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McGowan J, Kilias ES, Alacid E, Lipscombe J, Jenkins BH, Gharbi K, Kaithakottil GG, Macaulay IC, McTaggart S, Warring SD, Richards TA, Hall N, Swarbreck D. Identification of a non-canonical ciliate nuclear genetic code where UAA and UAG code for different amino acids. PLoS Genet 2023; 19:e1010913. [PMID: 37796765 PMCID: PMC10553269 DOI: 10.1371/journal.pgen.1010913] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 08/10/2023] [Indexed: 10/07/2023] Open
Abstract
The genetic code is one of the most highly conserved features across life. Only a few lineages have deviated from the "universal" genetic code. Amongst the few variants of the genetic code reported to date, the codons UAA and UAG virtually always have the same translation, suggesting that their evolution is coupled. Here, we report the genome and transcriptome sequencing of a novel uncultured ciliate, belonging to the Oligohymenophorea class, where the translation of the UAA and UAG stop codons have changed to specify different amino acids. Genomic and transcriptomic analyses revealed that UAA has been reassigned to encode lysine, while UAG has been reassigned to encode glutamic acid. We identified multiple suppressor tRNA genes with anticodons complementary to the reassigned codons. We show that the retained UGA stop codon is enriched in the 3'UTR immediately downstream of the coding region of genes, suggesting that there is functional drive to maintain tandem stop codons. Using a phylogenomics approach, we reconstructed the ciliate phylogeny and mapped genetic code changes, highlighting the remarkable number of independent genetic code changes within the Ciliophora group of protists. According to our knowledge, this is the first report of a genetic code variant where UAA and UAG encode different amino acids.
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Affiliation(s)
- Jamie McGowan
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | | | - Elisabet Alacid
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - James Lipscombe
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | | | - Karim Gharbi
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | | | - Iain C. Macaulay
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Seanna McTaggart
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Sally D. Warring
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | | | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - David Swarbreck
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
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2
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Luis TC, Barkas N, Carrelha J, Giustacchini A, Mazzi S, Norfo R, Wu B, Aliouat A, Guerrero JA, Rodriguez-Meira A, Bouriez-Jones T, Macaulay IC, Jasztal M, Zhu G, Ni H, Robson MJ, Blakely RD, Mead AJ, Nerlov C, Ghevaert C, Jacobsen SEW. Perivascular niche cells sense thrombocytopenia and activate hematopoietic stem cells in an IL-1 dependent manner. Nat Commun 2023; 14:6062. [PMID: 37770432 PMCID: PMC10539537 DOI: 10.1038/s41467-023-41691-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 09/11/2023] [Indexed: 09/30/2023] Open
Abstract
Hematopoietic stem cells (HSCs) residing in specialized niches in the bone marrow are responsible for the balanced output of multiple short-lived blood cell lineages in steady-state and in response to different challenges. However, feedback mechanisms by which HSCs, through their niches, sense acute losses of specific blood cell lineages remain to be established. While all HSCs replenish platelets, previous studies have shown that a large fraction of HSCs are molecularly primed for the megakaryocyte-platelet lineage and are rapidly recruited into proliferation upon platelet depletion. Platelets normally turnover in an activation-dependent manner, herein mimicked by antibodies inducing platelet activation and depletion. Antibody-mediated platelet activation upregulates expression of Interleukin-1 (IL-1) in platelets, and in bone marrow extracellular fluid in vivo. Genetic experiments demonstrate that rather than IL-1 directly activating HSCs, activation of bone marrow Lepr+ perivascular niche cells expressing IL-1 receptor is critical for the optimal activation of quiescent HSCs upon platelet activation and depletion. These findings identify a feedback mechanism by which activation-induced depletion of a mature blood cell lineage leads to a niche-dependent activation of HSCs to reinstate its homeostasis.
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Affiliation(s)
- Tiago C Luis
- Haematopoietic Stem Cell Biology Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK.
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK.
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London, W12 0NN, London, UK.
- Department of Life Sciences, Imperial College London, SW7 2AZ, London, UK.
| | - Nikolaos Barkas
- Haematopoietic Stem Cell Biology Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
| | - Joana Carrelha
- Haematopoietic Stem Cell Biology Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
| | - Alice Giustacchini
- Haematopoietic Stem Cell Biology Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
- Molecular and Cellular Immunology Section, UCL Great Ormond Street Institute of Child Health, London, UK
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
| | - Stefania Mazzi
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, SE-141 86, Stockholm, Sweden
| | - Ruggiero Norfo
- Haematopoietic Stem Cell Biology Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
| | - Bishan Wu
- Haematopoietic Stem Cell Biology Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
| | - Affaf Aliouat
- Haematopoietic Stem Cell Biology Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
| | - Jose A Guerrero
- Department of Haematology, University of Cambridge, Cambridge, UK
- National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
| | - Alba Rodriguez-Meira
- Haematopoietic Stem Cell Biology Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
| | - Tiphaine Bouriez-Jones
- Haematopoietic Stem Cell Biology Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
| | - Iain C Macaulay
- Haematopoietic Stem Cell Biology Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
- Earlham Institute, Norwich Research Park, NR4 7UZ, Norwich, UK
| | - Maria Jasztal
- Department of Haematology, University of Cambridge, Cambridge, UK
- National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
| | - Guangheng Zhu
- Toronto Platelet Immunobiology Group and Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, M5B 1W8, Canada
- CCOA Therapeutics Inc, Toronto, ON, M5B 1T8, Canada
| | - Heyu Ni
- Toronto Platelet Immunobiology Group and Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, M5B 1W8, Canada
- CCOA Therapeutics Inc, Toronto, ON, M5B 1T8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A1, Canada
- Canadian Blood Services Centre for Innovation, Toronto, ON, M5B 1W8, Canada
| | - Matthew J Robson
- Department of Biomedical Science, Charles E. Schmidt College of Medicine and Stiles-Nicholson Brain Institute, Florida Atlantic University, Jupiter, FL, 33458, USA
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Randy D Blakely
- Department of Biomedical Science, Charles E. Schmidt College of Medicine and Stiles-Nicholson Brain Institute, Florida Atlantic University, Jupiter, FL, 33458, USA
| | - Adam J Mead
- Haematopoietic Stem Cell Biology Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
| | - Claus Nerlov
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
| | - Cedric Ghevaert
- Department of Haematology, University of Cambridge, Cambridge, UK
- National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
| | - Sten Eirik W Jacobsen
- Haematopoietic Stem Cell Biology Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK.
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK.
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, SE-141 86, Stockholm, Sweden.
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77, Stockholm, Sweden.
- Department of Hematology, Karolinska University Hospital, Stockholm, Sweden.
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3
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Bell AM, Utting C, Dickie AC, Kucharczyk MW, Quillet R, Gutierrez-Mecinas M, Razlan AN, Cooper AH, Lan Y, Hachisuka J, Weir GA, Bannister K, Watanabe M, Kania A, Hoon MA, Macaulay IC, Denk F, Todd AJ. Deep sequencing of Phox2a nuclei reveals five classes of anterolateral system neurons. bioRxiv 2023:2023.08.20.553715. [PMID: 37786726 PMCID: PMC10541585 DOI: 10.1101/2023.08.20.553715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
The anterolateral system (ALS) is a major ascending pathway from the spinal cord that projects to multiple brain areas and underlies the perception of pain, itch and skin temperature. Despite its importance, our understanding of this system has been hampered by the considerable functional and molecular diversity of its constituent cells. Here we use fluorescence-activated cell sorting to isolate ALS neurons belonging to the Phox2a-lineage for single-nucleus RNA sequencing. We reveal five distinct clusters of ALS neurons (ALS1-5) and document their laminar distribution in the spinal cord using in situ hybridization. We identify 3 clusters of neurons located predominantly in laminae I-III of the dorsal horn (ALS1-3) and two clusters with cell bodies located in deeper laminae (ALS4 & ALS5). Our findings reveal the transcriptional logic that underlies ALS neuronal diversity in the adult mouse and uncover the molecular identity of two previously identified classes of projection neurons. We also show that these molecular signatures can be used to target groups of ALS neurons using retrograde viral tracing. Overall, our findings provide a valuable resource for studying somatosensory biology and targeting subclasses of ALS neurons.
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Affiliation(s)
- Andrew M. Bell
- School of Psychology and Neuroscience, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | | | - Allen C. Dickie
- School of Psychology and Neuroscience, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Mateusz W. Kucharczyk
- The Wolfson Centre for Age-Related Diseases, King’s College London, London WC2R 2LS, UK
- Laboratory of Neurophysiology, Department of Biochemical Toxicology, Faculty of Pharmacy, Jagiellonian University Medical College, PL30-668 Krakow, Poland
| | - Raphaëlle Quillet
- School of Psychology and Neuroscience, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Maria Gutierrez-Mecinas
- School of Psychology and Neuroscience, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Aimi N.B. Razlan
- School of Psychology and Neuroscience, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Andrew H. Cooper
- School of Psychology and Neuroscience, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | | | - Junichi Hachisuka
- School of Psychology and Neuroscience, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Greg A. Weir
- School of Psychology and Neuroscience, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Kirsty Bannister
- The Wolfson Centre for Age-Related Diseases, King’s College London, London WC2R 2LS, UK
| | - Masahiko Watanabe
- Department of Anatomy, Hokkaido University School of Medicine, Sapporo 060-8638, Japan
| | - Artur Kania
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC, H2W 1R7, Canada
| | - Mark A. Hoon
- Molecular Genetics Section, National Institute of Dental and Craniofacial Research/NIH, Bethesda, MD, USA
| | | | - Franziska Denk
- The Wolfson Centre for Age-Related Diseases, King’s College London, London WC2R 2LS, UK
| | - Andrew J. Todd
- School of Psychology and Neuroscience, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
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4
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Wojtowicz EE, Mistry JJ, Uzun V, Hellmich C, Scoones A, Chin DW, Kettyle LM, Grasso F, Lord AM, Wright DJ, Etherington GJ, Woll PS, Belderbos ME, Bowles KM, Nerlov C, Haerty W, Bystrykh LV, Jacobsen SEW, Rushworth SA, Macaulay IC. Panhematopoietic RNA barcoding enables kinetic measurements of nucleate and anucleate lineages and the activation of myeloid clones following acute platelet depletion. Genome Biol 2023; 24:152. [PMID: 37370129 PMCID: PMC10294477 DOI: 10.1186/s13059-023-02976-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Platelets and erythrocytes constitute over 95% of all hematopoietic stem cell output. However, the clonal dynamics of HSC contribution to these lineages remains largely unexplored. RESULTS We use lentiviral genetic labeling of mouse hematopoietic stem cells to quantify output from all lineages, nucleate, and anucleate, simultaneously linking these with stem and progenitor cell transcriptomic phenotypes using single-cell RNA-sequencing. We observe dynamic shifts of clonal behaviors through time in same-animal peripheral blood and demonstrate that acute platelet depletion shifts the output of multipotent hematopoietic stem cells to the exclusive production of platelets. Additionally, we observe the emergence of new myeloid-biased clones, which support short- and long-term production of blood cells. CONCLUSIONS Our approach enables kinetic studies of multi-lineage output in the peripheral blood and transcriptional heterogeneity of individual hematopoietic stem cells. Our results give a unique insight into hematopoietic stem cell reactivation upon platelet depletion and of clonal dynamics in both steady state and under stress.
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Affiliation(s)
- Edyta E Wojtowicz
- Earlham Institute, Norwich Research Park, Norwich, UK.
- Norwich Medical School, University of East Anglia, Norwich, UK.
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
- Department of Medicine, Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.
| | - Jayna J Mistry
- Earlham Institute, Norwich Research Park, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Vladimir Uzun
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Charlotte Hellmich
- Norwich Medical School, University of East Anglia, Norwich, UK
- Norfolk and Norwich University Hospital, Norwich, UK
| | - Anita Scoones
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Desmond W Chin
- Department of Medicine, Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Laura M Kettyle
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Medicine, Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Francesca Grasso
- Department of Medicine, Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Allegra M Lord
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Medicine, Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | | | | | - Petter S Woll
- Department of Medicine, Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | | | - Kristian M Bowles
- Norwich Medical School, University of East Anglia, Norwich, UK
- Norfolk and Norwich University Hospital, Norwich, UK
| | - Claus Nerlov
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Norwich, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Leonid V Bystrykh
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center of Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Sten Eirik W Jacobsen
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
- Department of Medicine, Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
| | | | - Iain C Macaulay
- Earlham Institute, Norwich Research Park, Norwich, UK.
- Norwich Medical School, University of East Anglia, Norwich, UK.
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5
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Mincarelli L, Uzun V, Wright D, Scoones A, Rushworth SA, Haerty W, Macaulay IC. Single-cell gene and isoform expression analysis reveals signatures of ageing in haematopoietic stem and progenitor cells. Commun Biol 2023; 6:558. [PMID: 37225862 PMCID: PMC10209181 DOI: 10.1038/s42003-023-04936-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/12/2023] [Indexed: 05/26/2023] Open
Abstract
Single-cell approaches have revealed that the haematopoietic hierarchy is a continuum of differentiation, from stem cell to committed progenitor, marked by changes in gene expression. However, many of these approaches neglect isoform-level information and thus do not capture the extent of alternative splicing within the system. Here, we present an integrated short- and long-read single-cell RNA-seq analysis of haematopoietic stem and progenitor cells. We demonstrate that over half of genes detected in standard short-read single-cell analyses are expressed as multiple, often functionally distinct, isoforms, including many transcription factors and key cytokine receptors. We observe global and HSC-specific changes in gene expression with ageing but limited impact of ageing on isoform usage. Integrating single-cell and cell-type-specific isoform landscape in haematopoiesis thus provides a new reference for comprehensive molecular profiling of heterogeneous tissues, as well as novel insights into transcriptional complexity, cell-type-specific splicing events and consequences of ageing.
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Affiliation(s)
- Laura Mincarelli
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom.
| | - Vladimir Uzun
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom
| | - David Wright
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom
| | - Anita Scoones
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom
| | - Stuart A Rushworth
- Norwich Medical School, The University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom.
| | - Iain C Macaulay
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom.
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6
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Bawn M, Hernandez J, Trampari E, Thilliez G, Quince C, Webber MA, Kingsley RA, Hall N, Macaulay IC. Single-cell genomics reveals population structures from in vitro evolutionary studies of Salmonella. Microb Genom 2022; 8. [PMID: 36125951 DOI: 10.1099/mgen.0.000871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Single-cell DNA sequencing has the potential to reveal detailed hierarchical structures in evolving populations of cells. Single cell approaches are increasingly used to study clonal evolution in human ageing and cancer but have not yet been deployed to study evolving clonal microbial populations. Here, we present an approach for single bacterial genomic analysis for in vitro evolution experiments using FACS isolation of individual bacteria followed by whole-genome amplification and sequencing. We apply this to the experimental evolution of a hypermutator strain of Salmonella in response to antibiotic stress (ciprofloxacin). By analysing sequence polymorphisms in individual cells from populations we identified the presence and prevalence of sub-populations which have acquired polymorphisms in genes previously demonstrated to be associated with ciprofloxacin susceptibility. We were also able to identify that the population exposed to antibiotic stress was able to develop resistance whilst maintaining diversity. This population structure could not be resolved from bulk sequence data, and our results show how high-throughput single-cell sequencing can enhance experimental studies of bacterial evolution.
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Affiliation(s)
- Matt Bawn
- Earlham Institute, Norwich Research Park, Norwich, NR1 7UZ, UK.,Quadram Institute, Norwich Research Park, Norwich, NR4 7UQ, UK
| | | | | | - Gaetan Thilliez
- Quadram Institute, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Christopher Quince
- Earlham Institute, Norwich Research Park, Norwich, NR1 7UZ, UK.,Quadram Institute, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Mark A Webber
- Quadram Institute, Norwich Research Park, Norwich, NR4 7UQ, UK.,Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7UA, UK
| | - Robert A Kingsley
- Quadram Institute, Norwich Research Park, Norwich, NR4 7UQ, UK.,School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK
| | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich, NR1 7UZ, UK.,School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK
| | - Iain C Macaulay
- Earlham Institute, Norwich Research Park, Norwich, NR1 7UZ, UK.,School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK
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7
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Ogbeide S, Giannese F, Mincarelli L, Macaulay IC. Into the multiverse: advances in single-cell multiomic profiling. Trends Genet 2022; 38:831-843. [PMID: 35537880 DOI: 10.1016/j.tig.2022.03.015] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 10/18/2022]
Abstract
Single-cell transcriptomic approaches have revolutionised the study of complex biological systems, with the routine measurement of gene expression in thousands of cells enabling construction of whole-organism cell atlases. However, the transcriptome is just one layer amongst many that coordinate to define cell type and state and, ultimately, function. In parallel with the widespread uptake of single-cell RNA-seq (scRNA-seq), there has been a rapid emergence of methods that enable multiomic profiling of individual cells, enabling parallel measurement of intercellular heterogeneity in the genome, epigenome, transcriptome, and proteomes. Linking measurements from each of these layers has the potential to reveal regulatory and functional mechanisms underlying cell behaviour in healthy development and disease.
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8
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Choudry FA, Bagger FO, Macaulay IC, Farrow S, Burden F, Kempster C, McKinney H, Olsen LR, Huang N, Downes K, Voet T, Uppal R, Martin JF, Mathur A, Ouwehand WH, Laurenti E, Teichmann SA, Frontini M. Transcriptional characterization of human megakaryocyte polyploidization and lineage commitment. J Thromb Haemost 2021; 19:1236-1249. [PMID: 33587817 DOI: 10.1111/jth.15271] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 02/09/2021] [Accepted: 02/12/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Megakaryocytes (MKs) originate from cells immuno-phenotypically indistinguishable from hematopoietic stem cells (HSCs), bypassing intermediate progenitors. They mature within the adult bone marrow and release platelets into the circulation. Until now, there have been no transcriptional studies of primary human bone marrow MKs. OBJECTIVES To characterize MKs and HSCs from human bone marrow using single-cell RNA sequencing, to investigate MK lineage commitment, maturation steps, and thrombopoiesis. RESULTS We show that MKs at different levels of polyploidization exhibit distinct transcriptional states. Although high levels of platelet-specific gene expression occur in the lower ploidy classes, as polyploidization increases, gene expression is redirected toward translation and posttranslational processing transcriptional programs, in preparation for thrombopoiesis. Our findings are in keeping with studies of MK ultrastructure and supersede evidence generated using in vitro cultured MKs. Additionally, by analyzing transcriptional signatures of a single HSC, we identify two MK-biased HSC subpopulations exhibiting unique differentiation kinetics. We show that human bone marrow MKs originate from these HSC subpopulations, supporting the notion that they display priming for MK differentiation. Finally, to investigate transcriptional changes in MKs associated with stress thrombopoiesis, we analyzed bone marrow MKs from individuals with recent myocardial infarction and found a specific gene expression signature. Our data support the modulation of MK differentiation in this thrombotic state. CONCLUSIONS Here, we use single-cell sequencing for the first time to characterize the human bone marrow MK transcriptome at different levels of polyploidization and investigate their differentiation from the HSC.
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Affiliation(s)
- Fizzah A Choudry
- Department of Hematology, University of Cambridge, Cambridge, UK
- Barts Heart Centre, Barts Health NHS Trust, London, UK
- Centre for Cardiovascular Medicine and Devices, Queen Mary University of London, London, UK
| | - Frederik O Bagger
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
- The Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
- Centre for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Iain C Macaulay
- The Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Samantha Farrow
- Department of Hematology, University of Cambridge, Cambridge, UK
| | - Frances Burden
- Department of Hematology, University of Cambridge, Cambridge, UK
| | - Carly Kempster
- Department of Hematology, University of Cambridge, Cambridge, UK
| | - Harriet McKinney
- Department of Hematology, University of Cambridge, Cambridge, UK
| | - Lars R Olsen
- Centre for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Ni Huang
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
- The Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Kate Downes
- Department of Hematology, University of Cambridge, Cambridge, UK
| | - Thierry Voet
- The Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Rakesh Uppal
- Barts Heart Centre, Barts Health NHS Trust, London, UK
- Centre for Cardiovascular Medicine and Devices, Queen Mary University of London, London, UK
| | - John F Martin
- Division of Medicine, University College London, London, UK
| | - Anthony Mathur
- Barts Heart Centre, Barts Health NHS Trust, London, UK
- Centre for Cardiovascular Medicine and Devices, Queen Mary University of London, London, UK
| | - Willem H Ouwehand
- Department of Hematology, University of Cambridge, Cambridge, UK
- The Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
- BHF Centre of Excellence, Division of Cardiovascular Medicine, Cambridge University Hospitals, Cambridge, UK
| | - Elisa Laurenti
- Department of Hematology, University of Cambridge, Cambridge, UK
| | - Sarah A Teichmann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
- The Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Mattia Frontini
- Department of Hematology, University of Cambridge, Cambridge, UK
- BHF Centre of Excellence, Division of Cardiovascular Medicine, Cambridge University Hospitals, Cambridge, UK
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9
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Brann DH, Tsukahara T, Weinreb C, Lipovsek M, Van den Berge K, Gong B, Chance R, Macaulay IC, Chou HJ, Fletcher RB, Das D, Street K, de Bezieux HR, Choi YG, Risso D, Dudoit S, Purdom E, Mill J, Hachem RA, Matsunami H, Logan DW, Goldstein BJ, Grubb MS, Ngai J, Datta SR. Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia. Sci Adv 2020; 6:eabc5801. [PMID: 32937591 PMCID: PMC10715684 DOI: 10.1126/sciadv.abc5801] [Citation(s) in RCA: 666] [Impact Index Per Article: 166.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/18/2020] [Indexed: 05/05/2023]
Abstract
Altered olfactory function is a common symptom of COVID-19, but its etiology is unknown. A key question is whether SARS-CoV-2 (CoV-2) - the causal agent in COVID-19 - affects olfaction directly, by infecting olfactory sensory neurons or their targets in the olfactory bulb, or indirectly, through perturbation of supporting cells. Here we identify cell types in the olfactory epithelium and olfactory bulb that express SARS-CoV-2 cell entry molecules. Bulk sequencing demonstrated that mouse, non-human primate and human olfactory mucosa expresses two key genes involved in CoV-2 entry, ACE2 and TMPRSS2. However, single cell sequencing revealed that ACE2 is expressed in support cells, stem cells, and perivascular cells, rather than in neurons. Immunostaining confirmed these results and revealed pervasive expression of ACE2 protein in dorsally-located olfactory epithelial sustentacular cells and olfactory bulb pericytes in the mouse. These findings suggest that CoV-2 infection of non-neuronal cell types leads to anosmia and related disturbances in odor perception in COVID-19 patients.
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Affiliation(s)
- David H Brann
- Harvard Medical School Department of Neurobiology, Boston MA 02115 USA
| | - Tatsuya Tsukahara
- Harvard Medical School Department of Neurobiology, Boston MA 02115 USA
| | - Caleb Weinreb
- Harvard Medical School Department of Neurobiology, Boston MA 02115 USA
| | - Marcela Lipovsek
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, London SE1 1UL, UK
| | - Koen Van den Berge
- Department of Statistics, University of California, Berkeley, CA 94720
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Boying Gong
- Division of Biostatistics, School of Public Health, University of California, Berkeley, CA 94720
| | - Rebecca Chance
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Iain C Macaulay
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Hsin-Jung Chou
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Russell B Fletcher
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Present address: Surrozen, Inc., South San Francisco, CA 94080
| | - Diya Das
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Berkeley Institute for Data Science, University of California, Berkeley
- Present address: Genentech, Inc., South San Francisco, CA 94080
| | - Kelly Street
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Hector Roux de Bezieux
- Division of Biostatistics, School of Public Health, University of California, Berkeley, CA 94720
- Center for Computational Biology, University of California, Berkeley, CA 94720
| | - Yoon-Gi Choi
- QB3 Functional Genomics Laboratory, University of California, Berkeley, CA 94720
| | - Davide Risso
- Department of Statistical Sciences, University of Padova, Padova, Italy
| | - Sandrine Dudoit
- Department of Statistics, University of California, Berkeley, CA 94720
- Division of Biostatistics, School of Public Health, University of California, Berkeley, CA 94720
| | - Elizabeth Purdom
- Department of Statistics, University of California, Berkeley, CA 94720
| | - Jonathan Mill
- University of Exeter Medical School, College of Medicine & Health, University of Exeter, Exeter EX2 5DW, UK
| | - Ralph Abi Hachem
- Duke University School of Medicine Department of Head and Neck Surgery & Communication Sciences, Durham, NC 27717 USA
| | - Hiroaki Matsunami
- Duke University School of Medicine Department of Molecular Genetics and Microbiology, Department of Neurobiology, Duke Institute for Brain Sciences, Durham, NC 27717 US
| | - Darren W Logan
- Waltham Petcare Science Institute, Leicestershire LE14 4RT, UK
| | - Bradley J Goldstein
- Duke University School of Medicine Department of Head and Neck Surgery & Communication Sciences, Durham, NC 27717 USA
| | - Matthew S Grubb
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, London SE1 1UL, UK
| | - John Ngai
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- QB3 Functional Genomics Laboratory, University of California, Berkeley, CA 94720
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA 94720
- Present address: National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
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10
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Abstract
Cells are a fundamental unit of life, and the ability to study the phenotypes and behaviors of individual cells is crucial to understanding the workings of complex biological systems. Cell phenotypes (epigenomic, transcriptomic, proteomic, and metabolomic) exhibit dramatic heterogeneity between and within the different cell types and states underlying cellular functional diversity. Cell genotypes can also display heterogeneity throughout an organism, in the form of somatic genetic variation-most notably in the emergence and evolution of tumors. Recent technical advances in single-cell isolation and the development of omics approaches sensitive enough to reveal these aspects of cell identity have enabled a revolution in the study of multicellular systems. In this review, we discuss the technologies available to resolve the genomes, epigenomes, transcriptomes, proteomes, and metabolomes of single cells from a wide variety of living systems.
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Affiliation(s)
- Laura Mincarelli
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZUnited Kingdom
| | - Ashleigh Lister
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZUnited Kingdom
| | - James Lipscombe
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZUnited Kingdom
| | - Iain C. Macaulay
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZUnited Kingdom
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11
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Shahbazi MN, Scialdone A, Skorupska N, Weberling A, Recher G, Zhu M, Jedrusik A, Devito LG, Noli L, Macaulay IC, Buecker C, Khalaf Y, Ilic D, Voet T, Marioni JC, Zernicka-Goetz M. Pluripotent state transitions coordinate morphogenesis in mouse and human embryos. Nature 2017; 552:239-243. [PMID: 29186120 PMCID: PMC5768241 DOI: 10.1038/nature24675] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 11/02/2017] [Indexed: 12/22/2022]
Abstract
The foundations of mammalian development lie in a cluster of embryonic epiblast stem cells. In response to extracellular matrix signalling, these cells undergo epithelialization and create an apical surface in contact with a cavity, a fundamental event for all subsequent development. Concomitantly, epiblast cells transit through distinct pluripotent states, before lineage commitment at gastrulation. These pluripotent states have been characterized at the molecular level, but their biological importance remains unclear. Here we show that exit from an unrestricted naive pluripotent state is required for epiblast epithelialization and generation of the pro-amniotic cavity in mouse embryos. Embryonic stem cells locked in the naive state are able to initiate polarization but fail to undergo lumenogenesis. Mechanistically, exit from naive pluripotency activates an Oct4-governed transcriptional program that results in expression of glycosylated sialomucin proteins and the vesicle tethering and fusion events of lumenogenesis. Similarly, exit of epiblasts from naive pluripotency in cultured human post-implantation embryos triggers amniotic cavity formation and developmental progression. Our results add tissue-level architecture as a new criterion for the characterization of different pluripotent states, and show the relevance of transitions between these states during development of the mammalian embryo.
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Affiliation(s)
- Marta N Shahbazi
- Mammalian Embryo and Stem Cell Group, University of Cambridge, Department of Physiology, Development and Neuroscience, Downing Street, Cambridge CB2 3EG, UK
| | - Antonio Scialdone
- EMBL-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - Natalia Skorupska
- Mammalian Embryo and Stem Cell Group, University of Cambridge, Department of Physiology, Development and Neuroscience, Downing Street, Cambridge CB2 3EG, UK
| | - Antonia Weberling
- Mammalian Embryo and Stem Cell Group, University of Cambridge, Department of Physiology, Development and Neuroscience, Downing Street, Cambridge CB2 3EG, UK
| | - Gaelle Recher
- Mammalian Embryo and Stem Cell Group, University of Cambridge, Department of Physiology, Development and Neuroscience, Downing Street, Cambridge CB2 3EG, UK
| | - Meng Zhu
- Mammalian Embryo and Stem Cell Group, University of Cambridge, Department of Physiology, Development and Neuroscience, Downing Street, Cambridge CB2 3EG, UK
| | - Agnieszka Jedrusik
- Mammalian Embryo and Stem Cell Group, University of Cambridge, Department of Physiology, Development and Neuroscience, Downing Street, Cambridge CB2 3EG, UK
| | - Liani G Devito
- Faculty of Life Sciences and Medicine, King's College London, Women's Health Academic Centre, Assisted Conception Unit, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Laila Noli
- Faculty of Life Sciences and Medicine, King's College London, Women's Health Academic Centre, Assisted Conception Unit, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Iain C Macaulay
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Christa Buecker
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Yakoub Khalaf
- Faculty of Life Sciences and Medicine, King's College London, Women's Health Academic Centre, Assisted Conception Unit, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Dusko Ilic
- Faculty of Life Sciences and Medicine, King's College London, Women's Health Academic Centre, Assisted Conception Unit, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Thierry Voet
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Herestraat 49, Leuven 3000, Belgium
| | - John C Marioni
- EMBL-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Magdalena Zernicka-Goetz
- Mammalian Embryo and Stem Cell Group, University of Cambridge, Department of Physiology, Development and Neuroscience, Downing Street, Cambridge CB2 3EG, UK
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12
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Kirschner K, Chandra T, Kiselev V, Flores-Santa Cruz D, Macaulay IC, Park HJ, Li J, Kent DG, Kumar R, Pask DC, Hamilton TL, Hemberg M, Reik W, Green AR. Proliferation Drives Aging-Related Functional Decline in a Subpopulation of the Hematopoietic Stem Cell Compartment. Cell Rep 2017; 19:1503-1511. [PMID: 28538171 PMCID: PMC5457484 DOI: 10.1016/j.celrep.2017.04.074] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 03/21/2017] [Accepted: 04/26/2017] [Indexed: 01/01/2023] Open
Abstract
Aging of the hematopoietic stem cell (HSC) compartment is characterized by lineage bias and reduced stem cell function, the molecular basis of which is largely unknown. Using single-cell transcriptomics, we identified a distinct subpopulation of old HSCs carrying a p53 signature indicative of stem cell decline alongside pro-proliferative JAK/STAT signaling. To investigate the relationship between JAK/STAT and p53 signaling, we challenged HSCs with a constitutively active form of JAK2 (V617F) and observed an expansion of the p53-positive subpopulation in old mice. Our results reveal cellular heterogeneity in the onset of HSC aging and implicate a role for JAK2V617F-driven proliferation in the p53-mediated functional decline of old HSCs.
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Affiliation(s)
- Kristina Kirschner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, Cambridgeshire CB2 0XY, UK; Department of Haematology, University of Cambridge, Cambridge, Cambridgeshire CB2 0XY, UK; Stem Cell Institute, University of Cambridge, Cambridge, Cambridgeshire CB2 0XY, UK; Institute for Cancer Sciences, University of Glasgow, Glasgow, Lanarkshire G61 1BD, UK.
| | - Tamir Chandra
- Epigenetics ISP, The Babraham Institute, Cambridge, Cambridgeshire CB22 3AT, UK; MRC Unit for Human Genetics, University of Edinburgh, Midlothian EH2 2XU, UK.
| | - Vladimir Kiselev
- The Wellcome Trust Sanger Institute, Cambridge, Cambridgeshire CB10 1SA, UK
| | - David Flores-Santa Cruz
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, Cambridgeshire CB2 0XY, UK
| | - Iain C Macaulay
- The Wellcome Trust Sanger Institute, Cambridge, Cambridgeshire CB10 1SA, UK
| | - Hyun Jun Park
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, Cambridgeshire CB2 0XY, UK
| | - Juan Li
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, Cambridgeshire CB2 0XY, UK
| | - David G Kent
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, Cambridgeshire CB2 0XY, UK
| | - Rupa Kumar
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, Cambridgeshire CB2 0XY, UK
| | - Dean C Pask
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, Cambridgeshire CB2 0XY, UK
| | - Tina L Hamilton
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, Cambridgeshire CB2 0XY, UK
| | - Martin Hemberg
- The Wellcome Trust Sanger Institute, Cambridge, Cambridgeshire CB10 1SA, UK
| | - Wolf Reik
- Epigenetics ISP, The Babraham Institute, Cambridge, Cambridgeshire CB22 3AT, UK; The Wellcome Trust Sanger Institute, Cambridge, Cambridgeshire CB10 1SA, UK.
| | - Anthony R Green
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, Cambridgeshire CB2 0XY, UK; Department of Haematology, University of Cambridge, Cambridge, Cambridgeshire CB2 0XY, UK; Stem Cell Institute, University of Cambridge, Cambridge, Cambridgeshire CB2 0XY, UK.
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13
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Svensson V, Natarajan KN, Ly LH, Miragaia RJ, Labalette C, Macaulay IC, Cvejic A, Teichmann SA. Power analysis of single-cell RNA-sequencing experiments. Nat Methods 2017; 14:381-387. [PMID: 28263961 PMCID: PMC5376499 DOI: 10.1038/nmeth.4220] [Citation(s) in RCA: 358] [Impact Index Per Article: 51.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 02/07/2017] [Indexed: 12/19/2022]
Abstract
Single-cell RNA sequencing (scRNA-seq) has become an established and powerful method to investigate transcriptomic cell-to-cell variation, thereby revealing new cell types and providing insights into developmental processes and transcriptional stochasticity. A key question is how the variety of available protocols compare in terms of their ability to detect and accurately quantify gene expression. Here, we assessed the protocol sensitivity and accuracy of many published data sets, on the basis of spike-in standards and uniform data processing. For our workflow, we developed a flexible tool for counting the number of unique molecular identifiers (https://github.com/vals/umis/). We compared 15 protocols computationally and 4 protocols experimentally for batch-matched cell populations, in addition to investigating the effects of spike-in molecular degradation. Our analysis provides an integrated framework for comparing scRNA-seq protocols.
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Affiliation(s)
- Valentine Svensson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Kedar Nath Natarajan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Lam-Ha Ly
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Ricardo J Miragaia
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Charlotte Labalette
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Iain C Macaulay
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Ana Cvejic
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Sarah A Teichmann
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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14
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Carmona SJ, Teichmann SA, Ferreira L, Macaulay IC, Stubbington MJT, Cvejic A, Gfeller D. Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types. Genome Res 2017; 27:451-461. [PMID: 28087841 PMCID: PMC5340972 DOI: 10.1101/gr.207704.116] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 01/12/2017] [Indexed: 12/30/2022]
Abstract
The immune system of vertebrate species consists of many different cell types that have distinct functional roles and are subject to different evolutionary pressures. Here, we first analyzed conservation of genes specific for all major immune cell types in human and mouse. Our results revealed higher gene turnover and faster evolution of trans-membrane proteins in NK cells compared with other immune cell types, and especially T cells, but similar conservation of nuclear and cytoplasmic protein coding genes. To validate these findings in a distant vertebrate species, we used single-cell RNA sequencing of lck:GFP cells in zebrafish and obtained the first transcriptome of specific immune cell types in a nonmammalian species. Unsupervised clustering and single-cell TCR locus reconstruction identified three cell populations, T cells, a novel type of NK-like cells, and a smaller population of myeloid-like cells. Differential expression analysis uncovered new immune-cell-specific genes, including novel immunoglobulin-like receptors, and neofunctionalization of recently duplicated paralogs. Evolutionary analyses confirmed the higher gene turnover of trans-membrane proteins in NK cells compared with T cells in fish species, suggesting that this is a general property of immune cell types across all vertebrates.
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Affiliation(s)
- Santiago J Carmona
- Ludwig Center for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - Sarah A Teichmann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, United Kingdom
| | - Lauren Ferreira
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge CB2 0XY, United Kingdom
- Wellcome Trust-Medical Research Council, Cambridge Stem Cell Institute, Cambridge CB2 1QR, United Kingdom
| | - Iain C Macaulay
- Sanger Institute-EBI Single-Cell Genomics Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, United Kingdom
| | - Michael J T Stubbington
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Ana Cvejic
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge CB2 0XY, United Kingdom
- Wellcome Trust-Medical Research Council, Cambridge Stem Cell Institute, Cambridge CB2 1QR, United Kingdom
| | - David Gfeller
- Ludwig Center for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
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15
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Abstract
Single-cell sequencing provides information that is not confounded by genotypic or phenotypic heterogeneity of bulk samples. Sequencing of one molecular type (RNA, methylated DNA or open chromatin) in a single cell, furthermore, provides insights into the cell's phenotype and links to its genotype. Nevertheless, only by taking measurements of these phenotypes and genotypes from the same single cells can such inferences be made unambiguously. In this review, we survey the first experimental approaches that assay, in parallel, multiple molecular types from the same single cell, before considering the challenges and opportunities afforded by these and future technologies. Unambiguous inference that a cellular phenotype is caused by a genotype can only be achieved by their measurement from the same single cell. Estimating RNA and DNA copy number abundance in single cells is now possible using a variety of experimental approaches. Parallel measurement of single-cell epigenomes and transcriptomes provides further insight into the regulation of cellular identity and phenotypes. Parallel measurement of single-cell transcriptomes and protein abundance (by FACS, proximity ligation assays/PEA or mass cytometry) allows insight into expression dynamics. Our understanding of cancer progression and diversity is likely to be advanced greatly by the multiomics investigation of single cells, as is our understanding of normal developmental and other disease processes. Ongoing technological advances will see improvements in the coverage, sensitivity of multiomics approaches, as well the number of analytes that can be surveyed in parallel.
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Affiliation(s)
- Iain C Macaulay
- Earlham Institute, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Chris P Ponting
- Sanger Institute - EBI Single-Cell Genomics Centre, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK; MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK.
| | - Thierry Voet
- Sanger Institute - EBI Single-Cell Genomics Centre, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK; Department of Human Genetics, University of Leuven, KU Leuven, Leuven, 3000, Belgium.
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16
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van der Weyden L, Arends MJ, Campbell AD, Bald T, Wardle-Jones H, Griggs N, Velasco-Herrera MDC, Tüting T, Sansom OJ, Karp NA, Clare S, Gleeson D, Ryder E, Galli A, Tuck E, Cambridge EL, Voet T, Macaulay IC, Wong K, Spiegel S, Speak AO, Adams DJ. Genome-wide in vivo screen identifies novel host regulators of metastatic colonization. Nature 2017; 541:233-236. [PMID: 28052056 PMCID: PMC5603286 DOI: 10.1038/nature20792] [Citation(s) in RCA: 161] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 11/15/2016] [Indexed: 12/17/2022]
Abstract
Metastasis is the leading cause of death for cancer patients. This multi-stage process requires tumour cells to survive in the circulation, extravasate at distant sites, then proliferate; it involves contributions from both the tumour cell and tumour microenvironment ('host', which includes stromal cells and the immune system). Studies suggest the early steps of the metastatic process are relatively efficient, with the post-extravasation regulation of tumour growth ('colonization') being critical in determining metastatic outcome. Here we show the results of screening 810 mutant mouse lines using an in vivo assay to identify microenvironmental regulators of metastatic colonization. We identify 23 genes that, when disrupted in mouse, modify the ability of tumour cells to establish metastatic foci, with 19 of these genes not previously demonstrated to play a role in host control of metastasis. The largest reduction in pulmonary metastasis was observed in sphingosine-1-phosphate (S1P) transporter spinster homologue 2 (Spns2)-deficient mice. We demonstrate a novel outcome of S1P-mediated regulation of lymphocyte trafficking, whereby deletion of Spns2, either globally or in a lymphatic endothelial-specific manner, creates a circulating lymphopenia and a higher percentage of effector T cells and natural killer (NK) cells present in the lung. This allows for potent tumour cell killing, and an overall decreased metastatic burden.
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Affiliation(s)
| | - Mark J Arends
- University of Edinburgh Division of Pathology, Edinburgh Cancer Research UK Cancer Centre, Institute of Genetics &Molecular Medicine, Edinburgh EH4 2XR, UK
| | | | - Tobias Bald
- Department of Dermatology, University Hospital Magdeburg, Magdeburg 39120, Germany
- Department of Immunology in Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston 4006, Australia
| | - Hannah Wardle-Jones
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Nicola Griggs
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | | | - Thomas Tüting
- Department of Dermatology, University Hospital Magdeburg, Magdeburg 39120, Germany
| | - Owen J Sansom
- Cancer Research UK Beatson Institute, Glasgow G61 1BD, UK
| | - Natasha A Karp
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Simon Clare
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Diane Gleeson
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Edward Ryder
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Antonella Galli
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Elizabeth Tuck
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Emma L Cambridge
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Thierry Voet
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
- Department of Human Genetics, University of Leuven (KU Leuven), Leuven, 3000, Belgium
| | - Iain C Macaulay
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Kim Wong
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Sarah Spiegel
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University School of Medicine, Richmond, Virginia 23298-0614, USA
| | - Anneliese O Speak
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - David J Adams
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
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17
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Luis TC, Luc S, Mizukami T, Boukarabila H, Thongjuea S, Woll PS, Azzoni E, Giustacchini A, Lutteropp M, Bouriez-Jones T, Vaidya H, Mead AJ, Atkinson D, Böiers C, Carrelha J, Macaulay IC, Patient R, Geissmann F, Nerlov C, Sandberg R, de Bruijn MFTR, Blackburn CC, Godin I, Jacobsen SEW. Initial seeding of the embryonic thymus by immune-restricted lympho-myeloid progenitors. Nat Immunol 2016; 17:1424-1435. [PMID: 27695000 DOI: 10.1038/ni.3576] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Accepted: 09/01/2016] [Indexed: 02/08/2023]
Abstract
The final stages of restriction to the T cell lineage occur in the thymus after the entry of thymus-seeding progenitors (TSPs). The identity and lineage potential of TSPs remains unclear. Because the first embryonic TSPs enter a non-vascularized thymic rudiment, we were able to directly image and establish the functional and molecular properties of embryonic thymopoiesis-initiating progenitors (T-IPs) before their entry into the thymus and activation of Notch signaling. T-IPs did not include multipotent stem cells or molecular evidence of T cell-restricted progenitors. Instead, single-cell molecular and functional analysis demonstrated that most fetal T-IPs expressed genes of and had the potential to develop into lymphoid as well as myeloid components of the immune system. Moreover, studies of embryos deficient in the transcriptional regulator RBPJ demonstrated that canonical Notch signaling was not involved in pre-thymic restriction to the T cell lineage or the migration of T-IPs.
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Affiliation(s)
- Tiago C Luis
- Haematopoietic Stem Cell Laboratory, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford OX3 9DS, United Kingdom
| | - Sidinh Luc
- Haematopoietic Stem Cell Laboratory, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford OX3 9DS, United Kingdom.,Hematopoietic Stem Cell Laboratory, Lund Stem Cell Center, Lund University, Klinikgatan 26, 221 84, Lund, Sweden.,MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Takuo Mizukami
- Haematopoietic Stem Cell Laboratory, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford OX3 9DS, United Kingdom
| | - Hanane Boukarabila
- Haematopoietic Stem Cell Laboratory, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford OX3 9DS, United Kingdom
| | - Supat Thongjuea
- Haematopoietic Stem Cell Laboratory, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford OX3 9DS, United Kingdom.,MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Petter S Woll
- Haematopoietic Stem Cell Laboratory, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford OX3 9DS, United Kingdom
| | - Emanuele Azzoni
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Alice Giustacchini
- Haematopoietic Stem Cell Laboratory, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford OX3 9DS, United Kingdom
| | - Michael Lutteropp
- Haematopoietic Stem Cell Laboratory, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford OX3 9DS, United Kingdom.,MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Tiphaine Bouriez-Jones
- Haematopoietic Stem Cell Laboratory, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford OX3 9DS, United Kingdom
| | - Harsh Vaidya
- Institute for Stem Cell Research, MRC Centre for Regenerative Medicine, University of Edinburgh, EH16 4UU Edinburgh, UK
| | - Adam J Mead
- Haematopoietic Stem Cell Laboratory, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford OX3 9DS, United Kingdom
| | - Deborah Atkinson
- Haematopoietic Stem Cell Laboratory, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford OX3 9DS, United Kingdom
| | - Charlotta Böiers
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, 22184 Lund, Sweden
| | - Joana Carrelha
- Haematopoietic Stem Cell Laboratory, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford OX3 9DS, United Kingdom
| | - Iain C Macaulay
- Haematopoietic Stem Cell Laboratory, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford OX3 9DS, United Kingdom
| | - Roger Patient
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Frederic Geissmann
- King's College London, Great Maze Pond, SE1 1UL London, UK.,Memorial Sloan Kettering Cancer Center, 417 East 68(th) Street, New York, NY 10065, USA
| | - Claus Nerlov
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institutet and Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden
| | - Marella F T R de Bruijn
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - C Clare Blackburn
- Institute for Stem Cell Research, MRC Centre for Regenerative Medicine, University of Edinburgh, EH16 4UU Edinburgh, UK
| | - Isabelle Godin
- Institut National de la Santé et de la Recherche Médicale U1170; Univ Paris-Sud, Université Paris-Saclay; Gustave Roussy, 114, rue Edouard Vaillant; Villejuif, F-94805, France
| | - Sten Eirik W Jacobsen
- Haematopoietic Stem Cell Laboratory, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford OX3 9DS, United Kingdom.,MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom.,Department of Cell and Molecular Biology, Wallenberg Institute for Regenerative Medicine and Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet and Karolinska University Hospital, 171 77 Stockholm, Sweden
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18
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Scialdone A, Tanaka Y, Jawaid W, Moignard V, Wilson NK, Macaulay IC, Marioni JC, Göttgens B. Resolving early mesoderm diversification through single-cell expression profiling. Nature 2016; 535:289-293. [PMID: 27383781 PMCID: PMC4947525 DOI: 10.1038/nature18633] [Citation(s) in RCA: 226] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 06/09/2016] [Indexed: 12/21/2022]
Abstract
In mammals, specification of the three major germ layers occurs during gastrulation, when cells ingressing through the primitive streak differentiate into the precursor cells of major organ systems. However, the molecular mechanisms underlying this process remain unclear, as numbers of gastrulating cells are very limited. In the mouse embryo at embryonic day 6.5, cells located at the junction between the extra-embryonic region and the epiblast on the posterior side of the embryo undergo an epithelial-to-mesenchymal transition and ingress through the primitive streak. Subsequently, cells migrate, either surrounding the prospective ectoderm contributing to the embryo proper, or into the extra-embryonic region to form the yolk sac, umbilical cord and placenta. Fate mapping has shown that mature tissues such as blood and heart originate from specific regions of the pre-gastrula epiblast, but the plasticity of cells within the embryo and the function of key cell-type-specific transcription factors remain unclear. Here we analyse 1,205 cells from the epiblast and nascent Flk1(+) mesoderm of gastrulating mouse embryos using single-cell RNA sequencing, representing the first transcriptome-wide in vivo view of early mesoderm formation during mammalian gastrulation. Additionally, using knockout mice, we study the function of Tal1, a key haematopoietic transcription factor, and demonstrate, contrary to previous studies performed using retrospective assays, that Tal1 knockout does not immediately bias precursor cells towards a cardiac fate.
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Affiliation(s)
- Antonio Scialdone
- EMBL-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust
Genome Campus, Cambridge, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Yosuke Tanaka
- Department of Haematology, Cambridge Institute for Medical Research,
University of Cambridge, Cambridge, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell
Institute, University of Cambridge, Cambridge, UK
| | - Wajid Jawaid
- Department of Haematology, Cambridge Institute for Medical Research,
University of Cambridge, Cambridge, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell
Institute, University of Cambridge, Cambridge, UK
| | - Victoria Moignard
- Department of Haematology, Cambridge Institute for Medical Research,
University of Cambridge, Cambridge, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell
Institute, University of Cambridge, Cambridge, UK
| | - Nicola K. Wilson
- Department of Haematology, Cambridge Institute for Medical Research,
University of Cambridge, Cambridge, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell
Institute, University of Cambridge, Cambridge, UK
| | | | - John C. Marioni
- EMBL-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust
Genome Campus, Cambridge, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
- CRUK Cambridge Institute, University of Cambridge, Cambridge,
UK
| | - Berthold Göttgens
- Department of Haematology, Cambridge Institute for Medical Research,
University of Cambridge, Cambridge, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell
Institute, University of Cambridge, Cambridge, UK
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19
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Goolam M, Scialdone A, Graham SJL, Macaulay IC, Jedrusik A, Hupalowska A, Voet T, Marioni JC, Zernicka-Goetz M. Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos. Cell 2016; 165:61-74. [PMID: 27015307 PMCID: PMC4819611 DOI: 10.1016/j.cell.2016.01.047] [Citation(s) in RCA: 272] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 11/10/2015] [Accepted: 01/22/2016] [Indexed: 01/08/2023]
Abstract
The major and essential objective of pre-implantation development is to establish embryonic and extra-embryonic cell fates. To address when and how this fundamental process is initiated in mammals, we characterize transcriptomes of all individual cells throughout mouse pre-implantation development. This identifies targets of master pluripotency regulators Oct4 and Sox2 as being highly heterogeneously expressed between blastomeres of the 4-cell embryo, with Sox21 showing one of the most heterogeneous expression profiles. Live-cell tracking demonstrates that cells with decreased Sox21 yield more extra-embryonic than pluripotent progeny. Consistently, decreasing Sox21 results in premature upregulation of the differentiation regulator Cdx2, suggesting that Sox21 helps safeguard pluripotency. Furthermore, Sox21 is elevated following increased expression of the histone H3R26-methylase CARM1 and is lowered following CARM1 inhibition, indicating the importance of epigenetic regulation. Therefore, our results indicate that heterogeneous gene expression, as early as the 4-cell stage, initiates cell-fate decisions by modulating the balance of pluripotency and differentiation.
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Affiliation(s)
- Mubeen Goolam
- Department of Physiology, Development & Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
| | - Antonio Scialdone
- European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK; Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Sarah J L Graham
- Department of Physiology, Development & Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
| | - Iain C Macaulay
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Agnieszka Jedrusik
- Department of Physiology, Development & Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
| | - Anna Hupalowska
- Department of Physiology, Development & Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
| | - Thierry Voet
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK; Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - John C Marioni
- European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK; Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK; Cancer Research UK-Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, UK.
| | - Magdalena Zernicka-Goetz
- Department of Physiology, Development & Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK.
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20
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Macaulay IC, Svensson V, Labalette C, Ferreira L, Hamey F, Voet T, Teichmann SA, Cvejic A. Single-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic Cells. Cell Rep 2016; 14:966-977. [PMID: 26804912 PMCID: PMC4742565 DOI: 10.1016/j.celrep.2015.12.082] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 10/30/2015] [Accepted: 12/16/2015] [Indexed: 12/21/2022] Open
Abstract
The transcriptional programs that govern hematopoiesis have been investigated primarily by population-level analysis of hematopoietic stem and progenitor cells, which cannot reveal the continuous nature of the differentiation process. Here we applied single-cell RNA-sequencing to a population of hematopoietic cells in zebrafish as they undergo thrombocyte lineage commitment. By reconstructing their developmental chronology computationally, we were able to place each cell along a continuum from stem cell to mature cell, refining the traditional lineage tree. The progression of cells along this continuum is characterized by a highly coordinated transcriptional program, displaying simultaneous suppression of genes involved in cell proliferation and ribosomal biogenesis as the expression of lineage specific genes increases. Within this program, there is substantial heterogeneity in the expression of the key lineage regulators. Overall, the total number of genes expressed, as well as the total mRNA content of the cell, decreases as the cells undergo lineage commitment.
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Affiliation(s)
- Iain C Macaulay
- Sanger Institute-EBI Single-Cell Genomics Centre, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Valentine Svensson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Charlotte Labalette
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK; Department of Haematology, University of Cambridge, Cambridge CB2 0PT, UK
| | - Lauren Ferreira
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK; Department of Haematology, University of Cambridge, Cambridge CB2 0PT, UK
| | - Fiona Hamey
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 1QR, UK
| | - Thierry Voet
- Sanger Institute-EBI Single-Cell Genomics Centre, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK; Department of Human Genetics, University of Leuven, Leuven 3000, Belgium
| | - Sarah A Teichmann
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ana Cvejic
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK; Department of Haematology, University of Cambridge, Cambridge CB2 0PT, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 1QR, UK.
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21
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Mayer CE, Žuklys S, Zhanybekova S, Ohigashi I, Teh HY, Sansom SN, Shikama-Dorn N, Hafen K, Macaulay IC, Deadman ME, Ponting CP, Takahama Y, Holländer GA. Dynamic spatio-temporal contribution of single β5t+ cortical epithelial precursors to the thymus medulla. Eur J Immunol 2016; 46:846-56. [PMID: 26694097 PMCID: PMC4832341 DOI: 10.1002/eji.201545995] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 11/24/2015] [Accepted: 12/17/2015] [Indexed: 01/20/2023]
Abstract
Intrathymic T‐cell development is critically dependent on cortical and medullary thymic epithelial cells (TECs). Both epithelial subsets originate during early thymus organogenesis from progenitor cells that express the thymoproteasome subunit β5t, a typical feature of cortical TECs. Using in vivo lineage fate mapping, we demonstrate in mice that β5t+ TEC progenitors give rise to the medullary TEC compartment early in life but significantly limit their contribution once the medulla has completely formed. Lineage‐tracing studies at single cell resolution demonstrate for young mice that the postnatal medulla is expanded from individual β5t+ cortical progenitors located at the cortico‐medullary junction. These results therefore not only define a developmental window during which the expansion of medulla is efficiently enabled by progenitors resident in the thymic cortex, but also reveal the spatio‐temporal dynamics that control the growth of the thymic medulla.
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Affiliation(s)
- Carlos E Mayer
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Saulius Žuklys
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | | | - Izumi Ohigashi
- Division of Experimental Immunology, Institute for Genome Research, University of Tokushima, Japan
| | - Hong-Ying Teh
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Stephen N Sansom
- The Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | | | - Katrin Hafen
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Iain C Macaulay
- Wellcome Trust Sanger Institute-EBI Single Cell Genomics Centre, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Mary E Deadman
- Department of Paediatrics and the Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Chris P Ponting
- Wellcome Trust Sanger Institute-EBI Single Cell Genomics Centre, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.,MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Yousuke Takahama
- Division of Experimental Immunology, Institute for Genome Research, University of Tokushima, Japan
| | - Georg A Holländer
- Department of Biomedicine, University of Basel, Basel, Switzerland.,Department of Paediatrics and the Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
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22
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Angermueller C, Clark SJ, Lee HJ, Macaulay IC, Teng MJ, Hu TX, Krueger F, Smallwood S, Ponting CP, Voet T, Kelsey G, Stegle O, Reik W. Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity. Nat Methods 2016; 13:229-232. [PMID: 26752769 PMCID: PMC4770512 DOI: 10.1038/nmeth.3728] [Citation(s) in RCA: 464] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 12/09/2015] [Indexed: 12/18/2022]
Abstract
We report scM&T-seq, a method for parallel single-cell genome-wide methylome and transcriptome sequencing, allowing discovery of associations between transcriptional and epigenetic variation. Profiling of 61 mouse embryonic stem cells confirmed known links between DNA methylation and transcription. Notably, the method reveals novel associations between heterogeneously methylated distal regulatory elements and transcription of key pluripotency genes.
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Affiliation(s)
- Christof Angermueller
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | | | - Heather J Lee
- Epigenetics Programme, Babraham Institute, Cambridge, UK.,Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | | | - Mabel J Teng
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Tim Xiaoming Hu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK.,Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.,Medical Research Council Functional Genomics Unit, University of Oxford, UK
| | - Felix Krueger
- Bioinformatics Group, Babraham Institute, Cambridge, UK
| | | | - Chris P Ponting
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.,Medical Research Council Functional Genomics Unit, University of Oxford, UK
| | - Thierry Voet
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.,Department of Human Genetics, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Gavin Kelsey
- Epigenetics Programme, Babraham Institute, Cambridge, UK
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Wolf Reik
- Epigenetics Programme, Babraham Institute, Cambridge, UK.,Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
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23
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Tarnawski L, Xian X, Monnerat G, Macaulay IC, Malan D, Borgman A, Wu SM, Fleischmann BK, Jovinge S. Integrin Based Isolation Enables Purification of Murine Lineage Committed Cardiomyocytes. PLoS One 2015; 10:e0135880. [PMID: 26323090 PMCID: PMC4556377 DOI: 10.1371/journal.pone.0135880] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 07/27/2015] [Indexed: 11/24/2022] Open
Abstract
In contrast to mature cardiomyocytes which have limited regenerative capacity, pluripotent stem cells represent a promising source for the generation of new cardiomyocytes. The tendency of pluripotent stem cells to form teratomas and the heterogeneity from various differentiation stages and cardiomyocyte cell sub-types, however, are major obstacles to overcome before this type of therapy could be applied in a clinical setting. Thus, the identification of extracellular markers for specific cardiomyocyte progenitors and mature subpopulations is of particular importance. The delineation of cardiomyocyte surface marker patterns not only serves as a means to derive homogeneous cell populations by FACS, but is also an essential tool to understand cardiac development. By using single-cell expression profiling in early mouse embryonic hearts, we found that a combination of integrin alpha-1, alpha-5, alpha-6 and N-cadherin enables isolation of lineage committed murine cardiomyocytes. Additionally, we were able to separate trabecular cardiomyocytes from solid ventricular myocardium and atrial murine cells. These cells exhibit expected subtype specific phenotype confirmed by electrophysiological analysis. We show that integrin expression can be used for the isolation of living, functional and lineage-specific murine cardiomyocytes.
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Affiliation(s)
- Laura Tarnawski
- Lund Strategic Research Center for Stem Cell Biology and Cell Therapy, Lund University, Lund, Sweden
| | - Xiaojie Xian
- Lund Strategic Research Center for Stem Cell Biology and Cell Therapy, Lund University, Lund, Sweden
| | - Gustavo Monnerat
- Institute of Physiology I, Life and Brain Center, Department of Cardiac Surgery, University of Bonn, Bonn, Germany; Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Iain C Macaulay
- Haematopoietic Stem Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, England
| | - Daniela Malan
- Institute of Physiology I, Life and Brain Center, Department of Cardiac Surgery, University of Bonn, Bonn, Germany
| | - Andrew Borgman
- Spectrum Health Fredrik Meijer Heart and Vascular Institute, Grand Rapids, Michigan, United States of America
| | - Sean M Wu
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford, California, United States of America; Stanford Cardiovascular Institute, Stanford, California, United States of America; Dept of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Bernd K Fleischmann
- Institute of Physiology I, Life and Brain Center, Department of Cardiac Surgery, University of Bonn, Bonn, Germany; Pharma Center Bonn, University of Bonn, Bonn, Germany
| | - Stefan Jovinge
- Lund Strategic Research Center for Stem Cell Biology and Cell Therapy, Lund University, Lund, Sweden; Van Andel Research Institute, Grand Rapids, Michigan, United States of America; Spectrum Health Fredrik Meijer Heart and Vascular Institute, Grand Rapids, Michigan, United States of America
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24
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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: 315] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [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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25
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Moignard V, Woodhouse S, Haghverdi L, Lilly AJ, Tanaka Y, Wilkinson AC, Buettner F, Macaulay IC, Jawaid W, Diamanti E, Nishikawa SI, Piterman N, Kouskoff V, Theis FJ, Fisher J, Göttgens B. Decoding the regulatory network of early blood development from single-cell gene expression measurements. Nat Biotechnol 2015; 33:269-276. [PMID: 25664528 PMCID: PMC4374163 DOI: 10.1038/nbt.3154] [Citation(s) in RCA: 288] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 01/16/2015] [Indexed: 11/16/2022]
Abstract
Reconstruction of the molecular pathways controlling organ development has been hampered by a lack of methods to resolve embryonic progenitor cells. Here we describe a strategy to address this problem that combines gene expression profiling of large numbers of single cells with data analysis based on diffusion maps for dimensionality reduction and network synthesis from state transition graphs. Applying the approach to hematopoietic development in the mouse embryo, we map the progression of mesoderm toward blood using single-cell gene expression analysis of 3,934 cells with blood-forming potential captured at four time points between E7.0 and E8.5. Transitions between individual cellular states are then used as input to develop a single-cell network synthesis toolkit to generate a computationally executable transcriptional regulatory network model of blood development. Several model predictions concerning the roles of Sox and Hox factors are validated experimentally. Our results demonstrate that single-cell analysis of a developing organ coupled with computational approaches can reveal the transcriptional programs that underpin organogenesis.
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Affiliation(s)
- Victoria Moignard
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Steven Woodhouse
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Laleh Haghverdi
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Mathematics, Technische Universität München, Garching, Germany
| | - Andrew J. Lilly
- Cancer Research UK Stem Cell Haematopoiesis Group, Paterson Institute for Cancer Research, University of Manchester, Manchester, UK
| | - Yosuke Tanaka
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Laboratory for Stem Cell Biology, RIKEN Center for Developmental Biology, Chuo-ku, Kobe, Japan
| | - Adam C. Wilkinson
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Florian Buettner
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Iain C. Macaulay
- Sanger Institute-EBI Single Cell Genomics Centre, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Wajid Jawaid
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, UK
| | - Evangelia Diamanti
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Shin-Ichi Nishikawa
- Laboratory for Stem Cell Biology, RIKEN Center for Developmental Biology, Chuo-ku, Kobe, Japan
| | - Nir Piterman
- Department of Computer Science, University of Leicester, Leicester, UK
| | - Valerie Kouskoff
- Cancer Research UK Stem Cell Haematopoiesis Group, Paterson Institute for Cancer Research, University of Manchester, Manchester, UK
| | - Fabian J. Theis
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Mathematics, Technische Universität München, Garching, Germany
| | - Jasmin Fisher
- Microsoft Research Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Berthold Göttgens
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
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26
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Sansom SN, Shikama-Dorn N, Zhanybekova S, Nusspaumer G, Macaulay IC, Deadman ME, Heger A, Ponting CP, Holländer GA. Population and single-cell genomics reveal the Aire dependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia. Genome Res 2014; 24:1918-31. [PMID: 25224068 PMCID: PMC4248310 DOI: 10.1101/gr.171645.113] [Citation(s) in RCA: 229] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2013] [Accepted: 09/12/2014] [Indexed: 12/18/2022]
Abstract
Promiscuous gene expression (PGE) by thymic epithelial cells (TEC) is essential for generating a diverse T cell antigen receptor repertoire tolerant to self-antigens, and thus for avoiding autoimmunity. Nevertheless, the extent and nature of this unusual expression program within TEC populations and single cells are unknown. Using deep transcriptome sequencing of carefully identified mouse TEC subpopulations, we discovered a program of PGE that is common between medullary (m) and cortical TEC, further elaborated in mTEC, and completed in mature mTEC expressing the autoimmune regulator gene (Aire). TEC populations are capable of expressing up to 19,293 protein-coding genes, the highest number of genes known to be expressed in any cell type. Remarkably, in mouse mTEC, Aire expression alone positively regulates 3980 tissue-restricted genes. Notably, the tissue specificities of these genes include known targets of autoimmunity in human AIRE deficiency. Led by the observation that genes induced by Aire expression are generally characterized by a repressive chromatin state in somatic tissues, we found these genes to be strongly associated with H3K27me3 marks in mTEC. Our findings are consistent with AIRE targeting and inducing the promiscuous expression of genes previously epigenetically silenced by Polycomb group proteins. Comparison of the transcriptomes of 174 single mTEC indicates that genes induced by Aire expression are transcribed stochastically at low cell frequency. Furthermore, when present, Aire expression-dependent transcript levels were 16-fold higher, on average, in individual TEC than in the mTEC population.
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Affiliation(s)
- Stephen N Sansom
- MRC Computational Genomics Analysis and Training Programme, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom;
| | - Noriko Shikama-Dorn
- Paediatric Immunology, Department of Biomedicine, University of Basel, and The Basel University Children's Hospital, Basel, 4058, Switzerland
| | - Saule Zhanybekova
- Paediatric Immunology, Department of Biomedicine, University of Basel, and The Basel University Children's Hospital, Basel, 4058, Switzerland
| | - Gretel Nusspaumer
- Paediatric Immunology, Department of Biomedicine, University of Basel, and The Basel University Children's Hospital, Basel, 4058, Switzerland
| | - Iain C Macaulay
- Wellcome Trust Sanger Institute-EBI Single Cell Genomics Centre, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Mary E Deadman
- Developmental Immunology, Department of Paediatrics, and the Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Andreas Heger
- MRC Computational Genomics Analysis and Training Programme, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom
| | - Chris P Ponting
- MRC Computational Genomics Analysis and Training Programme, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom; Wellcome Trust Sanger Institute-EBI Single Cell Genomics Centre, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Georg A Holländer
- Paediatric Immunology, Department of Biomedicine, University of Basel, and The Basel University Children's Hospital, Basel, 4058, Switzerland; Developmental Immunology, Department of Paediatrics, and the Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
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27
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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: 206] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 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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28
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Woll PS, Kjällquist U, Chowdhury O, Doolittle H, Wedge DC, Thongjuea S, Erlandsson R, Ngara M, Anderson K, Deng Q, Mead AJ, Stenson L, Giustacchini A, Duarte S, Giannoulatou E, Taylor S, Karimi M, Scharenberg C, Mortera-Blanco T, Macaulay IC, Clark SA, Dybedal I, Josefsen D, Fenaux P, Hokland P, Holm MS, Cazzola M, Malcovati L, Tauro S, Bowen D, Boultwood J, Pellagatti A, Pimanda JE, Unnikrishnan A, Vyas P, Göhring G, Schlegelberger B, Tobiasson M, Kvalheim G, Constantinescu SN, Nerlov C, Nilsson L, Campbell PJ, Sandberg R, Papaemmanuil E, Hellström-Lindberg E, Linnarsson S, Jacobsen SEW. Myelodysplastic syndromes are propagated by rare and distinct human cancer stem cells in vivo. Cancer Cell 2014; 25:794-808. [PMID: 24835589 DOI: 10.1016/j.ccr.2014.03.036] [Citation(s) in RCA: 227] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 02/12/2014] [Accepted: 03/31/2014] [Indexed: 12/14/2022]
Abstract
Evidence for distinct human cancer stem cells (CSCs) remains contentious and the degree to which different cancer cells contribute to propagating malignancies in patients remains unexplored. In low- to intermediate-risk myelodysplastic syndromes (MDS), we establish the existence of rare multipotent MDS stem cells (MDS-SCs), and their hierarchical relationship to lineage-restricted MDS progenitors. All identified somatically acquired genetic lesions were backtracked to distinct MDS-SCs, establishing their distinct MDS-propagating function in vivo. In isolated del(5q)-MDS, acquisition of del(5q) preceded diverse recurrent driver mutations. Sequential analysis in del(5q)-MDS revealed genetic evolution in MDS-SCs and MDS-progenitors prior to leukemic transformation. These findings provide definitive evidence for rare human MDS-SCs in vivo, with extensive implications for the targeting of the cells required and sufficient for MDS-propagation.
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Affiliation(s)
- Petter S Woll
- Haematopoietic Stem Cell Biology Laboratory, MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Una Kjällquist
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 65 Stockholm, Sweden
| | - Onima Chowdhury
- Haematopoietic Stem Cell Biology Laboratory, MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Helen Doolittle
- Haematopoietic Stem Cell Biology Laboratory, MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - David C Wedge
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA Cambridge, UK
| | - Supat Thongjuea
- Haematopoietic Stem Cell Biology Laboratory, MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Rikard Erlandsson
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 65 Stockholm, Sweden
| | - Mtakai Ngara
- Ludwig Institute for Cancer Research and Department of Cell and Molecular Biology, Karolinska Institute, 171 77 Stockholm, Sweden
| | - Kristina Anderson
- Department of Cellular Therapy, Norwegian Radium Hospital, Oslo University Hospital, 0130 Oslo, Norway
| | - Qiaolin Deng
- Ludwig Institute for Cancer Research and Department of Cell and Molecular Biology, Karolinska Institute, 171 77 Stockholm, Sweden
| | - Adam J Mead
- Haematopoietic Stem Cell Biology Laboratory, MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Laura Stenson
- Haematopoietic Stem Cell Biology Laboratory, MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Alice Giustacchini
- Haematopoietic Stem Cell Biology Laboratory, MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Sara Duarte
- Haematopoietic Stem Cell Biology Laboratory, MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Eleni Giannoulatou
- Computational Biology Research Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Stephen Taylor
- Computational Biology Research Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Mohsen Karimi
- Center for Hematology and Regenerative Medicine, Karolinska University Hospital Huddinge, 141 86 Stockholm, Sweden
| | - Christian Scharenberg
- Center for Hematology and Regenerative Medicine, Karolinska University Hospital Huddinge, 141 86 Stockholm, Sweden
| | - Teresa Mortera-Blanco
- Center for Hematology and Regenerative Medicine, Karolinska University Hospital Huddinge, 141 86 Stockholm, Sweden
| | - Iain C Macaulay
- Haematopoietic Stem Cell Biology Laboratory, MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Sally-Ann Clark
- Haematopoietic Stem Cell Biology Laboratory, MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Ingunn Dybedal
- Department of Hematology, Oslo University Hospital, Rikshospitalet, 0130 Oslo, Norway
| | - Dag Josefsen
- Department of Cellular Therapy, Norwegian Radium Hospital, Oslo University Hospital, 0130 Oslo, Norway
| | - Pierre Fenaux
- Hôpital Avicenne, Assistance Publique-Hôpitaux de Paris (AP-HP), Service d'hématologie clinique, 93000 Bobigny, France
| | - Peter Hokland
- Department of Hematology, Aarhus University Hospital, 8000 Aarhus, Denmark
| | - Mette S Holm
- Department of Hematology, Aarhus University Hospital, 8000 Aarhus, Denmark
| | - Mario Cazzola
- Department of Molecular Medicine, University of Pavia, and Department of Hematology Oncology, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Luca Malcovati
- Department of Molecular Medicine, University of Pavia, and Department of Hematology Oncology, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Sudhir Tauro
- Division of Medical Sciences, University of Dundee, Dundee DD1 9SY, Scotland, UK
| | - David Bowen
- St. James Institute of Oncology, St. James Hospital, Leeds LS9 7TF, UK
| | - Jacqueline Boultwood
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Oxford OX3 9DU, UK
| | - Andrea Pellagatti
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Oxford OX3 9DU, UK
| | - John E Pimanda
- Lowy Cancer Research Centre and the Prince of Wales Clinical School, University of New South Wales, Sydney 2052, Australia
| | - Ashwin Unnikrishnan
- Lowy Cancer Research Centre and the Prince of Wales Clinical School, University of New South Wales, Sydney 2052, Australia
| | - Paresh Vyas
- MRC Molecular Haematology Unit, Department of Haematology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Oxford University Hospital, NHS Trust, Oxford OX3 9DU, UK
| | - Gudrun Göhring
- Institute of Cell and Molecular Pathology, Hannover Medical School, 30625 Hannover, Germany
| | | | - Magnus Tobiasson
- Center for Hematology and Regenerative Medicine, Karolinska University Hospital Huddinge, 141 86 Stockholm, Sweden
| | - Gunnar Kvalheim
- Department of Cellular Therapy, Norwegian Radium Hospital, Oslo University Hospital, 0130 Oslo, Norway
| | - Stefan N Constantinescu
- Ludwig Institute for Cancer Research and de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Claus Nerlov
- MRC Molecular Haematology Unit, Department of Haematology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | | | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA Cambridge, UK
| | - Rickard Sandberg
- Ludwig Institute for Cancer Research and Department of Cell and Molecular Biology, Karolinska Institute, 171 77 Stockholm, Sweden
| | - Elli Papaemmanuil
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA Cambridge, UK
| | - Eva Hellström-Lindberg
- Center for Hematology and Regenerative Medicine, Karolinska University Hospital Huddinge, 141 86 Stockholm, Sweden
| | - Sten Linnarsson
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 65 Stockholm, Sweden
| | - Sten Eirik W Jacobsen
- Haematopoietic Stem Cell Biology Laboratory, MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Departments of Cell and Molecular Biology, Medicine Huddinge, and Laboratory Medicine, Huddinge, Karolinska Institutet and Center for Hematology and Regenerative Medicine, Karolinska University Hospital Huddinge, 141 86 Stockholm, Sweden.
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29
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Böiers C, Carrelha J, Lutteropp M, Luc S, Green JCA, Azzoni E, Woll PS, Mead AJ, Hultquist A, Swiers G, Perdiguero EG, Macaulay IC, Melchiori L, Luis TC, Kharazi S, Bouriez-Jones T, Deng Q, Pontén A, Atkinson D, Jensen CT, Sitnicka E, Geissmann F, Godin I, Sandberg R, de Bruijn MFTR, Jacobsen SEW. Lymphomyeloid contribution of an immune-restricted progenitor emerging prior to definitive hematopoietic stem cells. Cell Stem Cell 2013; 13:535-48. [PMID: 24054998 DOI: 10.1016/j.stem.2013.08.012] [Citation(s) in RCA: 184] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Revised: 07/21/2013] [Accepted: 08/28/2013] [Indexed: 02/07/2023]
Abstract
In jawed vertebrates, development of an adaptive immune-system is essential for protection of the born organism against otherwise life-threatening pathogens. Myeloid cells of the innate immune system are formed early in development, whereas lymphopoiesis has been suggested to initiate much later, following emergence of definitive hematopoietic stem cells (HSCs). Herein, we demonstrate that the embryonic lymphoid commitment process initiates earlier than previously appreciated, prior to emergence of definitive HSCs, through establishment of a previously unrecognized entirely immune-restricted and lymphoid-primed progenitor. Notably, this immune-restricted progenitor appears to first emerge in the yolk sac and contributes physiologically to the establishment of lymphoid and some myeloid components of the immune-system, establishing the lymphomyeloid lineage restriction process as an early and physiologically important lineage-commitment step in mammalian hematopoiesis.
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Affiliation(s)
- Charlotta Böiers
- Haematopoietic Stem Cell Laboratory, Lund Stem Cell Center, Lund University, 221 84 Lund, Sweden; Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, 221 84 Lund, Sweden
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30
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Sanjuan-Pla A, Macaulay IC, Jensen CT, Woll PS, Luis TC, Mead A, Moore S, Carella C, Matsuoka S, Bouriez Jones T, Chowdhury O, Stenson L, Lutteropp M, Green JCA, Facchini R, Boukarabila H, Grover A, Gambardella A, Thongjuea S, Carrelha J, Tarrant P, Atkinson D, Clark SA, Nerlov C, Jacobsen SEW. Platelet-biased stem cells reside at the apex of the haematopoietic stem-cell hierarchy. Nature 2013; 502:232-6. [PMID: 23934107 DOI: 10.1038/nature12495] [Citation(s) in RCA: 409] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 07/22/2013] [Indexed: 12/13/2022]
Abstract
The blood system is maintained by a small pool of haematopoietic stem cells (HSCs), which are required and sufficient for replenishing all human blood cell lineages at millions of cells per second throughout life. Megakaryocytes in the bone marrow are responsible for the continuous production of platelets in the blood, crucial for preventing bleeding--a common and life-threatening side effect of many cancer therapies--and major efforts are focused at identifying the most suitable cellular and molecular targets to enhance platelet production after bone marrow transplantation or chemotherapy. Although it has become clear that distinct HSC subsets exist that are stably biased towards the generation of lymphoid or myeloid blood cells, we are yet to learn whether other types of lineage-biased HSC exist or understand their inter-relationships and how differently lineage-biased HSCs are generated and maintained. The functional relevance of notable phenotypic and molecular similarities between megakaryocytes and bone marrow cells with an HSC cell-surface phenotype remains unclear. Here we identify and prospectively isolate a molecularly and functionally distinct mouse HSC subset primed for platelet-specific gene expression, with enhanced propensity for short- and long-term reconstitution of platelets. Maintenance of platelet-biased HSCs crucially depends on thrombopoietin, the primary extrinsic regulator of platelet development. Platelet-primed HSCs also frequently have a long-term myeloid lineage bias, can self-renew and give rise to lymphoid-biased HSCs. These findings show that HSC subtypes can be organized into a cellular hierarchy, with platelet-primed HSCs at the apex. They also demonstrate that molecular and functional priming for platelet development initiates already in a distinct HSC population. The identification of a platelet-primed HSC population should enable the rational design of therapies enhancing platelet output.
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Affiliation(s)
- Alejandra Sanjuan-Pla
- Institute for Stem Cell Research and MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH9 16UU, UK
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31
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Steele BM, Harper MT, Macaulay IC, Morrell CN, Perez-Tamayo A, Foy M, Habas R, Poole AW, Fitzgerald DJ, Maguire PB. Canonical Wnt signaling negatively regulates platelet function. Proc Natl Acad Sci U S A 2009; 106:19836-41. [PMID: 19901330 PMCID: PMC2785253 DOI: 10.1073/pnas.0906268106] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2009] [Indexed: 12/20/2022] Open
Abstract
Wnts regulate important intracellular signaling events, and dysregulation of the Wnt pathway has been linked to human disease. Here, we uncover numerous Wnt canonical effectors in human platelets where Wnts, their receptors, and downstream signaling components have not been previously described. We demonstrate that the Wnt3a ligand inhibits platelet adhesion, activation, dense granule secretion, and aggregation. Wnt3a also altered platelet shape change and inhibited the activation of the small GTPase RhoA. In addition, we found the Wnt-beta-catenin signaling pathway to be functional in platelets. Finally, disruption of the Wnt Frizzled 6 receptor in the mouse resulted in a hyperactivatory platelet phenotype and a reduced sensitivity to Wnt3a. Taken together our studies reveal a novel functional role for Wnt signaling in regulating anucleate platelet function and may provide a tractable target for future antiplatelet therapy.
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Affiliation(s)
- Brian M. Steele
- Conway Institute, School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Matthew T. Harper
- Department of Physiology and Pharmacology, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom
| | - Iain C. Macaulay
- Conway Institute, School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Craig N. Morrell
- Department of Molecular and Comparative Pathobiology, John Hopkins University School of Medicine, Baltimore, MD 21205; and
| | - Alita Perez-Tamayo
- Department of Molecular and Comparative Pathobiology, John Hopkins University School of Medicine, Baltimore, MD 21205; and
| | - Martina Foy
- Conway Institute, School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Raymond Habas
- Department of Biochemistry, Robert Wood Johnson School of Medicine, Piscataway, NJ 08854
| | - Alastair W. Poole
- Department of Physiology and Pharmacology, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom
| | - Desmond J. Fitzgerald
- Conway Institute, School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Patricia B. Maguire
- Conway Institute, School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
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32
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Burns P, Gusnanto A, Macaulay IC, Rankin A, Tom B, Langford CF, Dudbridge F, Ouwehand WH, Watkins NA. Identification of variation in the platelet transcriptome associated with glycoprotein 6 haplotype. Platelets 2008; 19:258-67. [PMID: 18569861 DOI: 10.1080/09537100801947434] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Platelet Glycoprotein VI (GPVI) is the activatory collagen signalling receptor that transmits an outside-in signal via the FcR gamma-chain. In Caucasians two GP6 haplotypes have been identified which encode GPVI isoforms that differ by five amino-acids. The minor haplotype is associated with a modest but statistically significant reduction in GPVI abundance and reduced downstream signalling events. As GPVI is also expressed on megakaryocytes, different GPVI isoforms may imprint on the platelet transcriptome. We investigated the association of GP6 haplotype with transcription by comparing the transcriptomes of platelets from individuals homozygous for the major ('a') and minor ('b') haplotypes to identify differentially expressed (DE) transcripts. Platelet RNA was isolated from apheresis concentrates from 16 'aa' donors and eight 'bb' donors. mRNA was amplified using a template-switching PCR based protocol and fluorescently labelled. Samples were randomly paired both within and between haplotypes and compared on a cDNA microarray. No consistently DE transcripts were identified within the 'aa' haplotype but 52 significantly DE transcripts were observed between haplotypes. Generally the fold differences were low (two to four-fold) but were confirmed by qRT-PCR for selected transcripts (TUBB1, P = 0.0004; VWF, P = 0.0126). The results of this study indicate that there are subtle differences between the platelet transcriptomes of individuals who differ by GP6 haplotype. The identification of DE genes may identify critical pathways and nodes not previously known to be involved in platelet development and function.
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Affiliation(s)
- Philippa Burns
- Department of Haematology, University of Cambridge and National Health Service Blood and Transplant, Cambridge, UK
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33
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Newland SA, Macaulay IC, Floto AR, de Vet EC, Ouwehand WH, Watkins NA, Lyons PA, Campbell DR. The novel inhibitory receptor G6B is expressed on the surface of platelets and attenuates platelet function in vitro. Blood 2007; 109:4806-9. [PMID: 17311996 DOI: 10.1182/blood-2006-09-047449] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The G6B cell-surface receptor, which contains a single Ig-like domain, has been shown to bind to SHP-1 and SHP-2 after phosphorylation of 2 immunoreceptor tyrosine-based inhibitory motifs (ITIMs) in its cytoplasmic tail, classifying this protein as a new member of the family of inhibitory receptors. In this study, we demonstrate by real-time polymerase chain reaction (PCR) and Western-blot analysis that G6B is expressed on platelets. Cross-linking of G6B with polyclonal antisera has a significant inhibitory effect on platelet aggregation and activation by agonists such as ADP and collagen-related peptide (CRP). This inhibitory function of G6B appears to operate in a calcium-independent manner. Our results suggest that G6B represents a novel inhibitory receptor found on the surface of platelets and that it could be an antithrombotic drug target.
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Affiliation(s)
- Stephen A Newland
- Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge, Addembrookes Hospital, Hills Road, Cambridge, UK
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34
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Macaulay IC, Tijssen MR, Thijssen-Timmer DC, Gusnanto A, Steward M, Burns P, Langford CF, Ellis PD, Dudbridge F, Zwaginga JJ, Watkins NA, van der Schoot CE, Ouwehand WH. Comparative gene expression profiling of in vitro differentiated megakaryocytes and erythroblasts identifies novel activatory and inhibitory platelet membrane proteins. Blood 2006; 109:3260-9. [PMID: 17192395 PMCID: PMC6485507 DOI: 10.1182/blood-2006-07-036269] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
To identify previously unknown platelet receptors we compared the transcriptomes of in vitro differentiated megakaryocytes (MKs) and erythroblasts (EBs). RNA was obtained from purified, biologically paired MK and EB cultures and compared using cDNA microarrays. Bioinformatical analysis of MK-up-regulated genes identified 151 transcripts encoding transmembrane domain-containing proteins. Although many of these were known platelet genes, a number of previously unidentified or poorly characterized transcripts were also detected. Many of these transcripts, including G6b, G6f, LRRC32, LAT2, and the G protein-coupled receptor SUCNR1, encode proteins with structural features or functions that suggest they may be involved in the modulation of platelet function. Immunoblotting on platelets confirmed the presence of the encoded proteins, and flow cytometric analysis confirmed the expression of G6b, G6f, and LRRC32 on the surface of platelets. Through comparative analysis of expression in platelets and other blood cells we demonstrated that G6b, G6f, and LRRC32 are restricted to the platelet lineage, whereas LAT2 and SUCNR1 were also detected in other blood cells. The identification of the succinate receptor SUCNR1 in platelets is of particular interest, because physiologically relevant concentrations of succinate were shown to potentiate the effect of low doses of a variety of platelet agonists.
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Affiliation(s)
- Iain C. Macaulay
- Department of Haematology, University of Cambridge, United Kingdom
- National Blood Service, Cambridge, United Kingdom
| | - Marloes R. Tijssen
- Department of Experimental Immunohaematology, Sanquin Research at Central Laboratory for the Blood Transfusion Service (CLB), Amsterdam, The Netherlands
- Landsteiner Laboratory, Academic Medical Center (AMC), University of Amsterdam, The Netherlands
| | - Daphne C. Thijssen-Timmer
- Department of Experimental Immunohaematology, Sanquin Research at Central Laboratory for the Blood Transfusion Service (CLB), Amsterdam, The Netherlands
| | - Arief Gusnanto
- Medical Research Council (MRC) Biostatistics Unit, Institute of Public Health, Cambridge, United Kingdom
| | | | - Philippa Burns
- Department of Haematology, University of Cambridge, United Kingdom
- National Blood Service, Cambridge, United Kingdom
| | | | - Peter D. Ellis
- Microarray Facility, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Frank Dudbridge
- Medical Research Council (MRC) Biostatistics Unit, Institute of Public Health, Cambridge, United Kingdom
| | - Jaap-Jan Zwaginga
- Department of Experimental Immunohaematology, Sanquin Research at Central Laboratory for the Blood Transfusion Service (CLB), Amsterdam, The Netherlands
- Landsteiner Laboratory, Academic Medical Center (AMC), University of Amsterdam, The Netherlands
- Department of Immunohematology–Blood Transfusion, Leiden University Medical Centre, Leiden, The Netherlands
| | - Nicholas A. Watkins
- Department of Haematology, University of Cambridge, United Kingdom
- National Blood Service, Cambridge, United Kingdom
| | - C. Ellen van der Schoot
- Department of Experimental Immunohaematology, Sanquin Research at Central Laboratory for the Blood Transfusion Service (CLB), Amsterdam, The Netherlands
- Landsteiner Laboratory, Academic Medical Center (AMC), University of Amsterdam, The Netherlands
- Department of Hematology, Amsterdam Medical Centre, University of Amsterdam, The Netherlands
| | - Willem H. Ouwehand
- Department of Haematology, University of Cambridge, United Kingdom
- National Blood Service, Cambridge, United Kingdom
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35
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Abstract
Proteomic and genomic technologies provide powerful tools for characterizing the multitude of events that occur in the anucleate platelet. These technologies are beginning to define the complete platelet transcriptome and proteome as well as the protein-protein interactions critical for platelet function. The integration of these results provides the opportunity to identify those proteins involved in discrete facets of platelet function. Here we summarize the findings of platelet proteome and transcriptome studies and their application to diseases of platelet function.
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Affiliation(s)
- Iain C Macaulay
- Department of Haematology, University of Cambridge, Cambridge, UK
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36
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Abstract
Historical studies, using Northern blot hybridization, RT-PCR and cDNA library construction have demonstrated the presence of a variety of mRNA molecules in platelets. The development of microarray technology has allowed further characterization of the transcripts represented in the platelet transcriptome. In this review, these studies will be summarized and their findings in relation to the study of platelet function and the identification of disease risk genes discussed.
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Affiliation(s)
- I C Macaulay
- Division of Transfusion Medicine, University of Cambridge, UK
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