/13/2022]
Abstract
Regulatory interactions mediated by transcription factors (TFs) make up complex networks that control cellular behavior. Fully understanding these gene regulatory networks (GRNs) offers greater insight into the consequences of disease-causing perturbations than can be achieved by studying single TF binding events in isolation. Chromosomal translocations of the lysine methyltransferase 2A (KMT2A) gene produce KMT2A fusion proteins such as KMT2A-AFF1 (previously MLL-AF4), causing poor prognosis acute lymphoblastic leukemias (ALLs) that sometimes relapse as acute myeloid leukemias (AMLs). KMT2A-AFF1 drives leukemogenesis through direct binding and inducing the aberrant overexpression of key genes, such as the anti-apoptotic factor BCL2 and the proto-oncogene MYC However, studying direct binding alone does not incorporate possible network-generated regulatory outputs, including the indirect induction of gene repression. To better understand the KMT2A-AFF1-driven regulatory landscape, we integrated ChIP-seq, patient RNA-seq, and CRISPR essentiality screens to generate a model GRN. This GRN identified several key transcription factors such as RUNX1 that regulate target genes downstream of KMT2A-AFF1 using feed-forward loop (FFL) and cascade motifs. A core set of nodes are present in both ALL and AML, and CRISPR screening revealed several factors that help mediate response to the drug venetoclax. Using our GRN, we then identified a KMT2A-AFF1:RUNX1 cascade that represses CASP9, as well as KMT2A-AFF1-driven FFLs that regulate BCL2 and MYC through combinatorial TF activity. This illustrates how our GRN can be used to better connect KMT2A-AFF1 behavior to downstream pathways that contribute to leukemogenesis, and potentially predict shifts in gene expression that mediate drug response.
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Affiliation(s)
- Joe R Harman
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, United Kingdom
| | - Ross Thorne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, United Kingdom
| | - Max Jamilly
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, United Kingdom
| | - Marta Tapia
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, United Kingdom
| | - Nicholas T Crump
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, United Kingdom
| | - Siobhan Rice
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, United Kingdom
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Department of Paediatrics, University of Oxford, Oxford, OX3 9DS, United Kingdom
| | - Ryan Beveridge
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, United Kingdom
- Virus Screening Facility, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, United Kingdom
| | - Edward Morrissey
- Center for Computational Biology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
| | - Marella F T R de Bruijn
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, United Kingdom
| | - Irene Roberts
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Department of Paediatrics, University of Oxford, Oxford, OX3 9DS, United Kingdom
- NIHR Oxford Biomedical Research Centre Haematology Theme, University of Oxford, Oxford, OX3 9DS, United Kingdom
| | - Anindita Roy
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Department of Paediatrics, University of Oxford, Oxford, OX3 9DS, United Kingdom
- NIHR Oxford Biomedical Research Centre Haematology Theme, University of Oxford, Oxford, OX3 9DS, United Kingdom
| | - Tudor A Fulga
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, United Kingdom
| | - Thomas A Milne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, United Kingdom
- NIHR Oxford Biomedical Research Centre Haematology Theme, University of Oxford, Oxford, OX3 9DS, United Kingdom
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7
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Harland LTG, Simon CS, Senft AD, Costello I, Greder L, Imaz-Rosshandler I, Göttgens B, Marioni JC, Bikoff EK, Porcher C, de Bruijn MFTR, Robertson EJ. Publisher Correction: The T-box transcription factor Eomesodermin governs haemogenic competence of yolk sac mesodermal progenitors. Nat Cell Biol 2021; 23:293. [PMID: 33574614 DOI: 10.1038/s41556-021-00645-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Luke T G Harland
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Claire S Simon
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.,Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anna D Senft
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.,National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Ita Costello
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Lucas Greder
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Ivan Imaz-Rosshandler
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Berthold Göttgens
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - John C Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK.,Wellcome Sanger Institute, Cambridge, UK.,CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | - Catherine Porcher
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Marella F T R de Bruijn
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.
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8
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Harland LTG, Simon CS, Senft AD, Costello I, Greder L, Imaz-Rosshandler I, Göttgens B, Marioni JC, Bikoff EK, Porcher C, de Bruijn MFTR, Robertson EJ. The T-box transcription factor Eomesodermin governs haemogenic competence of yolk sac mesodermal progenitors. Nat Cell Biol 2021; 23:61-74. [PMID: 33420489 PMCID: PMC7610381 DOI: 10.1038/s41556-020-00611-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 11/25/2020] [Indexed: 01/29/2023]
Abstract
Extra-embryonic mesoderm (ExM)-composed of the earliest cells that traverse the primitive streak-gives rise to the endothelium as well as haematopoietic progenitors in the developing yolk sac. How a specific subset of ExM becomes committed to a haematopoietic fate remains unclear. Here we demonstrate using an embryonic stem cell model that transient expression of the T-box transcription factor Eomesodermin (Eomes) governs haemogenic competency of ExM. Eomes regulates the accessibility of enhancers that the transcription factor stem cell leukaemia (SCL) normally utilizes to specify primitive erythrocytes and is essential for the normal development of Runx1+ haemogenic endothelium. Single-cell RNA sequencing suggests that Eomes loss of function profoundly blocks the formation of blood progenitors but not specification of Flk-1+ haematoendothelial progenitors. Our findings place Eomes at the top of the transcriptional hierarchy regulating early blood formation and suggest that haemogenic competence is endowed earlier during embryonic development than was previously appreciated.
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Affiliation(s)
- Luke T G Harland
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Claire S Simon
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anna D Senft
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Ita Costello
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Lucas Greder
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Ivan Imaz-Rosshandler
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Berthold Göttgens
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - John C Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | - Catherine Porcher
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Marella F T R de Bruijn
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.
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9
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Migueles RP, Shaw L, Rodrigues NP, May G, Henseleit K, Anderson KGV, Goker H, Jones CM, de Bruijn MFTR, Brickman JM, Enver T. Transcriptional regulation of Hhex in hematopoiesis and hematopoietic stem cell ontogeny. Dev Biol 2017; 424:236-245. [PMID: 28189604 DOI: 10.1016/j.ydbio.2016.12.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 11/25/2016] [Accepted: 12/19/2016] [Indexed: 11/28/2022]
Abstract
Hematopoietic stem cells (HSCs) emerge during development via an endothelial-to-hematopoietic transition from hemogenic endothelium of the dorsal aorta (DA). Using in situ hybridization and analysis of a knock-in RedStar reporter, we show that the transcriptional regulator Hhex is expressed in endothelium of the dorsal aorta (DA) and in clusters of putative HSCs as they are specified during murine development. We exploited this observation, using the Hhex locus to define cis regulatory elements, enhancers and interacting transcription factors that are both necessary and sufficient to support gene expression in the emerging HSC. We identify an evolutionarily conserved non-coding region (ECR) in the Hhex locus with the capacity to bind the hematopoietic-affiliated transcriptional regulators Gata2, SCL, Fli1, Pu.1 and Ets1/2. This region is sufficient to drive the expression of a transgenic GFP reporter in the DA endothelium and intra-aortic hematopoietic clusters. GFP-positive AGM cells co-expressed HSC-associated markers c-Kit, CD34, VE-Cadherin, and CD45, and were capable of multipotential differentiation and long term engraftment when transplanted into myelo-ablated recipients. The Hhex ECR was also sufficient to drive expression at additional blood sites including the yolk sac blood islands, fetal liver, vitelline and umbilical arteries and the adult bone marrow, suggesting a common mechanism for Hhex regulation throughout ontogenesis of the blood system. To explore the physiological requirement for the Hhex ECR region during hematoendothelial development, we deleted the ECR element from the endogenous locus in the context of a targeted Hhex-RedStar reporter allele. Results indicate a specific requirement for the ECR in blood-associated Hhex expression during development and further demonstrate a requirement for this region in the adult HSC compartment. Taken together, our results identified the ECR region as an enhancer both necessary and sufficient for gene expression in HSC development and homeostasis. The Hhex ECR thus appears to be a core node for the convergence of the transcription factor network that governs the emergence of HSCs.
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Affiliation(s)
- Rosa Portero Migueles
- MRC Centre for Regenerative Medicine - Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, EH16 4UU Edinburgh, UK
| | - Louise Shaw
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Neil P Rodrigues
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK; The European Cancer Stem Cell Research Institute, Cardiff University, School of Biosciences, Hadyn Ellis Building, Cardiff CF24 4HQ, UK
| | - Gillian May
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK; Stem Cell Laboratory, UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Korinna Henseleit
- MRC Centre for Regenerative Medicine - Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, EH16 4UU Edinburgh, UK
| | - Kathryn G V Anderson
- MRC Centre for Regenerative Medicine - Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, EH16 4UU Edinburgh, UK; The Danish Stem Cell Centre - DanStem, University of Copenhagen, 3B Blegdamsvej, DK-2200 Copenhagen, Denmark
| | - Hakan Goker
- Institute for Cancer Research, Chester Beatty Laboratories, London SW3 6JB, UK
| | - C Michael Jones
- Institute for Cancer Research, Chester Beatty Laboratories, London SW3 6JB, UK
| | - Marella F T R de Bruijn
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Joshua M Brickman
- MRC Centre for Regenerative Medicine - Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, EH16 4UU Edinburgh, UK; The Danish Stem Cell Centre - DanStem, University of Copenhagen, 3B Blegdamsvej, DK-2200 Copenhagen, Denmark.
| | - Tariq Enver
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK; Stem Cell Laboratory, UCL Cancer Institute, University College London, London WC1E 6DD, UK.
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10
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Yzaguirre AD, de Bruijn MFTR, Speck NA. The Role of Runx1 in Embryonic Blood Cell Formation. Advances in Experimental Medicine and Biology 2017; 962:47-64. [DOI: 10.1007/978-981-10-3233-2_4] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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11
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Luis TC, Luc S, Mizukami T, Boukarabila H, Thongjuea S, Woll PS, Azzoni E, Giustacchini A, Lutteropp M, Bouriez-Jones T, Vaidya H, Mead AJ, Atkinson D, Böiers C, Carrelha J, Macaulay IC, Patient R, Geissmann F, Nerlov C, Sandberg R, de Bruijn MFTR, Blackburn CC, Godin I, Jacobsen SEW. Initial seeding of the embryonic thymus by immune-restricted lympho-myeloid progenitors. Nat Immunol 2016; 17:1424-1435. [PMID: 27695000 DOI: 10.1038/ni.3576] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Accepted: 09/01/2016] [Indexed: 02/08/2023]
Abstract
The final stages of restriction to the T cell lineage occur in the thymus after the entry of thymus-seeding progenitors (TSPs). The identity and lineage potential of TSPs remains unclear. Because the first embryonic TSPs enter a non-vascularized thymic rudiment, we were able to directly image and establish the functional and molecular properties of embryonic thymopoiesis-initiating progenitors (T-IPs) before their entry into the thymus and activation of Notch signaling. T-IPs did not include multipotent stem cells or molecular evidence of T cell-restricted progenitors. Instead, single-cell molecular and functional analysis demonstrated that most fetal T-IPs expressed genes of and had the potential to develop into lymphoid as well as myeloid components of the immune system. Moreover, studies of embryos deficient in the transcriptional regulator RBPJ demonstrated that canonical Notch signaling was not involved in pre-thymic restriction to the T cell lineage or the migration of T-IPs.
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Affiliation(s)
- Tiago C Luis
- Haematopoietic Stem Cell Laboratory, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford OX3 9DS, United Kingdom
| | - Sidinh Luc
- Haematopoietic Stem Cell Laboratory, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford OX3 9DS, United Kingdom.,Hematopoietic Stem Cell Laboratory, Lund Stem Cell Center, Lund University, Klinikgatan 26, 221 84, Lund, Sweden.,MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Takuo Mizukami
- Haematopoietic Stem Cell Laboratory, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford OX3 9DS, United Kingdom
| | - Hanane Boukarabila
- Haematopoietic Stem Cell Laboratory, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford OX3 9DS, United Kingdom
| | - Supat Thongjuea
- Haematopoietic Stem Cell Laboratory, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford OX3 9DS, United Kingdom.,MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Petter S Woll
- Haematopoietic Stem Cell Laboratory, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford OX3 9DS, United Kingdom
| | - Emanuele Azzoni
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Alice Giustacchini
- Haematopoietic Stem Cell Laboratory, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford OX3 9DS, United Kingdom
| | - Michael Lutteropp
- Haematopoietic Stem Cell Laboratory, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford OX3 9DS, United Kingdom.,MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Tiphaine Bouriez-Jones
- Haematopoietic Stem Cell Laboratory, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford OX3 9DS, United Kingdom
| | - Harsh Vaidya
- Institute for Stem Cell Research, MRC Centre for Regenerative Medicine, University of Edinburgh, EH16 4UU Edinburgh, UK
| | - Adam J Mead
- Haematopoietic Stem Cell Laboratory, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford OX3 9DS, United Kingdom
| | - Deborah Atkinson
- Haematopoietic Stem Cell Laboratory, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford OX3 9DS, United Kingdom
| | - Charlotta Böiers
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, 22184 Lund, Sweden
| | - Joana Carrelha
- Haematopoietic Stem Cell Laboratory, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford OX3 9DS, United Kingdom
| | - Iain C Macaulay
- Haematopoietic Stem Cell Laboratory, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford OX3 9DS, United Kingdom
| | - Roger Patient
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Frederic Geissmann
- King's College London, Great Maze Pond, SE1 1UL London, UK.,Memorial Sloan Kettering Cancer Center, 417 East 68(th) Street, New York, NY 10065, USA
| | - Claus Nerlov
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institutet and Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden
| | - Marella F T R de Bruijn
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - C Clare Blackburn
- Institute for Stem Cell Research, MRC Centre for Regenerative Medicine, University of Edinburgh, EH16 4UU Edinburgh, UK
| | - Isabelle Godin
- Institut National de la Santé et de la Recherche Médicale U1170; Univ Paris-Sud, Université Paris-Saclay; Gustave Roussy, 114, rue Edouard Vaillant; Villejuif, F-94805, France
| | - Sten Eirik W Jacobsen
- Haematopoietic Stem Cell Laboratory, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford OX3 9DS, United Kingdom.,MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom.,Department of Cell and Molecular Biology, Wallenberg Institute for Regenerative Medicine and Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet and Karolinska University Hospital, 171 77 Stockholm, Sweden
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12
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Blobel GA, Bodine D, Brand M, Crispino J, de Bruijn MFTR, Nathan D, Papayannopoulou T, Porcher C, Strouboulis J, Zon L, Higgs DR, Stamatoyannopoulos G, Engel JD. An international effort to cure a global health problem: A report on the 19th Hemoglobin Switching Conference. Exp Hematol 2015; 43:821-37. [PMID: 26143582 DOI: 10.1016/j.exphem.2015.06.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 06/04/2015] [Accepted: 06/05/2015] [Indexed: 12/24/2022]
Abstract
Every 2 years since 1978, an international group of scientists, physicians, and other researchers meet to discuss the latest developments in the underlying etiology, mechanisms of action, and developmental acquisition of cellular and systemic defects exhibited and elicited by the most common inherited human disorders, the hemoglobinopathies. The 19th Hemoglobin Switching Conference, held in September 2014 at St. John's College in Oxford, once again exceeded all expectations by describing cutting edge research in cellular, molecular, developmental, and genomic advances focused on these diseases. The conference comprised about 60 short talks over 3 days by leading investigators in the field. This meeting report describes the highlights of the conference.
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Affiliation(s)
- Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David Bodine
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Marjorie Brand
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - John Crispino
- Division of Hematology/Oncology, Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
| | - Marella F T R de Bruijn
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital University of Oxford, Oxford, UK; BRC Blood Theme, NIHR Oxford Biomedical Centre, Oxford University Hospital, Oxford, UK
| | - David Nathan
- Division of Hematology and Oncology, Boston Children's Hospital, Departments of Pediatrics and Medicine, Harvard Medical School, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Catherine Porcher
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital University of Oxford, Oxford, UK; BRC Blood Theme, NIHR Oxford Biomedical Centre, Oxford University Hospital, Oxford, UK
| | - John Strouboulis
- Division of Molecular Oncology, Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece
| | - Len Zon
- Boston Children's Hospital/HHMI, Boston, MA, USA
| | - Douglas R Higgs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital University of Oxford, Oxford, UK; BRC Blood Theme, NIHR Oxford Biomedical Centre, Oxford University Hospital, Oxford, UK
| | | | - James Douglas Engel
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA.
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13
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Marks-Bluth J, Khanna A, Chandrakanthan V, Thoms J, Bee T, Eich C, Kang YC, Knezevic K, Qiao Q, Fitch S, Oxburgh L, Ottersbach K, Dzierzak E, de Bruijn MFTR, Pimanda JE. SMAD1 and SMAD5 Expression Is Coordinately Regulated by FLI1 and GATA2 during Endothelial Development. Mol Cell Biol 2015; 35:2165-72. [PMID: 25870111 PMCID: PMC4438244 DOI: 10.1128/mcb.00239-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 04/01/2015] [Accepted: 04/03/2015] [Indexed: 01/02/2023] Open
Abstract
The bone morphogenetic protein (BMP)/SMAD signaling pathway is a critical regulator of angiogenic sprouting and is involved in vascular development in the embryo. SMAD1 and SMAD5, the core mediators of BMP signaling, are vital for this activity, yet little is known about their transcriptional regulation in endothelial cells. Here, we have integrated multispecies sequence conservation, tissue-specific chromatin, in vitro reporter assay, and in vivo transgenic data to identify and validate Smad1+63 and the Smad5 promoter as tissue-specific cis-regulatory elements that are active in the developing endothelium. The activity of these elements in the endothelium was dependent on highly conserved ETS, GATA, and E-box motifs, and chromatin immunoprecipitation showed high levels of enrichment of FLI1, GATA2, and SCL at these sites in endothelial cell lines and E11 dorsal aortas in vivo. Knockdown of FLI1 and GATA2 but not SCL reduced the expression of SMAD1 and SMAD5 in endothelial cells in vitro. In contrast, CD31(+) cKit(-) endothelial cells harvested from embryonic day 9 (E9) aorta-gonad-mesonephros (AGM) regions of GATA2 null embryos showed reduced Smad1 but not Smad5 transcript levels. This is suggestive of a degree of in vivo selection where, in the case of reduced SMAD1 levels, endothelial cells with more robust SMAD5 expression have a selective advantage.
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Affiliation(s)
- Jonathon Marks-Bluth
- Lowy Cancer Research Centre and the Prince of Wales Clinical School, The University of New South Wales, Sydney, NSW, Australia The Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Anchit Khanna
- Lowy Cancer Research Centre and the Prince of Wales Clinical School, The University of New South Wales, Sydney, NSW, Australia
| | - Vashe Chandrakanthan
- Lowy Cancer Research Centre and the Prince of Wales Clinical School, The University of New South Wales, Sydney, NSW, Australia
| | - Julie Thoms
- Lowy Cancer Research Centre and the Prince of Wales Clinical School, The University of New South Wales, Sydney, NSW, Australia
| | - Thomas Bee
- Lowy Cancer Research Centre and the Prince of Wales Clinical School, The University of New South Wales, Sydney, NSW, Australia
| | - Christina Eich
- Erasmus MC Stem Cell Institute, Department of Cell Biology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Young Chan Kang
- Lowy Cancer Research Centre and the Prince of Wales Clinical School, The University of New South Wales, Sydney, NSW, Australia
| | - Kathy Knezevic
- Lowy Cancer Research Centre and the Prince of Wales Clinical School, The University of New South Wales, Sydney, NSW, Australia
| | - Qiao Qiao
- Lowy Cancer Research Centre and the Prince of Wales Clinical School, The University of New South Wales, Sydney, NSW, Australia
| | - Simon Fitch
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Leif Oxburgh
- Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, Maine, USA
| | - Katrin Ottersbach
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Elaine Dzierzak
- Erasmus MC Stem Cell Institute, Department of Cell Biology, Erasmus University Medical Center, Rotterdam, Netherlands The Queen's Medical Research Institute, College of Medicine and Veterinary Medicine, Edinburgh, United Kingdom
| | - Marella F T R de Bruijn
- The Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - John E Pimanda
- Lowy Cancer Research Centre and the Prince of Wales Clinical School, The University of New South Wales, Sydney, NSW, Australia Department of Haematology, Prince of Wales Hospital, Sydney, NSW, Australia
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14
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Wilkinson AC, Kawata VKS, Schütte J, Gao X, Antoniou S, Baumann C, Woodhouse S, Hannah R, Tanaka Y, Swiers G, Moignard V, Fisher J, Hidetoshi S, Tijssen MR, de Bruijn MFTR, Liu P, Göttgens B. Single-cell analyses of regulatory network perturbations using enhancer-targeting TALEs suggest novel roles for PU.1 during haematopoietic specification. Development 2014; 141:4018-30. [PMID: 25252941 PMCID: PMC4197694 DOI: 10.1242/dev.115709] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Transcription factors (TFs) act within wider regulatory networks to control cell identity and fate. Numerous TFs, including Scl (Tal1) and PU.1 (Spi1), are known regulators of developmental and adult haematopoiesis, but how they act within wider TF networks is still poorly understood. Transcription activator-like effectors (TALEs) are a novel class of genetic tool based on the modular DNA-binding domains of Xanthomonas TAL proteins, which enable DNA sequence-specific targeting and the manipulation of endogenous gene expression. Here, we report TALEs engineered to target the PU.1-14kb and Scl+40kb transcriptional enhancers as efficient new tools to perturb the expression of these key haematopoietic TFs. We confirmed the efficiency of these TALEs at the single-cell level using high-throughput RT-qPCR, which also allowed us to assess the consequences of both PU.1 activation and repression on wider TF networks during developmental haematopoiesis. Combined with comprehensive cellular assays, these experiments uncovered novel roles for PU.1 during early haematopoietic specification. Finally, transgenic mouse studies confirmed that the PU.1-14kb element is active at sites of definitive haematopoiesis in vivo and PU.1 is detectable in haemogenic endothelium and early committing blood cells. We therefore establish TALEs as powerful new tools to study the functionality of transcriptional networks that control developmental processes such as early haematopoiesis.
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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
| | - Viviane K S Kawata
- Cambridge Institute for Medical Research and Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK Division of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
| | - Judith Schütte
- Cambridge Institute for Medical Research and Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Xuefei Gao
- Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - Stella Antoniou
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Claudia Baumann
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Steven Woodhouse
- Cambridge Institute for Medical Research and Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Rebecca Hannah
- Cambridge Institute for Medical Research and Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Yosuke Tanaka
- Cambridge Institute for Medical Research and Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Gemma Swiers
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Victoria Moignard
- Cambridge Institute for Medical Research and Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Jasmin Fisher
- Microsoft Research Cambridge, 21 Station Road, Cambridge CB1 2FB, UK Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Shimauchi Hidetoshi
- Division of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
| | - Marloes R Tijssen
- Department of Haematology, University of Cambridge and National Health Service Blood and Transplant, Cambridge CB2 0PT, UK
| | - Marella F T R de Bruijn
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Pentao Liu
- Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - Berthold Göttgens
- Cambridge Institute for Medical Research and Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
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15
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Abstract
Definitive hematopoietic cells are generated de novo during ontogeny from a specialized subset of endothelium, the so-called hemogenic endothelium. In this review we give a brief overview of the identification of hemogenic endothelium, explore its links with the HSC lineage, and summarize recent insights into the nature of hemogenic endothelium and the microenvironmental and intrinsic regulators contributing to its transition into blood. Ultimately, a better understanding of the processes controlling the transition of endothelium into blood will advance the generation and expansion of hematopoietic stem cells for therapeutic purposes.
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Affiliation(s)
- Gemma Swiers
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Medicine, John Radcliffe Hospital, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, United Kingdom
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16
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Böiers C, Carrelha J, Lutteropp M, Luc S, Green JCA, Azzoni E, Woll PS, Mead AJ, Hultquist A, Swiers G, Perdiguero EG, Macaulay IC, Melchiori L, Luis TC, Kharazi S, Bouriez-Jones T, Deng Q, Pontén A, Atkinson D, Jensen CT, Sitnicka E, Geissmann F, Godin I, Sandberg R, de Bruijn MFTR, Jacobsen SEW. Lymphomyeloid contribution of an immune-restricted progenitor emerging prior to definitive hematopoietic stem cells. Cell Stem Cell 2013; 13:535-48. [PMID: 24054998 DOI: 10.1016/j.stem.2013.08.012] [Citation(s) in RCA: 184] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Revised: 07/21/2013] [Accepted: 08/28/2013] [Indexed: 02/07/2023]
Abstract
In jawed vertebrates, development of an adaptive immune-system is essential for protection of the born organism against otherwise life-threatening pathogens. Myeloid cells of the innate immune system are formed early in development, whereas lymphopoiesis has been suggested to initiate much later, following emergence of definitive hematopoietic stem cells (HSCs). Herein, we demonstrate that the embryonic lymphoid commitment process initiates earlier than previously appreciated, prior to emergence of definitive HSCs, through establishment of a previously unrecognized entirely immune-restricted and lymphoid-primed progenitor. Notably, this immune-restricted progenitor appears to first emerge in the yolk sac and contributes physiologically to the establishment of lymphoid and some myeloid components of the immune-system, establishing the lymphomyeloid lineage restriction process as an early and physiologically important lineage-commitment step in mammalian hematopoiesis.
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Affiliation(s)
- Charlotta Böiers
- Haematopoietic Stem Cell Laboratory, Lund Stem Cell Center, Lund University, 221 84 Lund, Sweden; Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, 221 84 Lund, Sweden
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17
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Mirshekar-Syahkal B, Haak E, Kimber GM, van Leusden K, Harvey K, O'Rourke J, Laborda J, Bauer SR, de Bruijn MFTR, Ferguson-Smith AC, Dzierzak E, Ottersbach K. Dlk1 is a negative regulator of emerging hematopoietic stem and progenitor cells. Haematologica 2012; 98:163-71. [PMID: 22801971 DOI: 10.3324/haematol.2012.070789] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The first mouse adult-repopulating hematopoietic stem cells emerge in the aorta-gonad-mesonephros region at embryonic day (E) 10.5. Their numbers in this region increase thereafter and begin to decline at E12.5, thus pointing to the possible existence of both positive and negative regulators of emerging hematopoietic stem cells. Our recent expression analysis of the aorta-gonad-mesonephros region showed that the Delta-like homologue 1 (Dlk1) gene is up-regulated in the region of the aorta-gonad-mesonephros where hematopoietic stem cells are preferentially located. To analyze its function, we studied Dlk1 expression in wild-type and hematopoietic stem cell-deficient embryos and determined hematopoietic stem and progenitor cell activity in Dlk1 knockout and overexpressing mice. Its role in hematopoietic support was studied in co-culture experiments using stromal cell lines that express varying levels of Dlk1. We show here that Dlk1 is expressed in the smooth muscle layer of the dorsal aorta and the ventral sub-aortic mesenchyme, where its expression is dependent on the hematopoietic transcription factor Runx1. We further demonstrate that Dlk1 has a negative impact on hematopoietic stem and progenitor cell activity in the aorta-gonad-mesonephros region in vivo, which is recapitulated in co-cultures of hematopoietic stem cells on stromal cells that express varying levels of Dlk1. This negative effect of Dlk1 on hematopoietic stem and progenitor cell activity requires the membrane-bound form of the protein and cannot be recapitulated by soluble Dlk1. Together, these data suggest that Dlk1 expression by cells of the aorta-gonad-mesonephros hematopoietic microenvironment limits hematopoietic stem cell expansion and is, to our knowledge, the first description of such a negative regulator in this tissue.
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Affiliation(s)
- Bahar Mirshekar-Syahkal
- Department of Haematology, Cambridge Institute for Medical Research, Wellcome Trust & MRC Stem Cell Institute, University of Cambridge, Cambridge, UK
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18
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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: 531] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
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Affiliation(s)
- Nicola K Wilson
- University of Cambridge Department of Haematology, Cambridge Institute for Medical Research, Hills Road, Cambridge, CB2 0XY, UK
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19
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Abstract
Three recent Nature papers use time-lapse confocal imaging to visualize the birth of blood cells from the aortic endothelium. Two studies (Bertrand et al., 2010; Kissa and Herbomel, 2010) utilize the zebrafish embryo, while the third (Boisset et al., 2010) develops a novel technique to image the mouse aorta.
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Affiliation(s)
- Gemma Swiers
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
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20
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Nottingham WT, Jarratt A, Burgess M, Speck CL, Cheng JF, Prabhakar S, Rubin EM, Li PS, Sloane-Stanley J, Kong-A-San J, de Bruijn MFTR. Runx1-mediated hematopoietic stem-cell emergence is controlled by a Gata/Ets/SCL-regulated enhancer. Blood 2007; 110:4188-97. [PMID: 17823307 PMCID: PMC2234795 DOI: 10.1182/blood-2007-07-100883] [Citation(s) in RCA: 188] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The transcription factor Runx1/AML1 is an important regulator of hematopoiesis and is critically required for the generation of the first definitive hematopoietic stem cells (HSCs) in the major vasculature of the mouse embryo. As a pivotal factor in HSC ontogeny, its transcriptional regulation is of high interest but is largely undefined. In this study, we used a combination of comparative genomics and chromatin analysis to identify a highly conserved 531-bp enhancer located at position + 23.5 in the first intron of the 224-kb mouse Runx1 gene. We show that this enhancer contributes to the early hematopoietic expression of Runx1. Transcription factor binding in vivo and analysis of the mutated enhancer in transient transgenic mouse embryos implicate Gata2 and Ets proteins as critical factors for its function. We also show that the SCL/Lmo2/Ldb-1 complex is recruited to the enhancer in vivo. Importantly, transplantation experiments demonstrate that the intronic Runx1 enhancer targets all definitive HSCs in the mouse embryo, suggesting that it functions as a crucial cis-regulatory element that integrates the Gata, Ets, and SCL transcriptional networks to initiate HSC generation.
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Affiliation(s)
- Wade T Nottingham
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK
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21
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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: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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22
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North TE, Stacy T, Matheny CJ, Speck NA, de Bruijn MFTR. Runx1 is expressed in adult mouse hematopoietic stem cells and differentiating myeloid and lymphoid cells, but not in maturing erythroid cells. ACTA ACUST UNITED AC 2004; 22:158-68. [PMID: 14990855 DOI: 10.1634/stemcells.22-2-158] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The transcription factor Runx1 marks all functional hematopoietic stem cells (HSCs) in the embryo and is required for their generation. Mutations in Runx1 are found in approximately 25% of acute leukemias and in familial platelet disorder, suggesting a role for Runx1 in adult hematopoiesis as well. A comprehensive analysis of Runx1 expression in adult hematopoiesis is lacking. Here we show that Runx1 is expressed in functional HSCs in the adult mouse, as well as in cells with spleen colony-forming unit (CFU) and culture CFU capacities. Additionally, we document Runx1 expression in all hematopoietic lineages at the single cell level. Runx1 is expressed in the majority of myeloid cells and in a smaller proportion of lymphoid cells. Runx1 expression substantially decreases during erythroid differentiation. We also document effects of reduced Runx1 levels on adult hematopoiesis.
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Affiliation(s)
- Trista E North
- Department of Biochemistry, Dartmouth Medical School, Hanover, New Hampshire, USA. (Current address for Dr. de Bruijn) MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, United Kingdom
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23
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Abstract
Core binding factors are heterodimeric transcription factors containing a DNA binding Runx1, Runx2, or Runx3 subunit, along with a non DNA binding CBF beta subunit. All four subunits are required at one or more stages of hematopoiesis. This review describes the role of Runx1 and CBF beta in the initiation of hematopoiesis in the embryo, and in the emergence of hematopoietic stem cells. We also discuss the later stages of hematopoiesis for which members of the core binding factor family are required, as well as the recently described roles for these proteins in autoimmunity.
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Affiliation(s)
- Marella F T R de Bruijn
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford OX3 9DS, UK
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24
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Baumeister T, Rössner S, Pech G, de Bruijn MFTR, Leenen PJM, Schuler G, Lutz MB. Interleukin-3Ralpha+ myeloid dendritic cells and mast cells develop simultaneously from different bone marrow precursors in cultures with interleukin-3. J Invest Dermatol 2003; 121:280-8. [PMID: 12880419 DOI: 10.1046/j.1523-1747.2003.12380.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The distinct developmental routes of dendritic cells and mast cells from murine bone marrow cultures with interleukin-3 are unclear. We found that short-term bone marrow cultures with interleukin-3 after 8-10 d consist of about 10%-30% dendritic cells and 70%-90% mast cell precursors, and only after 4-6 wk do homogeneous populations of mast cells emerge. Phenotypical and functional analysis of interleukin-3/dendritic cells revealed a high similarity with myeloid dendritic cells generated with granulocyte-macrophage colony stimulating factor in the expression of myeloid dendritic cell markers (CD11c+ B220- CD8alpha- CD11b+), major histocompatibility complex II and costimulatory molecules, endocytosis, maturation potential, interleukin-12 production, and T cell priming. Interleukin-3/dendritic cells expressed higher levels of interleukin-3 receptor, however. To dissect the interleukin-3/dendritic cell and mast cell development, we sorted fresh bone marrow cells into six subsets by the antibodies ER-MP12 (CD31) and ER-MP20 (Ly-6C). Both interelukin-3/dendritic cells and granulocyte-macrophage colony stimulating factor/dendritic cells develop from the same bone marrow populations, including the ER-MP12neg, ER-MP20high bone marrow monocytes. In contrast, mast cells only developed from ER-MP12(int+high), ER-MP20neg bone marrow cell subsets, indicating that different precursors exist for interleukin-3/dendritic cells and mast cells. Established mast cell cultures could not be converted to dendritic cells or stimulated to express major histocompatibility complex II molecules in vitro or home to lymph node T cell areas in vivo. In summary, we show that dendritic cells generated from bone marrow precursors with interleukin-3 are clearly myeloid and develop via a different pathway compared to bone marrow mast cells.
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Affiliation(s)
- Thomas Baumeister
- Department of Dermatology, University of Erlangen, Erlangen, Germany
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25
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Abstract
The lineage relationship of dendritic cells (DC) with other hematopoietic cell types has been studied extensively, resulting in the identification of different bone marrow (BM) progenitors that give rise to distinct DC types. However, the identity of the different maturation stages of DC precursors in the BM remains unclear. In this study we define the in vivo developmental steps of the myeloid DC lineage in mouse BM. To this end, BM cells were separated according to their expression of CD31 (ER-MP12), Ly-6C (ER-MP20) and ER-MP58 antigens, and stimulated to develop into myeloid DC, using granulocyte macrophage colony stimulating factor as a specific growth factor. DC developed from three BM subpopulations: ER-MP12(hi)/20(-) (early blast cells), ER-MP12(+)/20(+) (myeloid blasts) and ER-MP12(-)/20(hi) (monocytes). The kinetic and phenotypic features of DC developing in vitro indicate that the three populations represent successive maturation stages of myeloid DC precursors. Within the earliest ER-MP12(hi)/20(-) population, DC precursors exclusively occurred in the myeloid-restricted ER-MP58(hi) subset. By using switch cultures, we show that these BM precursor subpopulations, when stimulated to develop into macrophages using macrophage colony stimulating factor, retain the ability to develop into myeloid DC until advanced stages of maturation. Together, these findings support a common ER-MP12/20-defined differentiation pathway for both macrophages and myeloid DC throughout their BM development.
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Affiliation(s)
- Tatjana Nikolic
- Department of Immunology, Erasmus MC, University Medical Center, PO Box 1738, 3000 DR Rotterdam, The Netherlands. t.nikolic@erasmusmc
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26
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de Bruijn MFTR, Ma X, Robin C, Ottersbach K, Sanchez MJ, Dzierzak E. Hematopoietic stem cells localize to the endothelial cell layer in the midgestation mouse aorta. Immunity 2002; 16:673-83. [PMID: 12049719 DOI: 10.1016/s1074-7613(02)00313-8] [Citation(s) in RCA: 317] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The emergence of the first adult hematopoietic stem cells (HSCs) during mammalian ontogeny has been under intense investigation. It is as yet unresolved whether these first HSCs are derived from intraembryonic hemangioblasts, hemogenic endothelial cells, or other progenitors. Thus, to examine the spatial generation of functional HSCs within the mouse embryo, we used the well-known HSC marker, Sca-1, and a transgenic approach with an Ly-6A (Sca-1) GFP marker gene. Our results show that this transgene marker is expressed in all functional HSCs in the midgestation aorta. Immunohistology of aorta-gonads-mesonephros (AGM) regions show that GFP(+) cells are specifically localized to the endothelial layer lining the wall of the dorsal aorta but not to the mesenchyme, strongly suggesting that HSC activity arises within a few cells within the endothelium of the major vasculature.
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27
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North TE, de Bruijn MFTR, Stacy T, Talebian L, Lind E, Robin C, Binder M, Dzierzak E, Speck NA. Runx1 expression marks long-term repopulating hematopoietic stem cells in the midgestation mouse embryo. Immunity 2002; 16:661-72. [PMID: 12049718 DOI: 10.1016/s1074-7613(02)00296-0] [Citation(s) in RCA: 457] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Hematopoietic stem cells (HSCs) are first found in the aorta-gonad-mesonephros region and vitelline and umbilical arteries of the midgestation mouse embryo. Runx1 (AML1), the DNA binding subunit of a core binding factor, is required for the emergence and/or subsequent function of HSCs. We show that all HSCs in the embryo express Runx1. Furthermore, HSCs in Runx1(+/-) embryos are heterogeneous and include CD45(+) cells, endothelial cells, and mesenchymal cells. Comparison with wild-type embryos showed that the distribution of HSCs among these various cell populations is sensitive to Runx1 dosage. These data provide the first morphological description of embryonic HSCs and contribute new insight into their cellular origin.
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Affiliation(s)
- Trista E North
- Department of Biochemistry, Dartmouth Medical School, Hanover, NH 03755, USA
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28
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Oostendorp RAJ, Harvey KN, Kusadasi N, de Bruijn MFTR, Saris C, Ploemacher RE, Medvinsky AL, Dzierzak EA. Stromal cell lines from mouse aorta-gonads-mesonephros subregions are potent supporters of hematopoietic stem cell activity. Blood 2002; 99:1183-9. [PMID: 11830464 DOI: 10.1182/blood.v99.4.1183] [Citation(s) in RCA: 137] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The aorta-gonads-mesonephros (AGM) region autonomously generates the first adult repopulating hematopoietic stem cells (HSCs) in the mouse embryo. HSC activity is initially localized to the dorsal aorta and mesenchyme (AM) and vitelline and umbilical arteries. Thereafter, HSC activity is found in the urogenital ridges (UGs), yolk sac, and liver. As increasing numbers of HSCs are generated, it is thought that these sites provide supportive microenvironments in which HSCs are harbored until the bone marrow microenvironment is established. However, little is known about the supportive cells within these midgestational sites, and particularly which microenvironment is most supportive for HSC growth and maintenance. Thus, to better understand the cells and molecules involved in hematopoietic support in the midgestation embryo, more than 100 stromal cell lines and clones were established from these sites. Numerous stromal clones were found to maintain hematopoietic progenitors and HSCs to a similar degree as, or better than, previously described murine stromal lines. Both the AM and UG subregions of the AGM produced many supportive clones, with the most highly HSC-supportive clone being derived from the UGs. Interestingly, the liver at this stage yielded only few supportive stromal clones. These results strongly suggest that during midgestation, not only the AM but also the UG subregion provides a potent microenvironment for growth and maintenance of the first HSCs.
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