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Lozano-Velasco E, Garcia-Padilla C, Carmona-Garcia M, Gonzalez-Diaz A, Arequipa-Rendon A, Aranega AE, Franco D. MEF2C Directly Interacts with Pre-miRNAs and Distinct RNPs to Post-Transcriptionally Regulate miR-23a-miR-27a-miR-24-2 microRNA Cluster Member Expression. Noncoding RNA 2024; 10:32. [PMID: 38804364 PMCID: PMC11130849 DOI: 10.3390/ncrna10030032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 05/11/2024] [Accepted: 05/15/2024] [Indexed: 05/29/2024] Open
Abstract
Transcriptional regulation constitutes a key step in gene expression regulation. Myocyte enhancer factor 2C (MEF2C) is a transcription factor of the MADS box family involved in the early development of several cell types, including muscle cells. Over the last decade, a novel layer of complexity modulating gene regulation has emerged as non-coding RNAs have been identified, impacting both transcriptional and post-transcriptional regulation. microRNAs represent the most studied and abundantly expressed subtype of small non-coding RNAs, and their functional roles have been widely documented. On the other hand, our knowledge of the transcriptional and post-transcriptional regulatory mechanisms that drive microRNA expression is still incipient. We recently demonstrated that MEF2C is able to transactivate the long, but not short, regulatory element upstream of the miR-23a-miR-27a-miR-24-2 transcriptional start site. However, MEF2C over-expression and silencing, respectively, displayed distinct effects on each of the miR-23a-miR-27a-miR-24-2 mature cluster members without affecting pri-miRNA expression levels, thus supporting additional MEF2C-driven regulatory mechanisms. Within this study, we demonstrated a complex post-transcriptional regulatory mechanism directed by MEF2C in the regulation of miR-23a-miR-27a-miR-24-2 cluster members, distinctly involving different domains of the MEF2C transcription factor and the physical interaction with pre-miRNAs and Ksrp, HnRNPa3 and Ddx17 transcripts.
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Affiliation(s)
- Estefanía Lozano-Velasco
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (E.L.-V.); (C.G.-P.); (M.C.-G.); (A.G.-D.); (A.A.-R.); (A.E.A.)
- Fundación Medina, 18016 Granada, Spain
| | - Carlos Garcia-Padilla
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (E.L.-V.); (C.G.-P.); (M.C.-G.); (A.G.-D.); (A.A.-R.); (A.E.A.)
- Department of Anatomy, Embryology and Zoology, School of Medicine, University of Extremadura, 06006 Badajoz, Spain
| | - Miguel Carmona-Garcia
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (E.L.-V.); (C.G.-P.); (M.C.-G.); (A.G.-D.); (A.A.-R.); (A.E.A.)
| | - Alba Gonzalez-Diaz
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (E.L.-V.); (C.G.-P.); (M.C.-G.); (A.G.-D.); (A.A.-R.); (A.E.A.)
| | - Angela Arequipa-Rendon
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (E.L.-V.); (C.G.-P.); (M.C.-G.); (A.G.-D.); (A.A.-R.); (A.E.A.)
| | - Amelia E. Aranega
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (E.L.-V.); (C.G.-P.); (M.C.-G.); (A.G.-D.); (A.A.-R.); (A.E.A.)
- Fundación Medina, 18016 Granada, Spain
| | - Diego Franco
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (E.L.-V.); (C.G.-P.); (M.C.-G.); (A.G.-D.); (A.A.-R.); (A.E.A.)
- Fundación Medina, 18016 Granada, Spain
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Ma Z, Sugimura R, Lui KO. The role of m6A mRNA modification in normal and malignant hematopoiesis. J Leukoc Biol 2024; 115:100-115. [PMID: 37195903 DOI: 10.1093/jleuko/qiad061] [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: 01/13/2023] [Revised: 05/04/2023] [Accepted: 05/01/2023] [Indexed: 05/19/2023] Open
Abstract
Hematopoiesis is a highly orchestrated biological process sustaining the supply of leukocytes involved in the maintenance of immunity, O2 and CO2 exchange, and wound healing throughout the lifetime of an animal, including humans. During early hematopoietic cell development, several waves of hematopoiesis require the precise regulation of hematopoietic ontogeny as well as the maintenance of hematopoietic stem and progenitor cells in the hematopoietic tissues, such as the fetal liver and bone marrow. Recently, emerging evidence has suggested the critical role of m6A messenger RNA (mRNA) modification, an epigenetic modification dynamically regulated by its effector proteins, in the generation and maintenance of hematopoietic cells during embryogenesis. In the adulthood, m6A has also been demonstrated to be involved in the functional maintenance of hematopoietic stem and progenitor cells in the bone marrow and umbilical cord blood, as well as the progression of malignant hematopoiesis. In this review, we focus on recent progress in identifying the biological functions of m6A mRNA modification, its regulators, and downstream gene targets during normal and pathological hematopoiesis. We propose that targeting m6A mRNA modification could offer novel insights into therapeutic development against abnormal and malignant hematopoietic cell development in the future.
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Affiliation(s)
- Zhangjing Ma
- Department of Chemical Pathology, and Li Ka Shing Institute of Health Science, Prince of Wales Hospital, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Rio Sugimura
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam , Hong Kong, China
| | - Kathy O Lui
- Department of Chemical Pathology, and Li Ka Shing Institute of Health Science, Prince of Wales Hospital, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Nanshan District, Shenzhen, China
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Herrejon Chavez F, Luo H, Cifani P, Pine A, Chu EL, Joshi S, Barin E, Schurer A, Chan M, Chang K, Han GYQ, Pierson AJ, Xiao M, Yang X, Kuehm LM, Hong Y, Nguyen DTT, Chiosis G, Kentsis A, Leslie C, Vu LP, Kharas MG. RNA binding protein SYNCRIP maintains proteostasis and self-renewal of hematopoietic stem and progenitor cells. Nat Commun 2023; 14:2290. [PMID: 37085479 PMCID: PMC10121618 DOI: 10.1038/s41467-023-38001-x] [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: 04/23/2022] [Accepted: 04/11/2023] [Indexed: 04/23/2023] Open
Abstract
Tissue homeostasis is maintained after stress by engaging and activating the hematopoietic stem and progenitor compartments in the blood. Hematopoietic stem cells (HSCs) are essential for long-term repopulation after secondary transplantation. Here, using a conditional knockout mouse model, we revealed that the RNA-binding protein SYNCRIP is required for maintenance of blood homeostasis especially after regenerative stress due to defects in HSCs and progenitors. Mechanistically, we find that SYNCRIP loss results in a failure to maintain proteome homeostasis that is essential for HSC maintenance. SYNCRIP depletion results in increased protein synthesis, a dysregulated epichaperome, an accumulation of misfolded proteins and induces endoplasmic reticulum stress. Additionally, we find that SYNCRIP is required for translation of CDC42 RHO-GTPase, and loss of SYNCRIP results in defects in polarity, asymmetric segregation, and dilution of unfolded proteins. Forced expression of CDC42 recovers polarity and in vitro replating activities of HSCs. Taken together, we uncovered a post-transcriptional regulatory program that safeguards HSC self-renewal capacity and blood homeostasis.
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Affiliation(s)
- Florisela Herrejon Chavez
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hanzhi Luo
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Paolo Cifani
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Alli Pine
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eren L Chu
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pharmacology, Weill Cornell School of Medical Sciences, New York, NY, USA
| | - Suhasini Joshi
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ersilia Barin
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Pharmacology Program of the Weill Cornell Graduate School of Medicine Sciences, New York, NY, USA
| | - Alexandra Schurer
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mandy Chan
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kathryn Chang
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Grace Y Q Han
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aspen J Pierson
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael Xiao
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Xuejing Yang
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Yuning Hong
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Diu T T Nguyen
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Gabriela Chiosis
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alex Kentsis
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Departments of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Medical College of Cornell University, New York, NY, USA
| | - Christina Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ly P Vu
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Terry Fox Laboratory, British Columbia Cancer Research Centre, Vancouver, BC, Canada.
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada.
| | - Michael G Kharas
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Bain FM, Che JLC, Jassinskaja M, Kent DG. Lessons from early life: understanding development to expand stem cells and treat cancers. Development 2022; 149:277217. [PMID: 36217963 PMCID: PMC9724165 DOI: 10.1242/dev.201070] [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] [Indexed: 01/25/2023]
Abstract
Haematopoietic stem cell (HSC) self-renewal is a process that is essential for the development and homeostasis of the blood system. Self-renewal expansion divisions, which create two daughter HSCs from a single parent HSC, can be harnessed to create large numbers of HSCs for a wide range of cell and gene therapies, but the same process is also a driver of the abnormal expansion of HSCs in diseases such as cancer. Although HSCs are first produced during early embryonic development, the key stage and location where they undergo maximal expansion is in the foetal liver, making this tissue a rich source of data for deciphering the molecules driving HSC self-renewal. Another equally interesting stage occurs post-birth, several weeks after HSCs have migrated to the bone marrow, when HSCs undergo a developmental switch and adopt a more dormant state. Characterising these transition points during development is key, both for understanding the evolution of haematological malignancies and for developing methods to promote HSC expansion. In this Spotlight article, we provide an overview of some of the key insights that studying HSC development have brought to the fields of HSC expansion and translational medicine, many of which set the stage for the next big breakthroughs in the field.
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Affiliation(s)
- Fiona M. Bain
- Department of Biology, York Biomedical Research Institute, University of York, York, YO10 5DD, UK
| | - James L. C. Che
- Department of Biology, York Biomedical Research Institute, University of York, York, YO10 5DD, UK
| | - Maria Jassinskaja
- Department of Biology, York Biomedical Research Institute, University of York, York, YO10 5DD, UK
| | - David G. Kent
- Department of Biology, York Biomedical Research Institute, University of York, York, YO10 5DD, UK
- Author for correspondence ()
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Hematopoietic Stem and Progenitor Cell Maintenance and Multiple Lineage Differentiation Is an Integral Function of NFATc1. Cells 2022; 11:cells11132012. [PMID: 35805096 PMCID: PMC9265824 DOI: 10.3390/cells11132012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 06/21/2022] [Indexed: 12/10/2022] Open
Abstract
Hematopoietic stem and progenitor cell (HSPC) maintenance and the differentiation of various lineages is a highly complex but precisely regulated process. Multiple signaling pathways and an array of transcription factors influence HSPC maintenance and the differentiation of individual lineages to constitute a functional hematopoietic system. Nuclear factor of activated T cell (NFAT) family transcription factors have been studied in the context of development and function of multiple mature hematopoietic lineage cells. However, until now their contribution in HSPC physiology and HSPC differentiation to multiple hematopoietic lineages has remained poorly understood. Here, we show that NFAT proteins, specifically NFATc1, play an indispensable role in the maintenance of HSPCs. In the absence of NFATc1, very few HSPCs develop in the bone marrow, which are functionally defective. In addition to HSPC maintenance, NFATc1 also critically regulates differentiation of lymphoid, myeloid, and erythroid lineage cells from HSPCs. Deficiency of NFATc1 strongly impaired, while enhanced NFATc1 activity augmented, the differentiation of these lineages, which further attested to the vital involvement of NFATc1 in regulating hematopoiesis. Hematopoietic defects due to lack of NFATc1 activity can lead to severe pathologies such as lymphopenia, myelopenia, and a drastically reduced lifespan underlining the critical role NFATc1 plays in HSPC maintenance and in the differentaion of various lineages. Our findings suggest that NFATc1 is a critical component of the myriad signaling and transcriptional regulators that are essential to maintain normal hematopoiesis.
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Cova G, Taroni C, Deau MC, Cai Q, Mittelheisser V, Philipps M, Jung M, Cerciat M, Le Gras S, Thibault-Carpentier C, Jost B, Carlsson L, Thornton AM, Shevach EM, Kirstetter P, Kastner P, Chan S. Helios represses megakaryocyte priming in hematopoietic stem and progenitor cells. J Exp Med 2021; 218:e20202317. [PMID: 34459852 PMCID: PMC8406645 DOI: 10.1084/jem.20202317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 05/28/2021] [Accepted: 07/27/2021] [Indexed: 12/13/2022] Open
Abstract
Our understanding of cell fate decisions in hematopoietic stem cells is incomplete. Here, we show that the transcription factor Helios is highly expressed in murine hematopoietic stem and progenitor cells (HSPCs), where it is required to suppress the separation of the platelet/megakaryocyte lineage from the HSPC pool. Helios acts mainly in quiescent cells, where it directly represses the megakaryocyte gene expression program in cells as early as the stem cell stage. Helios binding promotes chromatin compaction, notably at the regulatory regions of platelet-specific genes recognized by the Gata2 and Runx1 transcriptional activators, implicated in megakaryocyte priming. Helios null HSPCs are biased toward the megakaryocyte lineage at the expense of the lymphoid and partially resemble cells of aging animals. We propose that Helios acts as a guardian of HSPC pluripotency by continuously repressing the megakaryocyte fate, which in turn allows downstream lymphoid priming to take place. These results highlight the importance of negative and positive priming events in lineage commitment.
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Affiliation(s)
- Giovanni Cova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Chiara Taroni
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Marie-Céline Deau
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Qi Cai
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Vincent Mittelheisser
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Muriel Philipps
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Matthieu Jung
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Plateforme GenomEast, Infrastructure France Génomique, Illkirch, France
| | - Marie Cerciat
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Plateforme GenomEast, Infrastructure France Génomique, Illkirch, France
| | - Stéphanie Le Gras
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Plateforme GenomEast, Infrastructure France Génomique, Illkirch, France
| | - Christelle Thibault-Carpentier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Plateforme GenomEast, Infrastructure France Génomique, Illkirch, France
| | - Bernard Jost
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Plateforme GenomEast, Infrastructure France Génomique, Illkirch, France
| | - Leif Carlsson
- Umeå Center for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Angela M. Thornton
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Ethan M. Shevach
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Peggy Kirstetter
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Philippe Kastner
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Faculté de Médecine, Université de Strasbourg, Strasbourg, France
| | - Susan Chan
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch, France
- Université de Strasbourg, Illkirch, France
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Randhawa V, Kumar M. An integrated network analysis approach to identify potential key genes, transcription factors, and microRNAs regulating human hematopoietic stem cell aging. Mol Omics 2021; 17:967-984. [PMID: 34605522 DOI: 10.1039/d1mo00199j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hematopoietic stem cells (HSCs) undergo functional deterioration with increasing age that causes loss of their self-renewal and regenerative potential. Despite various efforts, significant success in identifying molecular regulators of HSC aging has not been achieved, one prime reason being the non-availability of appropriate human HSC samples. To demonstrate the scope of integrating and re-analyzing the HSC transcriptomics data available, we used existing tools and databases to structure a sequential data analysis pipeline to predict potential candidate genes, transcription factors, and microRNAs simultaneously. This sequential approach comprises (i) collecting matched young and aged mice HSC sample datasets, (ii) identifying differentially expressed genes, (iii) identifying human homologs of differentially expressed genes, (iv) inferring gene co-expression network modules, and (v) inferring the microRNA-transcription factor-gene regulatory network. Systems-level analyses of HSC interaction networks provided various insights based on which several candidates were predicted. For example, 16 HSC aging-related candidate genes were predicted (e.g., CD38, BRCA1, AGTR1, GSTM1, etc.) from GCN analysis. Following this, the shortest path distance-based analyses of the regulatory network predicted several novel candidate miRNAs and TFs. Among these, miR-124-3p was a common regulator in candidate gene modules, while TFs MYC and SP1 were identified to regulate various candidate genes. Based on the regulatory interactions among candidate genes, TFs, and miRNAs, a potential regulation model of biological processes in each of the candidate modules was predicted, which provided systems-level insights into the molecular complexity of each module to regulate HSC aging.
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Affiliation(s)
- Vinay Randhawa
- Virology Unit and Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific & Industrial Research, Chandigarh-160036, India.
| | - Manoj Kumar
- Virology Unit and Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific & Industrial Research, Chandigarh-160036, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
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Vaughan KL, Franchini AM, Kern HG, Lawrence BP. The Aryl Hydrocarbon Receptor Modulates Murine Hematopoietic Stem Cell Homeostasis and Influences Lineage-Biased Stem and Progenitor Cells. Stem Cells Dev 2021; 30:970-980. [PMID: 34428990 PMCID: PMC8851211 DOI: 10.1089/scd.2021.0096] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/09/2021] [Indexed: 12/24/2022] Open
Abstract
The core function of hematopoietic stem and progenitor cells (HSPCs) is to provide lifelong production of all lineages of the blood and immune cells. The mechanisms that modulate HSPC homeostasis and lineage biasing are not fully understood. Growing evidence implicates the aryl hydrocarbon receptor (AHR), an environment-sensing transcription factor, as a regulator of hematopoiesis. AHR ligands modulate the frequency of mature hematopoietic cells in the bone marrow and periphery, while HSPCs from mice lacking AHR (AHR KO) have increased proliferation. Yet, whether AHR modulates HSPC lineage potential and directs differentiation toward specific lineage-biased progenitors is not well understood. This study revealed that AHR KO mice have an increased proportion of myeloid-biased HSCs and myeloid-biased multipotent progenitor (MPP3) cells. Utilizing inducible AHR knockout mice (iAHR KO), it was discovered that acute deletion of AHR doubled the number of MPP3 cells and altered the composition of downstream lineage-committed progenitors, such as increased frequency of pregranulocyte/premonocyte committed progenitors. Furthermore, in vivo antagonism of the AHR led to a 2.5-fold increase in the number of MPP3 cells and promoted myeloid-biased differentiation. Using hematopoietic-specific conditional AHR knockout mice (AHRVav1) revealed that increased frequency of myeloid-biased HSCs and myeloid-biased progenitors is driven by AHR signaling that is intrinsic to the hematopoietic compartment. These findings demonstrate that the AHR plays a pivotal role in regulating steady-state hematopoiesis, influencing HSPC homeostasis and lineage potential. In addition, the data presented provide potential insight into how deliberate modulation of AHR signaling could help with the treatment of a broad range of diseases that require the hematopoietic compartment.
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Affiliation(s)
- Keegan L. Vaughan
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Anthony M. Franchini
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Harrison G. Kern
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - B. Paige Lawrence
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
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9
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Xie SZ, Kaufmann KB, Wang W, Chan-Seng-Yue M, Gan OI, Laurenti E, Garcia-Prat L, Takayanagi SI, Ng SWK, Xu C, Zeng AGX, Jin L, McLeod J, Wagenblast E, Mitchell A, Kennedy JA, Liu Q, Boutzen H, Kleinau M, Jargstorf J, Holmes G, Zhang Y, Voisin V, Bader GD, Wang JCY, Hannun YA, Luberto C, Schroeder T, Minden MD, Dick JE. Sphingosine-1-phosphate receptor 3 potentiates inflammatory programs in normal and leukemia stem cells to promote differentiation. Blood Cancer Discov 2021; 2:32-53. [PMID: 33458693 PMCID: PMC7116590 DOI: 10.1158/2643-3230.bcd-20-0155] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/27/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022] Open
Abstract
Acute myeloid leukemia (AML) is a caricature of normal hematopoiesis, driven from leukemia stem cells (LSC) that share some hematopoietic stem cell (HSC) programs including responsiveness to inflammatory signaling. Although inflammation dysregulates mature myeloid cells and influences stemness programs and lineage determination in HSC by activating stress myelopoiesis, such roles in LSC are poorly understood. Here, we show that S1PR3, a receptor for the bioactive lipid sphingosine-1-phosphate, is a central regulator which drives myeloid differentiation and activates inflammatory programs in both HSC and LSC. S1PR3-mediated inflammatory signatures varied in a continuum from primitive to mature myeloid states across AML patient cohorts, each with distinct phenotypic and clinical properties. S1PR3 was high in LSC and blasts of mature myeloid samples with linkages to chemosensitivity, while S1PR3 activation in primitive samples promoted LSC differentiation leading to eradication. Our studies open new avenues for therapeutic target identification specific for each AML subset.
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Affiliation(s)
- Stephanie Z Xie
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
| | - Kerstin B Kaufmann
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Weijia Wang
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Michelle Chan-Seng-Yue
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Olga I Gan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Elisa Laurenti
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Laura Garcia-Prat
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Shin-Ichiro Takayanagi
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Cell Therapy Project, R&D Division, Kirin Holdings Company, Limited, Kanagawa, Japan
| | - Stanley W K Ng
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - ChangJiang Xu
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Andy G X Zeng
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Liqing Jin
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jessica McLeod
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Elvin Wagenblast
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Amanda Mitchell
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - James A Kennedy
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Division of Medical Oncology and Hematology, Department of Medicine, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Qiang Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Héléna Boutzen
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Melissa Kleinau
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Joseph Jargstorf
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Gareth Holmes
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Yang Zhang
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Veronique Voisin
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jean C Y Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Division of Medical Oncology and Hematology, Department of Medicine, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Yusuf A Hannun
- Stony Brook Cancer Center and Departments of Medicine, Biochemistry, and Pathology, Stony Brook University, Stony Brook, New York
| | - Chiara Luberto
- Department of Physiology and Biophysics, Stony Brook School of Medicine, Stony Brook, New York
| | - Timm Schroeder
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Division of Medical Oncology and Hematology, Department of Medicine, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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10
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Yang J, Zhao S, Ma D. Biological Characteristics and Regulation of Early Megakaryocytopoiesis. Stem Cell Rev Rep 2020; 15:652-663. [PMID: 31230184 DOI: 10.1007/s12015-019-09905-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
For decades, megakaryocytopoiesis is believed to occur following a classical binary hierarchical developmental model. This model is based on an analysis of predefined flow-sorted cell populations by using cell surface markers. However, this classical model has been challenged by increasing evidences obtained with new techniques which integrating flow cytometric, transcriptomic and functional data at single-cell level and with lineage tracing technique. These recent advances in megakaryocytopoiesis proposed that commitment of haematopoietic stem cells (HSCs) towards megakaryocytic lineage occurs in much earlier stage than that postulated in the classical model. There may exist multipotent but megakaryocyte (MK)/platelet-biased HSCs within HSC compartment and even HSCs can directly differentiate into MKs in steady state or in response to stress. In this review, we focus on recent findings about differentiation from commitment of HSCs to MK and its regulation, and discuss future directions in this research field.
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Affiliation(s)
- Jingang Yang
- Department of Experimental Medicine, General Hospital of Northern Theatre Command, 83 Wenhua Road, Shenhe District, Shenyang, Liaoning, People's Republic of China
| | - Song Zhao
- Department of Experimental Medicine, General Hospital of Northern Theatre Command, 83 Wenhua Road, Shenhe District, Shenyang, Liaoning, People's Republic of China
| | - Dongchu Ma
- Department of Experimental Medicine, General Hospital of Northern Theatre Command, 83 Wenhua Road, Shenhe District, Shenyang, Liaoning, People's Republic of China.
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11
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Loughran SJ, Haas S, Wilkinson AC, Klein AM, Brand M. Lineage commitment of hematopoietic stem cells and progenitors: insights from recent single cell and lineage tracing technologies. Exp Hematol 2020; 88:1-6. [PMID: 32653531 DOI: 10.1016/j.exphem.2020.07.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 12/31/2022]
Abstract
Blood production is essential to maintain human health, and even small perturbations in hematopoiesis can cause disease. Hematopoiesis has therefore been the focus of much research for many years. Experiments determining the lineage potentials of hematopoietic stem and progenitor cells (HSPCs) in vitro and after transplantation revealed a hierarchy of progenitor cell states, where differentiating cells undergo lineage commitment-a series of irreversible changes that progressively restrict their potential. New technologies have recently been developed that allow for a more detailed analysis of the molecular states and fates of differentiating HSPCs. Proteomic and lineage-tracing approaches, alongside single-cell transcriptomic analyses, have recently helped to reveal the biological complexity underlying lineage commitment during hematopoiesis. Recent insights from these new technologies were presented by Dr. Marjorie Brand and Dr. Allon Klein in the Summer 2019 ISEH Webinar, and are discussed in this Perspective.
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Affiliation(s)
- Stephen J Loughran
- Wellcome-MRC Cambridge Stem Cell Institute and Department of Haematology, University of Cambridge, Cambridge, United Kingdom.
| | - Simon Haas
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine and Division of Stem Cells and Cancer, DKFZ German Cancer Research Centre, Heidelberg, Germany
| | - Adam C Wilkinson
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA; Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Allon M Klein
- Department of Systems Biology, Harvard Medical School, Boston, MA
| | - Marjorie Brand
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada
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12
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Wilkinson AC, Nakauchi H. Stabilizing hematopoietic stem cells in vitro. Curr Opin Genet Dev 2020; 64:1-5. [PMID: 32570191 DOI: 10.1016/j.gde.2020.05.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/22/2020] [Accepted: 05/24/2020] [Indexed: 12/17/2022]
Abstract
Hematopoietic stem cells (HSCs) can regenerate all lineages of the adult blood and immune systems long-term following transplantation via a combination of self-renewal and multipotent differentiation. HSCs are therefore an important cell type in both basic research and in the clinic, where HSC transplantation is a curative therapy for a range of diseases. However, as a rare bone marrow cell population, the characterization and collection of HSCs can often be challenging. This has led to a large search for in vitro culture conditions that support the growth of functional HSCs and the in vitro stabilization of the HSC state represents a major goal in the field. Here, we review recent progress towards stabilizing HSCs in vitro.
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Affiliation(s)
- Adam C Wilkinson
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
| | - Hiromitsu Nakauchi
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Division of Stem Cell Therapy, Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan.
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13
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Abstract
The self-renewal capacity of multipotent haematopoietic stem cells (HSCs) supports blood system homeostasis throughout life and underlies the curative capacity of clinical HSC transplantation therapies. However, despite extensive characterization of the HSC state in the adult bone marrow and embryonic fetal liver, the mechanism of HSC self-renewal has remained elusive. This Review presents our current understanding of HSC self-renewal in vivo and ex vivo, and discusses important advances in ex vivo HSC expansion that are providing new biological insights and offering new therapeutic opportunities.
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14
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Poplineau M, Vernerey J, Platet N, N'guyen L, Hérault L, Esposito M, Saurin AJ, Guilouf C, Iwama A, Duprez E. PLZF limits enhancer activity during hematopoietic progenitor aging. Nucleic Acids Res 2019; 47:4509-4520. [PMID: 30892634 PMCID: PMC6511862 DOI: 10.1093/nar/gkz174] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 03/04/2019] [Accepted: 03/08/2019] [Indexed: 12/19/2022] Open
Abstract
PLZF (promyelocytic leukemia zinc finger) is a transcription factor acting as a global regulator of hematopoietic commitment. PLZF displays an epigenetic specificity by recruiting chromatin-modifying factors but little is known about its role in remodeling chromatin of cells committed toward a given specific hematopoietic lineage. In murine myeloid progenitors, we decipher a new role for PLZF in restraining active genes and enhancers by targeting acetylated lysine 27 of Histone H3 (H3K27ac). Functional analyses reveal that active enhancers bound by PLZF are involved in biological processes related to metabolism and associated with hematopoietic aging. Comparing the epigenome of young and old myeloid progenitors, we reveal that H3K27ac variation at active enhancers is a hallmark of hematopoietic aging. Taken together, these data suggest that PLZF, associated with active enhancers, appears to restrain their activity as an epigenetic gatekeeper of hematopoietic aging.
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Affiliation(s)
- Mathilde Poplineau
- Epigenetic Factors in Normal and Malignant Hematopoiesis, Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France.,Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Julien Vernerey
- Epigenetic Factors in Normal and Malignant Hematopoiesis, Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Nadine Platet
- Epigenetic Factors in Normal and Malignant Hematopoiesis, Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Lia N'guyen
- Epigenetic Factors in Normal and Malignant Hematopoiesis, Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Léonard Hérault
- Epigenetic Factors in Normal and Malignant Hematopoiesis, Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Michela Esposito
- Gustave Roussy, Université Paris-Saclay, Inserm U1170, CNRS Villejuif, France
| | | | - Christel Guilouf
- Gustave Roussy, Université Paris-Saclay, Inserm U1170, CNRS Villejuif, France
| | - Atsushi Iwama
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan.,Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Estelle Duprez
- Epigenetic Factors in Normal and Malignant Hematopoiesis, Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
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15
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Wilkinson AC, Ryan DJ, Kucinski I, Wang W, Yang J, Nestorowa S, Diamanti E, Tsang JCH, Wang J, Campos LS, Yang F, Fu B, Wilson N, Liu P, Gottgens B. Expanded potential stem cell media as a tool to study human developmental hematopoiesis in vitro. Exp Hematol 2019; 76:1-12.e5. [PMID: 31326613 PMCID: PMC6859476 DOI: 10.1016/j.exphem.2019.07.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 07/09/2019] [Accepted: 07/11/2019] [Indexed: 01/05/2023]
Abstract
Pluripotent stem cell (PSC) differentiation in vitro represents a powerful and tractable model to study mammalian development and an unlimited source of cells for regenerative medicine. Within hematology, in vitro PSC hematopoiesis affords novel insights into blood formation and represents an exciting potential approach to generate hematopoietic and immune cell types for transplantation and transfusion. Most studies to date have focused on in vitro hematopoiesis from mouse PSCs and human PSCs. However, differences in mouse and human PSC culture protocols have complicated the translation of discoveries between these systems. We recently developed a novel chemical media formulation, expanded potential stem cell medium (EPSCM), that maintains mouse PSCs in a unique cellular state and extraembryonic differentiation capacity. Herein, we describe how EPSCM can be directly used to stably maintain human PSCs. We further demonstrate that human PSCs maintained in EPSCM can spontaneously form embryoid bodies and undergo in vitro hematopoiesis using a simple differentiation protocol, similar to mouse PSC differentiation. EPSCM-maintained human PSCs generated at least two hematopoietic cell populations, which displayed distinct transcriptional profiles by RNA-sequencing (RNA-seq) analysis. EPSCM also supports gene targeting using homologous recombination, affording generation of an SPI1 (PU.1) reporter PSC line to study and track in vitro hematopoiesis. EPSCM therefore provides a useful tool not only to study pluripotency but also hematopoietic cell specification and developmental-lineage commitment.
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Affiliation(s)
- Adam C Wilkinson
- Department of Haematology, Wellcome & MRC Cambridge Stem Cell Institute, Cambridge, UK
| | - David J Ryan
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Iwo Kucinski
- Department of Haematology, Wellcome & MRC Cambridge Stem Cell Institute, Cambridge, UK
| | - Wei Wang
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Jian Yang
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Sonia Nestorowa
- Department of Haematology, Wellcome & MRC Cambridge Stem Cell Institute, Cambridge, UK
| | - Evangelia Diamanti
- Department of Haematology, Wellcome & MRC Cambridge Stem Cell Institute, Cambridge, UK
| | | | - Juexuan Wang
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Lia S Campos
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Fengtang Yang
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Beiyuan Fu
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Nicola Wilson
- Department of Haematology, Wellcome & MRC Cambridge Stem Cell Institute, Cambridge, UK
| | - Pentao Liu
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK; School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, Stem Cell and Regenerative Medicine Consortium, University of Hong Kong, Hong Kong, China
| | - Berthold Gottgens
- Department of Haematology, Wellcome & MRC Cambridge Stem Cell Institute, Cambridge, UK.
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16
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Tan TK, Zhang C, Sanda T. Oncogenic transcriptional program driven by TAL1 in T-cell acute lymphoblastic leukemia. Int J Hematol 2018; 109:5-17. [PMID: 30145780 DOI: 10.1007/s12185-018-2518-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 07/21/2018] [Accepted: 08/06/2018] [Indexed: 12/12/2022]
Abstract
TAL1/SCL is a prime example of an oncogenic transcription factor that is abnormally expressed in acute leukemia due to the replacement of regulator elements. This gene has also been recognized as an essential regulator of hematopoiesis. TAL1 expression is strictly regulated in a lineage- and stage-specific manner. Such precise control is crucial for the switching of the transcriptional program. The misexpression of TAL1 in immature thymocytes leads to a widespread series of orchestrated downstream events that affect several different cellular machineries, resulting in a lethal consequence, namely T-cell acute lymphoblastic leukemia (T-ALL). In this article, we will discuss the transcriptional regulatory network and downstream target genes, including protein-coding genes and non-coding RNAs, controlled by TAL1 in normal hematopoiesis and T-cell leukemogenesis.
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Affiliation(s)
- Tze King Tan
- Cancer Science Institute of Singapore, National University of Singapore, Centre for Translational Medicine, 14 Medical Drive, #12-01, Singapore, 117599, Singapore
| | - Chujing Zhang
- Cancer Science Institute of Singapore, National University of Singapore, Centre for Translational Medicine, 14 Medical Drive, #12-01, Singapore, 117599, Singapore
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, National University of Singapore, Centre for Translational Medicine, 14 Medical Drive, #12-01, Singapore, 117599, Singapore. .,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.
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17
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Wilkinson AC, Yamazaki S. The hematopoietic stem cell diet. Int J Hematol 2018; 107:634-641. [PMID: 29605874 DOI: 10.1007/s12185-018-2451-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 03/27/2018] [Indexed: 02/07/2023]
Abstract
Hematopoietic stem cells (HSCs) are responsible for sustaining life-long blood formation or hematopoiesis and are also used clinically in a form of bone marrow transplantation, a curative cellular therapy for a range of hematological diseases. HSCs are maintained throughout adult life by a complex biological niche or microenvironment, which is thought to be composed of a range of cellular, molecular, and metabolic components. The metabolic components of the HSC niche have become of increasing interest over the past few years. It is now well-recognized that metabolic activity is intimately linked to HSC function, and dysregulation of these metabolic pathways result in hematological pathologies such as leukemia. Here, we review the recent progress in this field including our current understanding of the "dietary" requirements of HSCs and how nutrition influences HSC activity. These recent findings have suggested promising new metabolic approaches to improve clinical HSC transplantation and leukemia therapies.
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Affiliation(s)
- Adam C Wilkinson
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Satoshi Yamazaki
- Division of Stem Cell Therapy, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan.
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18
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Single-Cell Sequencing in Normal and Malignant Hematopoiesis. Hemasphere 2018; 2:e34. [PMID: 31723762 PMCID: PMC6745901 DOI: 10.1097/hs9.0000000000000034] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 01/19/2018] [Accepted: 01/22/2018] [Indexed: 12/31/2022] Open
Abstract
Hematopoiesis is one of the best studied adult stem-cell systems, with a differentiation hierarchy progressing from immature hematopoietic stem cells to over 10 distinct mature cell types. Recent technological breakthroughs now make it possible to define transcriptional profiles in thousands of individual cells. Facilitated by the wealth of prior data on cell purification and analysis strategies, hematopoiesis has been one of the earliest experimental systems to which many of these new single-cell sequencing technologies have been applied. In this review, the authors focus on recent studies, which have shed light on heterogeneity within individual populations as well as the relationships between populations, and also attempt to characterize the differences between normal and disease/perturbed states.
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19
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Leong WZ, Tan SH, Ngoc PCT, Amanda S, Yam AWY, Liau WS, Gong Z, Lawton LN, Tenen DG, Sanda T. ARID5B as a critical downstream target of the TAL1 complex that activates the oncogenic transcriptional program and promotes T-cell leukemogenesis. Genes Dev 2018; 31:2343-2360. [PMID: 29326336 PMCID: PMC5795782 DOI: 10.1101/gad.302646.117] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 11/30/2017] [Indexed: 12/13/2022]
Abstract
Leong et al. identified ARID5B as a collaborating oncogenic factor involved in the transcriptional program in T-ALL. ARID5B positively regulates the expression of TAL1 and its regulatory partners and also activates the expression of the oncogene MYC. The oncogenic transcription factor TAL1/SCL induces an aberrant transcriptional program in T-cell acute lymphoblastic leukemia (T-ALL) cells. However, the critical factors that are directly activated by TAL1 and contribute to T-ALL pathogenesis are largely unknown. Here, we identified AT-rich interactive domain 5B (ARID5B) as a collaborating oncogenic factor involved in the transcriptional program in T-ALL. ARID5B expression is down-regulated at the double-negative 2–4 stages in normal thymocytes, while it is induced by the TAL1 complex in human T-ALL cells. The enhancer located 135 kb upstream of the ARID5B gene locus is activated under a superenhancer in T-ALL cells but not in normal T cells. Notably, ARID5B-bound regions are associated predominantly with active transcription. ARID5B and TAL1 frequently co-occupy target genes and coordinately control their expression. ARID5B positively regulates the expression of TAL1 and its regulatory partners. ARID5B also activates the expression of the oncogene MYC. Importantly, ARID5B is required for the survival and growth of T-ALL cells, and forced expression of ARID5B in immature thymocytes results in thymus retention, differentiation arrest, radioresistance, and tumor formation in zebrafish. Our results indicate that ARID5B reinforces the oncogenic transcriptional program by positively regulating the TAL1-induced regulatory circuit and MYC in T-ALL, thereby contributing to T-cell leukemogenesis.
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Affiliation(s)
- Wei Zhong Leong
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore
| | - Shi Hao Tan
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore
| | - Phuong Cao Thi Ngoc
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore
| | - Stella Amanda
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore
| | - Alice Wei Yee Yam
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore
| | - Wei-Siang Liau
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore
| | - Zhiyuan Gong
- Department of Biological Sciences, National University of Singapore, 117543 Singapore
| | - Lee N Lawton
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore
| | - Daniel G Tenen
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore.,Harvard Medical School, Boston, Massachusetts 02215, USA.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 117599 Singapore
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 117599 Singapore
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20
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Rossmann MP, Orkin SH, Chute JP. Hematopoietic Stem Cell Biology. Hematology 2018. [DOI: 10.1016/b978-0-323-35762-3.00009-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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21
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Liang OD, So EY, Egan PC, Goldberg LR, Aliotta JM, Wu KQ, Dubielecka PM, Ventetuolo CE, Reginato AM, Quesenberry PJ, Klinger JR. Endothelial to haematopoietic transition contributes to pulmonary arterial hypertension. Cardiovasc Res 2017; 113:1560-1573. [PMID: 29016733 PMCID: PMC5852529 DOI: 10.1093/cvr/cvx161] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 03/16/2017] [Accepted: 08/10/2017] [Indexed: 12/22/2022] Open
Abstract
AIMS The pathogenic mechanisms of pulmonary arterial hypertension (PAH) remain unclear, but involve dysfunctional endothelial cells (ECs), dysregulated immunity and inflammation in the lung. We hypothesize that a developmental process called endothelial to haematopoietic transition (EHT) contributes to the pathogenesis of pulmonary hypertension (PH). We sought to determine the role of EHT in mouse models of PH, to characterize specific cell types involved in this process, and to identify potential therapeutic targets to prevent disease progression. METHODS AND RESULTS When transgenic mice with fluorescence protein ZsGreen-labelled ECs were treated with Sugen/hypoxia (Su/Hx) combination to induce PH, the percentage of ZsGreen+ haematopoietic cells in the peripheral blood, primarily of myeloid lineage, significantly increased. This occurrence coincided with the depletion of bone marrow (BM) ZsGreen+ c-kit+ CD45- endothelial progenitor cells (EPCs), which could be detected accumulating in the lung upon PH-induction. Quantitative RT-PCR based gene array analysis showed that key transcription factors driving haematopoiesis were expressed in these EPCs. When transplanted into lethally irradiated recipient mice, the BM-derived EPCs exhibited long-term engraftment and haematopoietic differentiation capability, indicating these EPCs are haemogenic in nature. Specific inhibition of the critical haematopoietic transcription factor Runx1 blocked the EHT process in vivo, prevented egress of the BM EPCs and ultimately attenuated PH progression in Su/Hx- as well as in monocrotaline-induced PH in mice. Thus, myeloid-skewed EHT promotes the development of PH and inhibition of this process prevents disease progression in mouse models of PH. Furthermore, high levels of Runx1 expression were found in circulating CD34+ CD133+ EPCs isolated from peripheral blood of patients with PH, supporting the clinical relevance of our proposed mechanism of EHT. CONCLUSION EHT contributes to the pathogenesis of PAH. The transcription factor Runx1 may be a novel therapeutic target for the treatment of PAH.
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Affiliation(s)
- Olin D. Liang
- Division of Hematology/Oncology, Department of Medicine
- Center for Regenerative Medicine, Department of Orthopaedics
| | - Eui-Young So
- Division of Hematology/Oncology, Department of Medicine
- Center for Regenerative Medicine, Department of Orthopaedics
| | | | | | - Jason M. Aliotta
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine
| | - Keith Q. Wu
- Center for Regenerative Medicine, Department of Orthopaedics
| | | | - Corey E. Ventetuolo
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine
| | - Anthony M. Reginato
- Division of Rheumatology, Department of Medicine, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI 02903, USA
| | | | - James R. Klinger
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine
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22
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Wilkinson AC, Nakauchi H, Göttgens B. Mammalian Transcription Factor Networks: Recent Advances in Interrogating Biological Complexity. Cell Syst 2017; 5:319-331. [PMID: 29073372 PMCID: PMC5928788 DOI: 10.1016/j.cels.2017.07.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 06/29/2017] [Accepted: 07/20/2017] [Indexed: 12/11/2022]
Abstract
Transcription factor (TF) networks are a key determinant of cell fate decisions in mammalian development and adult tissue homeostasis and are frequently corrupted in disease. However, our inability to experimentally resolve and interrogate the complexity of mammalian TF networks has hampered the progress in this field. Recent technological advances, in particular large-scale genome-wide approaches, single-cell methodologies, live-cell imaging, and genome editing, are emerging as important technologies in TF network biology. Several recent studies even suggest a need to re-evaluate established models of mammalian TF networks. Here, we provide a brief overview of current and emerging methods to define mammalian TF networks. We also discuss how these emerging technologies facilitate new ways to interrogate complex TF networks, consider the current open questions in the field, and comment on potential future directions and biomedical applications.
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Affiliation(s)
- Adam C Wilkinson
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - Hiromitsu Nakauchi
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA; Division of Stem Cell Therapy, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Berthold Göttgens
- Department of Haematology, Cambridge Institute for Medical Research and Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0XY, UK.
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23
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Tan SH, Bertulfo FC, Sanda T. Leukemia-Initiating Cells in T-Cell Acute Lymphoblastic Leukemia. Front Oncol 2017; 7:218. [PMID: 29034206 PMCID: PMC5627022 DOI: 10.3389/fonc.2017.00218] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 09/01/2017] [Indexed: 12/26/2022] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is a hematological malignancy characterized by the clonal proliferation of immature T-cell precursors. T-ALL has many similar pathophysiological features to acute myeloid leukemia, which has been extensively studied in the establishment of the cancer stem cell (CSC) theory, but the CSC concept in T-ALL is still debatable. Although leukemia-initiating cells (LICs), which can generate leukemia in a xenograft setting, have been found in both human T-ALL patients and animal models, the nature and origin of LICs are largely unknown. In this review, we discuss recent studies on LICs in T-ALL and the potential mechanisms of LIC emergence in this disease. We focus on the oncogenic transcription factors TAL1, LMO2, and NOTCH1 and highlight the significance of the transcriptional regulatory programs in normal hematopoietic stem cells and T-ALL.
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Affiliation(s)
- Shi Hao Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Fatima Carla Bertulfo
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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24
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Hamey FK, Nestorowa S, Kinston SJ, Kent DG, Wilson NK, Göttgens B. Reconstructing blood stem cell regulatory network models from single-cell molecular profiles. Proc Natl Acad Sci U S A 2017; 114:5822-5829. [PMID: 28584094 PMCID: PMC5468644 DOI: 10.1073/pnas.1610609114] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Adult blood contains a mixture of mature cell types, each with specialized functions. Single hematopoietic stem cells (HSCs) have been functionally shown to generate all mature cell types for the lifetime of the organism. Differentiation of HSCs toward alternative lineages must be balanced at the population level by the fate decisions made by individual cells. Transcription factors play a key role in regulating these decisions and operate within organized regulatory programs that can be modeled as transcriptional regulatory networks. As dysregulation of single HSC fate decisions is linked to fatal malignancies such as leukemia, it is important to understand how these decisions are controlled on a cell-by-cell basis. Here we developed and applied a network inference method, exploiting the ability to infer dynamic information from single-cell snapshot expression data based on expression profiles of 48 genes in 2,167 blood stem and progenitor cells. This approach allowed us to infer transcriptional regulatory network models that recapitulated differentiation of HSCs into progenitor cell types, focusing on trajectories toward megakaryocyte-erythrocyte progenitors and lymphoid-primed multipotent progenitors. By comparing these two models, we identified and subsequently experimentally validated a difference in the regulation of nuclear factor, erythroid 2 (Nfe2) and core-binding factor, runt domain, alpha subunit 2, translocated to, 3 homolog (Cbfa2t3h) by the transcription factor Gata2. Our approach confirms known aspects of hematopoiesis, provides hypotheses about regulation of HSC differentiation, and is widely applicable to other hierarchical biological systems to uncover regulatory relationships.
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Affiliation(s)
- Fiona K Hamey
- Department of Haematology, Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge Institute for Medical Research, Cambridge CB2 0XY, United Kingdom
| | - Sonia Nestorowa
- Department of Haematology, Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge Institute for Medical Research, Cambridge CB2 0XY, United Kingdom
| | - Sarah J Kinston
- Department of Haematology, Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge Institute for Medical Research, Cambridge CB2 0XY, United Kingdom
| | - David G Kent
- Department of Haematology, Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge Institute for Medical Research, Cambridge CB2 0XY, United Kingdom
| | - Nicola K Wilson
- Department of Haematology, Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge Institute for Medical Research, Cambridge CB2 0XY, United Kingdom
| | - Berthold Göttgens
- Department of Haematology, Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge Institute for Medical Research, Cambridge CB2 0XY, United Kingdom
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25
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Liau WS, Ngoc PCT, Sanda T. Roles of the RUNX1 Enhancer in Normal Hematopoiesis and Leukemogenesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 962:139-147. [PMID: 28299656 DOI: 10.1007/978-981-10-3233-2_10] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Enhancers are regulatory elements in genomic DNA that contain specific sequence motifs that are bound by DNA-binding transcription factors. The activity of enhancers is tightly regulated in an integrated and combinatorial manner, thus yielding complex patterns of transcription in different tissues. Identifying enhancers is crucial to understanding the physiological and pathogenic roles of their target genes. The RUNX1 intronic enhancer, eR1, acts in cis to regulate RUNX1 gene expression in hematopoietic stem cells (HSCs) and hemogenic endothelial cells. RUNX1 and other hematopoietic transcription factors TAL1/SCL, GATA2, PU.1, LMO2 and LDB1 bind at this region. Interestingly, recent studies have revealed that this region is involved in a large cluster of enhancers termed a super-enhancer. The RUNX1 super-enhancer is observed in normal HSCs and T-cell acute lymphoblastic leukemia cells. In this review, we describe the discovery of eR1 and its roles in normal development and leukemogenesis, as well as its potential applications in stem cell research.
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Affiliation(s)
- Wei-Siang Liau
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Phuong Cao Thi Ngoc
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore. .,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.
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26
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Ma S, Kemmeren P, Aliferis CF, Statnikov A. An Evaluation of Active Learning Causal Discovery Methods for Reverse-Engineering Local Causal Pathways of Gene Regulation. Sci Rep 2016; 6:22558. [PMID: 26939894 PMCID: PMC4778024 DOI: 10.1038/srep22558] [Citation(s) in RCA: 3] [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: 04/02/2015] [Accepted: 02/17/2016] [Indexed: 12/15/2022] Open
Abstract
Reverse-engineering of causal pathways that implicate diseases and vital cellular functions is a fundamental problem in biomedicine. Discovery of the local causal pathway of a target variable (that consists of its direct causes and direct effects) is essential for effective intervention and can facilitate accurate diagnosis and prognosis. Recent research has provided several active learning methods that can leverage passively observed high-throughput data to draft causal pathways and then refine the inferred relations with a limited number of experiments. The current study provides a comprehensive evaluation of the performance of active learning methods for local causal pathway discovery in real biological data. Specifically, 54 active learning methods/variants from 3 families of algorithms were applied for local causal pathways reconstruction of gene regulation for 5 transcription factors in S. cerevisiae. Four aspects of the methods' performance were assessed, including adjacency discovery quality, edge orientation accuracy, complete pathway discovery quality, and experimental cost. The results of this study show that some methods provide significant performance benefits over others and therefore should be routinely used for local causal pathway discovery tasks. This study also demonstrates the feasibility of local causal pathway reconstruction in real biological systems with significant quality and low experimental cost.
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Affiliation(s)
- Sisi Ma
- Center for Health Informatics and Bioinformatics, New York University Medical Center, New York, New York, USA
| | - Patrick Kemmeren
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center, Utrecht, The Netherlands
| | - Constantin F. Aliferis
- Institute for Health Informatics, Academic Health Center, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Alexander Statnikov
- Center for Health Informatics and Bioinformatics, New York University Medical Center, New York, New York, USA
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27
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Genetic and Epigenetic Mechanisms That Maintain Hematopoietic Stem Cell Function. Stem Cells Int 2015; 2016:5178965. [PMID: 26798358 PMCID: PMC4699043 DOI: 10.1155/2016/5178965] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 09/03/2015] [Accepted: 09/09/2015] [Indexed: 01/15/2023] Open
Abstract
All hematopoiesis cells develop from multipotent progenitor cells. Hematopoietic stem cells (HSC) have the ability to develop into all blood lineages but also maintain their stemness. Different molecular mechanisms have been identified that are crucial for regulating quiescence and self-renewal to maintain the stem cell pool and for inducing proliferation and lineage differentiation. The stem cell niche provides the microenvironment to keep HSC in a quiescent state. Furthermore, several transcription factors and epigenetic modifiers are involved in this process. These create modifications that regulate the cell fate in a more or less reversible and dynamic way and contribute to HSC homeostasis. In addition, HSC respond in a unique way to DNA damage. These mechanisms also contribute to the regulation of HSC function and are essential to ensure viability after DNA damage. How HSC maintain their quiescent stage during the entire life is still matter of ongoing research. Here we will focus on the molecular mechanisms that regulate HSC function.
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28
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Hong SH, Kim KS, Oh IH. Concise review: Exploring miRNAs--toward a better understanding of hematopoiesis. Stem Cells 2015; 33:1-7. [PMID: 25132287 DOI: 10.1002/stem.1810] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 07/14/2014] [Indexed: 12/12/2022]
Abstract
Hematopoiesis is governed by a multidimensional regulatory network involving both intrinsic and extrinsic factors that control self-renewal and differentiation of hematopoietic stem cells (HSCs) through the coordination of influences that affect cell fate. Increasing evidence indicates that microRNAs (miRNAs), short noncoding RNAs of approximately 22 nucleotides, play a central role in orchestrating these regulatory mechanisms to modulate the multiple entities of hematopoietic function in a cell-type specific manner, including self-renewal, lineage commitment, and survival of HSCs as well as their microenvironmental crosstalk. Here, we summarize the current understanding regarding the regulatory effects of miRNA on hematopoietic cells, thus enlightening their role in fine-tuning HSC function and hematopoietic homeostasis.
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Affiliation(s)
- Seok-Ho Hong
- Department of Internal Medicine, School of Medicine, Stem Cell Institute, Kangwon National University, Chuncheon, South Korea
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29
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Peng X, Dong M, Ma L, Jia XE, Mao J, Jin C, Chen Y, Gao L, Liu X, Ma K, Wang L, Du T, Jin Y, Huang Q, Li K, Zon LI, Liu T, Deng M, Zhou Y, Xi X, Zhou Y, Chen S. A point mutation of zebrafish c-cbl gene in the ring finger domain produces a phenotype mimicking human myeloproliferative disease. Leukemia 2015; 29:2355-65. [PMID: 26104663 DOI: 10.1038/leu.2015.154] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 05/09/2015] [Accepted: 05/12/2015] [Indexed: 12/12/2022]
Abstract
Controlled self-renewal and differentiation of hematopoietic stem/progenitor cells (HSPCs) are critical for vertebrate development and survival. These processes are tightly regulated by the transcription factors, signaling molecules and epigenetic factors. Impaired regulations of their function could result in hematological malignancies. Using a large-scale zebrafish N-ethyl-N-nitrosourea mutagenesis screening, we identified a line named LDD731, which presented significantly increased HSPCs in hematopoietic organs. Further analysis revealed that the cells of erythroid/myeloid lineages in definitive hematopoiesis were increased while the primitive hematopoiesis was not affected. The homozygous mutation was lethal with a median survival time around 14-15 days post fertilization. The causal mutation was located by positional cloning in the c-cbl gene, the human ortholog of which, c-CBL, is found frequently mutated in myeloproliferative neoplasms (MPN) or acute leukemia. Sequence analysis showed the mutation in LDD731 caused a histidine-to-tyrosine substitution of the amino acid codon 382 within the RING finger domain of c-Cbl. Moreover, the myeloproliferative phenotype in zebrafish seemed dependent on the Flt3 (fms-like tyrosine kinase 3) signaling, consistent with that observed in both mice and humans. Our study may shed new light on the pathogenesis of MPN and provide a useful in vivo vertebrate model of this syndrome for screening drugs.
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Affiliation(s)
- X Peng
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, RuiJin Hospital, Shanghai Jiao Tong University (SJTU) School of Medicine, and Collaborative Innovation Center of Systems Biomedicine, SJTU, Shanghai, China
| | - M Dong
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences and Graduate University, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - L Ma
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, RuiJin Hospital, Shanghai Jiao Tong University (SJTU) School of Medicine, and Collaborative Innovation Center of Systems Biomedicine, SJTU, Shanghai, China.,Shanghai Center for Systems Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - X-E Jia
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences and Graduate University, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - J Mao
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, RuiJin Hospital, Shanghai Jiao Tong University (SJTU) School of Medicine, and Collaborative Innovation Center of Systems Biomedicine, SJTU, Shanghai, China
| | - C Jin
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences and Graduate University, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Y Chen
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, RuiJin Hospital, Shanghai Jiao Tong University (SJTU) School of Medicine, and Collaborative Innovation Center of Systems Biomedicine, SJTU, Shanghai, China
| | - L Gao
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences and Graduate University, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - X Liu
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, RuiJin Hospital, Shanghai Jiao Tong University (SJTU) School of Medicine, and Collaborative Innovation Center of Systems Biomedicine, SJTU, Shanghai, China
| | - K Ma
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences and Graduate University, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - L Wang
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences and Graduate University, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - T Du
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, RuiJin Hospital, Shanghai Jiao Tong University (SJTU) School of Medicine, and Collaborative Innovation Center of Systems Biomedicine, SJTU, Shanghai, China
| | - Y Jin
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, RuiJin Hospital, Shanghai Jiao Tong University (SJTU) School of Medicine, and Collaborative Innovation Center of Systems Biomedicine, SJTU, Shanghai, China
| | - Q Huang
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, RuiJin Hospital, Shanghai Jiao Tong University (SJTU) School of Medicine, and Collaborative Innovation Center of Systems Biomedicine, SJTU, Shanghai, China
| | - K Li
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, RuiJin Hospital, Shanghai Jiao Tong University (SJTU) School of Medicine, and Collaborative Innovation Center of Systems Biomedicine, SJTU, Shanghai, China
| | - L I Zon
- Stem Cell Program at Boston Children's Hospital, Hematology/Oncology Program at Children's Hospital and Dana Faber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Boston, MA, USA
| | - T Liu
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, RuiJin Hospital, Shanghai Jiao Tong University (SJTU) School of Medicine, and Collaborative Innovation Center of Systems Biomedicine, SJTU, Shanghai, China.,Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences and Graduate University, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - M Deng
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences and Graduate University, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Y Zhou
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences and Graduate University, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - X Xi
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, RuiJin Hospital, Shanghai Jiao Tong University (SJTU) School of Medicine, and Collaborative Innovation Center of Systems Biomedicine, SJTU, Shanghai, China
| | - Y Zhou
- Stem Cell Program at Boston Children's Hospital, Hematology/Oncology Program at Children's Hospital and Dana Faber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - S Chen
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, RuiJin Hospital, Shanghai Jiao Tong University (SJTU) School of Medicine, and Collaborative Innovation Center of Systems Biomedicine, SJTU, Shanghai, China
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30
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Wilson NK, Kent DG, Buettner F, Shehata M, Macaulay IC, Calero-Nieto FJ, Sánchez Castillo M, Oedekoven CA, Diamanti E, Schulte R, Ponting CP, Voet T, Caldas C, Stingl J, Green AR, Theis FJ, Göttgens B. Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations. Cell Stem Cell 2015; 16:712-24. [PMID: 26004780 PMCID: PMC4460190 DOI: 10.1016/j.stem.2015.04.004] [Citation(s) in RCA: 327] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 02/26/2015] [Accepted: 04/10/2015] [Indexed: 01/27/2023]
Abstract
Heterogeneity within the self-renewal durability of adult hematopoietic stem cells (HSCs) challenges our understanding of the molecular framework underlying HSC function. Gene expression studies have been hampered by the presence of multiple HSC subtypes and contaminating non-HSCs in bulk HSC populations. To gain deeper insight into the gene expression program of murine HSCs, we combined single-cell functional assays with flow cytometric index sorting and single-cell gene expression assays. Through bioinformatic integration of these datasets, we designed an unbiased sorting strategy that separates non-HSCs away from HSCs, and single-cell transplantation experiments using the enriched population were combined with RNA-seq data to identify key molecules that associate with long-term durable self-renewal, producing a single-cell molecular dataset that is linked to functional stem cell activity. Finally, we demonstrated the broader applicability of this approach for linking key molecules with defined cellular functions in another stem cell system.
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Affiliation(s)
- Nicola K Wilson
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute and Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - David G Kent
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute and Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Florian Buettner
- Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Mona Shehata
- Department of Oncology and Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, UK
| | - Iain C Macaulay
- Single Cell Genomics Centre, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Fernando J Calero-Nieto
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute and Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Manuel Sánchez Castillo
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute and Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Caroline A Oedekoven
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute and Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Evangelia Diamanti
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute and Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Reiner Schulte
- Head of Flow Cytometry, Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Chris P Ponting
- Single Cell Genomics Centre, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; MRC Computational Genomics Analysis and Training Programme, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK
| | - Thierry Voet
- Single Cell Genomics Centre, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Carlos Caldas
- Department of Oncology and Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, UK
| | - John Stingl
- Department of Oncology and Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, UK
| | - Anthony R Green
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute and Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; Department of Mathematics, Technische Universität München, Boltzmannstraße 3, 85748 Garching, Germany
| | - Berthold Göttgens
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute and Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK.
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31
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Polycomb repressive complex 2 component Suz12 is required for hematopoietic stem cell function and lymphopoiesis. Blood 2015; 126:167-75. [PMID: 26036803 DOI: 10.1182/blood-2014-12-615898] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Accepted: 05/27/2015] [Indexed: 01/12/2023] Open
Abstract
Polycomb repressive complex 2 (PRC2) is a chromatin modifier that regulates stem cells in embryonic and adult tissues. Loss-of-function studies of PRC2 components have been complicated by early embryonic dependence on PRC2 activity and the partial functional redundancy of enhancer of zeste homolog 1 (Ezh1) and enhancer of zeste homolog 2 (Ezh2), which encode the enzymatic component of PRC2. Here, we investigated the role of PRC2 in hematopoiesis by conditional deletion of suppressor of zeste 12 protein homolog (Suz12), a core component of PRC2. Complete loss of Suz12 resulted in failure of hematopoiesis, both in the embryo and the adult, with a loss of maintenance of hematopoietic stem cells (HSCs). In contrast, partial loss of PRC2 enhanced HSC self-renewal. Although Suz12 was required for lymphoid development, deletion in individual blood cell lineages revealed that it was dispensable for the development of granulocytic, monocytic, and megakaryocytic cells. Collectively, these data reveal the multifaceted role of PRC2 in hematopoiesis, with divergent dose-dependent effects in HSC and distinct roles in maturing blood cells. Because PRC2 is a potential target for cancer therapy, the significant consequences of modest changes in PRC2 activity, as well as the cell and developmental stage-specific effects, will need to be carefully considered in any therapeutic context.
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Rabenhorst U, Thalheimer F, Gerlach K, Kijonka M, Böhm S, Krause D, Vauti F, Arnold HH, Schroeder T, Schnütgen F, von Melchner H, Rieger M, Zörnig M. Single-Stranded DNA-Binding Transcriptional Regulator FUBP1 Is Essential for Fetal and Adult Hematopoietic Stem Cell Self-Renewal. Cell Rep 2015; 11:1847-55. [DOI: 10.1016/j.celrep.2015.05.038] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 05/08/2015] [Accepted: 05/23/2015] [Indexed: 12/21/2022] Open
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Hematopoietic stem cells: concepts, definitions, and the new reality. Blood 2015; 125:2605-13. [PMID: 25762175 DOI: 10.1182/blood-2014-12-570200] [Citation(s) in RCA: 345] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 02/03/2015] [Indexed: 12/25/2022] Open
Abstract
Hematopoietic stem cell (HSC) research took hold in the 1950s with the demonstration that intravenously injected bone marrow cells can rescue irradiated mice from lethality by reestablishing blood cell production. Attempts to quantify the cells responsible led to the discovery of serially transplantable, donor-derived, macroscopic, multilineage colonies detectable on the spleen surface 1 to 2 weeks posttransplant. The concept of self-renewing multipotent HSCs was born, but accompanied by perplexing evidence of great variability in the outcomes of HSC self-renewal divisions. The next 60 years saw an explosion in the development and use of more refined tools for assessing the behavior of prospectively purified subsets of hematopoietic cells with blood cell-producing capacity. These developments have led to the formulation of increasingly complex hierarchical models of hematopoiesis and a growing list of intrinsic and extrinsic elements that regulate HSC cycling status, viability, self-renewal, and lineage outputs. More recent examination of these properties in individual, highly purified HSCs and analyses of their perpetuation in clonally generated progeny HSCs have now provided definitive evidence of linearly transmitted heterogeneity in HSC states. These results anticipate the need and use of emerging new technologies to establish models that will accommodate such pluralistic features of HSCs and their control mechanisms.
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34
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Liu S, Xu Y, Zhou Z, Feng B, Huang H. Progress and challenges in generating functional hematopoietic stem/progenitor cells from human pluripotent stem cells. Cytotherapy 2015; 17:344-58. [PMID: 25680303 DOI: 10.1016/j.jcyt.2015.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 01/03/2015] [Accepted: 01/06/2015] [Indexed: 11/25/2022]
Abstract
The generation of hematopoietic stem cells (HSCs) from human pluripotent stem cells (hPSCs) in vitro holds great potential for providing alternative sources of donor cells for clinical HSC transplantation. However, the low efficiency of current protocols for generating blood lineages and the dysfunction identified in hPSC-derived hematopoietic cells limit their use for full hematopoietic reconstitution in clinics. This review outlines the current understanding of in vitro hematopoietic differentiation from hPSCs, emphasizes the intrinsic and extrinsic molecular mechanisms that are attributed to the aberrant phenotype and function in hPSC-derived hematopoietic cells, pinpoints the current challenges to develop the truly functional HSCs from hPSCs for clinical applications and explores their potential solutions.
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Affiliation(s)
- Senquan Liu
- Bone Marrow Transplantation Centre, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yulin Xu
- Bone Marrow Transplantation Centre, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Zijing Zhou
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Bo Feng
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; SBS Core Laboratory, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.
| | - He Huang
- Bone Marrow Transplantation Centre, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China.
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35
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The histone demethylase Jarid1b is required for hematopoietic stem cell self-renewal in mice. Blood 2015; 125:2075-8. [PMID: 25655602 DOI: 10.1182/blood-2014-08-596734] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Jarid1b/KDM5b is a histone demethylase that regulates self-renewal and differentiation in stem cells and cancer; however, its function in hematopoiesis is unclear. Here, we find that Jarid1b is highly expressed in primitive hematopoietic compartments and is overexpressed in acute myeloid leukemias. Constitutive genetic deletion of Jarid1b did not impact steady-state hematopoiesis. In contrast, acute deletion of Jarid1b from bone marrow increased peripheral blood T cells and, following secondary transplantation, resulted in loss of bone marrow reconstitution. Our results reveal that deletion of Jarid1b compromises hematopoietic stem cell (HSC) self-renewal capacity and suggest that Jarid1b is a positive regulator of HSC potential.
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36
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Sánchez-Castillo M, Ruau D, Wilkinson AC, Ng FSL, Hannah R, Diamanti E, Lombard P, Wilson NK, Gottgens B. CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities. Nucleic Acids Res 2014; 43:D1117-23. [PMID: 25270877 PMCID: PMC4384009 DOI: 10.1093/nar/gku895] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
CODEX (http://codex.stemcells.cam.ac.uk/) is a user-friendly database for the direct access and interrogation of publicly available next-generation sequencing (NGS) data, specifically aimed at experimental biologists. In an era of multi-centre genomic dataset generation, CODEX provides a single database where these samples are collected, uniformly processed and vetted. The main drive of CODEX is to provide the wider scientific community with instant access to high-quality NGS data, which, irrespective of the publishing laboratory, is directly comparable. CODEX allows users to immediately visualize or download processed datasets, or compare user-generated data against the database's cumulative knowledge-base. CODEX contains four types of NGS experiments: transcription factor chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq), histone modification ChIP-Seq, DNase-Seq and RNA-Seq. These are largely encompassed within two specialized repositories, HAEMCODE and ESCODE, which are focused on haematopoiesis and embryonic stem cell samples, respectively. To date, CODEX contains over 1000 samples, including 221 unique TFs and 93 unique cell types. CODEX therefore provides one of the most complete resources of publicly available NGS data for the direct interrogation of transcriptional programmes that regulate cellular identity and fate in the context of mammalian development, homeostasis and disease.
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Affiliation(s)
- Manuel Sánchez-Castillo
- Department of Haematology, Wellcome Trust-MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - David Ruau
- Department of Haematology, Wellcome Trust-MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Adam C Wilkinson
- Department of Haematology, Wellcome Trust-MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Felicia S L Ng
- Department of Haematology, Wellcome Trust-MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Rebecca Hannah
- Department of Haematology, Wellcome Trust-MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Evangelia Diamanti
- Department of Haematology, Wellcome Trust-MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Patrick Lombard
- Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Nicola K Wilson
- Department of Haematology, Wellcome Trust-MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Berthold Gottgens
- Department of Haematology, Wellcome Trust-MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
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37
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Chen L, Kostadima M, Martens JH, Canu G, Garcia SP, Turro E, Downes K, Macaulay IC, Bielczyk-Maczynska E, Coe S, Farrow S, Poudel P, Burden F, Jansen SB, Astle WJ, Attwood A, Bariana T, de Bono B, Breschi A, Chambers JC, Consortium BRIDGE, Choudry FA, Clarke L, Coupland P, van der Ent M, Erber WN, Jansen JH, Favier R, Fenech ME, Foad N, Freson K, van Geet C, Gomez K, Guigo R, Hampshire D, Kelly AM, Kerstens HH, Kooner JS, Laffan M, Lentaigne C, Labalette C, Martin T, Meacham S, Mumford A, Nürnberg S, Palumbo E, van der Reijden BA, Richardson D, Sammut SJ, Slodkowicz G, Tamuri AU, Vasquez L, Voss K, Watt S, Westbury S, Flicek P, Loos R, Goldman N, Bertone P, Read RJ, Richardson S, Cvejic A, Soranzo N, Ouwehand WH, Stunnenberg HG, Frontini M, Rendon A. Transcriptional diversity during lineage commitment of human blood progenitors. Science 2014; 345:1251033. [PMID: 25258084 PMCID: PMC4254742 DOI: 10.1126/science.1251033] [Citation(s) in RCA: 215] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Blood cells derive from hematopoietic stem cells through stepwise fating events. To characterize gene expression programs driving lineage choice, we sequenced RNA from eight primary human hematopoietic progenitor populations representing the major myeloid commitment stages and the main lymphoid stage. We identified extensive cell type-specific expression changes: 6711 genes and 10,724 transcripts, enriched in non-protein-coding elements at early stages of differentiation. In addition, we found 7881 novel splice junctions and 2301 differentially used alternative splicing events, enriched in genes involved in regulatory processes. We demonstrated experimentally cell-specific isoform usage, identifying nuclear factor I/B (NFIB) as a regulator of megakaryocyte maturation-the platelet precursor. Our data highlight the complexity of fating events in closely related progenitor populations, the understanding of which is essential for the advancement of transplantation and regenerative medicine.
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Affiliation(s)
- Lu Chen
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Myrto Kostadima
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Joost H.A. Martens
- Department of Molecular Biology, Radboud University, Nijmegen, the Netherlands
| | - Giovanni Canu
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Sara P. Garcia
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Ernest Turro
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Iain C. Macaulay
- Sanger Institute-EBI Single-Cell Genomics Centre, Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Ewa Bielczyk-Maczynska
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Sophia Coe
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Samantha Farrow
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Pawan Poudel
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Frances Burden
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Sjoert B.G. Jansen
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - William J. Astle
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Medical Research Council Biostatistics Unit, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Antony Attwood
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Tadbir Bariana
- Department of Haematology, University College London Cancer Institute, London, United Kingdom
- The Katharine Dormandy Haemophilia Centre and Thrombosis Unit, Royal Free NHS Trust, London, United Kingdom
| | - Bernard de Bono
- CHIME Institute, University College London, Archway Campus, London, United Kingdom
- Auckland Bioengineering Institute, University of Auckland, New Zealand
| | - Alessandra Breschi
- Centre for Genomic Regulation and University Pompeu Fabra, Barcelona, Spain
| | - John C. Chambers
- Imperial College Healthcare NHS Trust, DuCane Road, London, United Kingdom
- Ealing Hospital NHS Trust, Southall, Middlesex, United Kingdom
| | | | - Fizzah A. Choudry
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Paul Coupland
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Martijn van der Ent
- Department of Molecular Biology, Radboud University, Nijmegen, the Netherlands
| | - Wendy N. Erber
- Pathology and Laboratory Medicine, University of Western Australia, Crawley, Western Australia, Australia
| | - Joop H. Jansen
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rémi Favier
- Assistance Publique-Hopitaux de Paris, Institut National de la Santé et de la Recherche Médicale U1009, Villejuif, France
| | - Matthew E. Fenech
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Nicola Foad
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Kathleen Freson
- Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium
| | - Chris van Geet
- Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium
| | - Keith Gomez
- The Katharine Dormandy Haemophilia Centre and Thrombosis Unit, Royal Free NHS Trust, London, United Kingdom
| | - Roderic Guigo
- Centre for Genomic Regulation and University Pompeu Fabra, Barcelona, Spain
| | - Daniel Hampshire
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Anne M. Kelly
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | | | - Jaspal S. Kooner
- Imperial College Healthcare NHS Trust, DuCane Road, London, United Kingdom
- Ealing Hospital NHS Trust, Southall, Middlesex, United Kingdom
| | - Michael Laffan
- Department of Haematology, Hammersmith Campus, Imperial College Academic Health Sciences Centre, Imperial College London, London, United Kingdom
| | - Claire Lentaigne
- Department of Haematology, Hammersmith Campus, Imperial College Academic Health Sciences Centre, Imperial College London, London, United Kingdom
| | - Charlotte Labalette
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Tiphaine Martin
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Twin Research & Genetic Epidemiology, Genetics & Molecular Medicine Division, St Thomas’ Hospital, King’s College, London, United Kingdom
| | - Stuart Meacham
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Andrew Mumford
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Sylvia Nürnberg
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Emilio Palumbo
- Centre for Genomic Regulation and University Pompeu Fabra, Barcelona, Spain
| | - Bert A. van der Reijden
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - David Richardson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Stephen J. Sammut
- Department of Oncology, Addenbrooke’s Cambridge University Hospital NHS Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Cancer Research United Kingdom, Cambridge Institute, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Greg Slodkowicz
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Asif U. Tamuri
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Louella Vasquez
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Katrin Voss
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Stephen Watt
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Sarah Westbury
- School of Clinical Sciences, University of Bristol, United Kingdom
| | - Paul Flicek
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Remco Loos
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Nick Goldman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Paul Bertone
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Genome Biology and Developmental Biology Units, European Molecular Biology Laboratory, Heidelberg, Germany
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Randy J. Read
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Sylvia Richardson
- Medical Research Council Biostatistics Unit, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Ana Cvejic
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Nicole Soranzo
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Willem H. Ouwehand
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | | | - Mattia Frontini
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Augusto Rendon
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Medical Research Council Biostatistics Unit, Cambridge Biomedical Campus, Cambridge, United Kingdom
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38
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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] [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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39
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Hofmann MC. Stem cells and nanomaterials. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 811:255-75. [PMID: 24683036 DOI: 10.1007/978-94-017-8739-0_13] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Because of their ability to self-renew and differentiate into many cell types, stem cells offer the potential to be used for tissue regeneration and engineering. Much progress has recently been made in our understanding of the biology of stem cells and our ability to manipulate their proliferation and differentiation to obtain functional tissues. Similarly, nanomaterials have been recently developed that will accelerate discovery of mechanisms driving stem cell fate and their utilization in medicine. Nanoparticles have been developed that allow the labeling and tracking of stem cells and their differentiated phenotype within an organism. Nanosurfaces are engineered that mimic the extracellular matrix to which stem cells adhere and migrate. Scaffolds made of functionalized nanofibers can now be used to grow stem cells and regenerate damaged tissues and organs. However, the small scale of nanomaterials induces changes in their chemical and physical properties that might modify their interactions with cells and tissues, and render them toxic to stem cells. Therefore a thorough understanding of stem cell-nanomaterial interactions is still necessary not only to accelerate the success of medical treatments but also to ensure the safety of the tools provided by these novel technologies.
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Affiliation(s)
- Marie-Claude Hofmann
- Department of Endocrine Neoplasia and Hormonal Disorders, University of Texas MD Anderson Cancer Center, Houston, TX, USA,
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Ratliff ML, Templeton TD, Ward JM, Webb CF. The Bright Side of Hematopoiesis: Regulatory Roles of ARID3a/Bright in Human and Mouse Hematopoiesis. Front Immunol 2014; 5:113. [PMID: 24678314 PMCID: PMC3958700 DOI: 10.3389/fimmu.2014.00113] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 03/04/2014] [Indexed: 12/12/2022] Open
Abstract
ARID3a/Bright is a DNA-binding protein that was originally discovered for its ability to increase immunoglobulin transcription in antigen-activated B cells. It interacts with DNA as a dimer through its ARID, or A/T-rich interacting domain. In association with other proteins, ARID3a increased transcription of the immunoglobulin heavy chain and led to improved chromatin accessibility of the heavy chain enhancer. Constitutive expression of ARID3a in B lineage cells resulted in autoantibody production, suggesting its regulation is important. Abnormal ARID3a expression has also been associated with increased proliferative capacity and malignancy. Roles for ARID3a in addition to interactions with the immunoglobulin locus were suggested by transgenic and knockout mouse models. Over-expression of ARID3a resulted in skewing of mature B cell subsets and altered gene expression patterns of follicular B cells, whereas loss of function resulted in loss of B1 lineage B cells and defects in hematopoiesis. More recent studies showed that loss of ARID3a in adult somatic cells promoted developmental plasticity, alterations in gene expression patterns, and lineage fate decisions. Together, these data suggest new regulatory roles for ARID3a. The genes influenced by ARID3a are likely to play pivotal roles in lineage decisions, highlighting the importance of this understudied transcription factor.
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Affiliation(s)
- Michelle L Ratliff
- Immunobiology and Cancer Research, Oklahoma Medical Research Foundation , Oklahoma City, OK , USA
| | - Troy D Templeton
- Department of Cell Biology, University of Oklahoma Health Sciences Center , Oklahoma City, OK , USA
| | - Julie M Ward
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center , Oklahoma City, OK , USA
| | - Carol F Webb
- Immunobiology and Cancer Research, Oklahoma Medical Research Foundation , Oklahoma City, OK , USA ; Department of Cell Biology, University of Oklahoma Health Sciences Center , Oklahoma City, OK , USA ; Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center , Oklahoma City, OK , USA
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Ruiz MA. Cell therapy in Brazil: time for reflection. Rev Bras Hematol Hemoter 2013; 35:296-8. [PMID: 24255604 PMCID: PMC3832301 DOI: 10.5581/1516-8484.20130117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Accepted: 09/01/2013] [Indexed: 11/27/2022] Open
Affiliation(s)
- Milton Artur Ruiz
- Editor-in-chief. Revista Brasileira de Hematologia e Hemoterapia -RBHH
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