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Yayon N, Kedlian VR, Boehme L, Suo C, Wachter B, Beuschel RT, Amsalem O, Polanski K, Koplev S, Tuck E, Dann E, Van Hulle J, Perera S, Putteman T, Predeus AV, Dabrowska M, Richardson L, Tudor C, Kreins AY, Engelbert J, Stephenson E, Kleshchevnikov V, De Rita F, Crossland D, Bosticardo M, Pala F, Prigmore E, Chipampe NJ, Prete M, Fei L, To K, Barker RA, He X, Van Nieuwerburgh F, Bayraktar O, Patel M, Davies GE, Haniffa MA, Uhlmann V, Notarangelo LD, Germain RN, Radtke AJ, Marioni JC, Taghon T, Teichmann SA. A spatial human thymus cell atlas mapped to a continuous tissue axis. bioRxiv 2023:2023.10.25.562925. [PMID: 37986877 PMCID: PMC10659407 DOI: 10.1101/2023.10.25.562925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
T cells develop from circulating precursors, which enter the thymus and migrate throughout specialised sub-compartments to support maturation and selection. This process starts already in early fetal development and is highly active until the involution of the thymus in adolescence. To map the micro-anatomical underpinnings of this process in pre- vs. post-natal states, we undertook a spatially resolved analysis and established a new quantitative morphological framework for the thymus, the Cortico-Medullary Axis. Using this axis in conjunction with the curation of a multimodal single-cell, spatial transcriptomics and high-resolution multiplex imaging atlas, we show that canonical thymocyte trajectories and thymic epithelial cells are highly organised and fully established by post-conception week 12, pinpoint TEC progenitor states, find that TEC subsets and peripheral tissue genes are associated with Hassall's Corpuscles and uncover divergence in the pace and drivers of medullary entry between CD4 vs. CD8 T cell lineages. These findings are complemented with a holistic toolkit for spatial analysis and annotation, providing a basis for a detailed understanding of T lymphocyte development.
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Affiliation(s)
- Nadav Yayon
- Wellcome Sanger Institute, Cellular Genetics, Cambridge, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
| | | | - Lena Boehme
- Ghent University, Department of Diagnostic Sciences, Ghent, Belgium
| | - Chenqu Suo
- Wellcome Sanger Institute, Cellular Genetics, Cambridge, United Kingdom
| | - Brianna Wachter
- National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, Bethesda, MD, United States
| | - Rebecca T Beuschel
- National Institute of Allergy and Infectious Diseases, NIH, Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Bethesda, MD, United States
| | - Oren Amsalem
- Beth Israel Deaconess Medical Center, Harvard Medical School, Division of Endocrinology, Diabetes and Metabolism, Boston, MA, United States
| | | | - Simon Koplev
- Wellcome Sanger Institute, Cellular Genetics, Cambridge, United Kingdom
| | - Elizabeth Tuck
- Wellcome Sanger Institute, Cellular Genetics, Cambridge, United Kingdom
| | - Emma Dann
- Wellcome Sanger Institute, Cellular Genetics, Cambridge, United Kingdom
| | - Jolien Van Hulle
- Ghent University, Department of Diagnostic Sciences, Ghent, Belgium
| | - Shani Perera
- Wellcome Sanger Institute, Cellular Genetics, Cambridge, United Kingdom
| | - Tom Putteman
- Ghent University, Department of Diagnostic Sciences, Ghent, Belgium
| | | | - Monika Dabrowska
- Wellcome Sanger Institute, Cellular Genetics, Cambridge, United Kingdom
| | - Laura Richardson
- Wellcome Sanger Institute, Cellular Genetics, Cambridge, United Kingdom
| | - Catherine Tudor
- Wellcome Sanger Institute, Cellular Genetics, Cambridge, United Kingdom
| | - Alexandra Y Kreins
- Great Ormond Street Hospital for Children NHS Foundation Trust, Department of Immunology and Gene Therapy, London, United Kingdom
- UCL Great Ormond Street Institute of Child Health, Infection, Immunity and Inflammation Research & Teaching Department, London, United Kingdom
| | - Justin Engelbert
- Newcastle University, Biosciences Institute, Faculty of Medical Sciences, Newcastle upon Tyne, United Kingdom
| | - Emily Stephenson
- Newcastle University, Biosciences Institute, Faculty of Medical Sciences, Newcastle upon Tyne, United Kingdom
| | | | - Fabrizio De Rita
- Freeman Hospital, Department of Adult Congenital Heart Disease and Paediatric Cardiology/Cardiothoracic Surgery, Newcastle upon Tyne, United Kingdom
| | - David Crossland
- Freeman Hospital, Department of Adult Congenital Heart Disease and Paediatric Cardiology/Cardiothoracic Surgery, Newcastle upon Tyne, United Kingdom
| | - Marita Bosticardo
- National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, Bethesda, MD, United States
| | - Francesca Pala
- National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, Bethesda, MD, United States
| | - Elena Prigmore
- Wellcome Sanger Institute, Cellular Genetics, Cambridge, United Kingdom
| | | | - Martin Prete
- Wellcome Sanger Institute, Cellular Genetics, Cambridge, United Kingdom
| | - Lijiang Fei
- Wellcome Sanger Institute, Cellular Genetics, Cambridge, United Kingdom
| | - Ken To
- Wellcome Sanger Institute, Cellular Genetics, Cambridge, United Kingdom
| | - Roger A Barker
- University of Cambridge, John van Geest Centre for Brain Repair, Department of Clinical Neurosciences and Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
| | - Xiaoling He
- University of Cambridge, John van Geest Centre for Brain Repair, Department of Clinical Neurosciences and Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
| | - Filip Van Nieuwerburgh
- Ghent University, Laboratory of Pharmaceutical Biotechnology, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Omer Bayraktar
- Wellcome Sanger Institute, Cellular Genetics, Cambridge, United Kingdom
| | - Minal Patel
- Wellcome Sanger Institute, Cellular Genetics, Cambridge, United Kingdom
| | - Graham E Davies
- Great Ormond Street Hospital for Children NHS Foundation Trust, Department of Immunology and Gene Therapy, London, United Kingdom
- UCL Great Ormond Street Institute of Child Health, Infection, Immunity and Inflammation Research & Teaching Department, London, United Kingdom
| | - Muzlifah A Haniffa
- Wellcome Sanger Institute, Cellular Genetics, Cambridge, United Kingdom
- Newcastle University, Biosciences Institute, Faculty of Medical Sciences, Newcastle upon Tyne, United Kingdom
| | - Virginie Uhlmann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
| | - Luigi D Notarangelo
- National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, Bethesda, MD, United States
| | - Ronald N Germain
- National Institute of Allergy and Infectious Diseases, NIH, Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Bethesda, MD, United States
| | - Andrea J Radtke
- National Institute of Allergy and Infectious Diseases, NIH, Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Bethesda, MD, United States
| | - John C Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
- University of Cambridge, Cancer Research UK, Cambridge, United Kingdom
| | - Tom Taghon
- Ghent University, Department of Diagnostic Sciences, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Cellular Genetics, Cambridge, United Kingdom
- University of Cambridge, Cavendish Laboratory, Cambridge, United Kingdom
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2
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Goh I, Botting RA, Rose A, Webb S, Engelbert J, Gitton Y, Stephenson E, Londoño MQ, Mather M, Mende N, Imaz-Rosshandler I, Yang L, Horsfall D, Basurto-Lozada D, Chipampe NJ, Rook V, Lee JTH, Ton ML, Keitley D, Mazin P, Vijayabaskar M, Hannah R, Gambardella L, Green K, Ballereau S, Inoue M, Tuck E, Lorenzi V, Kwakwa K, Alsinet C, Olabi B, Miah M, Admane C, Popescu DM, Acres M, Dixon D, Ness T, Coulthard R, Lisgo S, Henderson DJ, Dann E, Suo C, Kinston SJ, Park JE, Polanski K, Marioni J, van Dongen S, Meyer KB, de Bruijn M, Palis J, Behjati S, Laurenti E, Wilson NK, Vento-Tormo R, Chédotal A, Bayraktar O, Roberts I, Jardine L, Göttgens B, Teichmann SA, Haniffa M. Yolk sac cell atlas reveals multiorgan functions during human early development. Science 2023; 381:eadd7564. [PMID: 37590359 PMCID: PMC7614978 DOI: 10.1126/science.add7564] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [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: 07/04/2022] [Accepted: 07/03/2023] [Indexed: 08/19/2023]
Abstract
The extraembryonic yolk sac (YS) ensures delivery of nutritional support and oxygen to the developing embryo but remains ill-defined in humans. We therefore assembled a comprehensive multiomic reference of the human YS from 3 to 8 postconception weeks by integrating single-cell protein and gene expression data. Beyond its recognized role as a site of hematopoiesis, we highlight roles in metabolism, coagulation, vascular development, and hematopoietic regulation. We reconstructed the emergence and decline of YS hematopoietic stem and progenitor cells from hemogenic endothelium and revealed a YS-specific accelerated route to macrophage production that seeds developing organs. The multiorgan functions of the YS are superseded as intraembryonic organs develop, effecting a multifaceted relay of vital functions as pregnancy proceeds.
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Affiliation(s)
- Issac Goh
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | - Rachel A. Botting
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | - Antony Rose
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | - Simone Webb
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | | | - Yorick Gitton
- Sorbonne Université, INSERM, CNRS, Institut de la Vision,
Paris, France
| | - Emily Stephenson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | | | - Michael Mather
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | - Nicole Mende
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell
Institute, CB2 0AW, UK
| | - Ivan Imaz-Rosshandler
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell
Institute, CB2 0AW, UK
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus,
CD2 0QH, UK
| | - Lu Yang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Dave Horsfall
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | - Daniela Basurto-Lozada
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | - Nana-Jane Chipampe
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Victoria Rook
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Jimmy Tsz Hang Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Mai-Linh Ton
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell
Institute, CB2 0AW, UK
| | - Daniel Keitley
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Department of Zoology, University of Cambridge, Cambridge UK
| | - Pavel Mazin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - M.S. Vijayabaskar
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell
Institute, CB2 0AW, UK
| | - Rebecca Hannah
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell
Institute, CB2 0AW, UK
| | - Laure Gambardella
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Kile Green
- Translational and Clinical Research Institute, Newcastle University,
NE2 4HH, UK
| | - Stephane Ballereau
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Megumi Inoue
- Sorbonne Université, INSERM, CNRS, Institut de la Vision,
Paris, France
| | - Elizabeth Tuck
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Valentina Lorenzi
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Kwasi Kwakwa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Clara Alsinet
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Centre Nacional d’Analisi Genomica-Centre de Regulacio
Genomica (CNAG-CRG), Barcelona Institute of Science and Technology (BIST),
Barcelona, Spain
| | - Bayanne Olabi
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | - Mohi Miah
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | - Chloe Admane
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | | | - Meghan Acres
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | - David Dixon
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | - Thomas Ness
- NovoPath, Department of Pathology, Newcastle Hospitals NHS
Foundation Trust, Newcastle upon Tyne, UK
| | - Rowen Coulthard
- NovoPath, Department of Pathology, Newcastle Hospitals NHS
Foundation Trust, Newcastle upon Tyne, UK
| | - Steven Lisgo
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | | | - Emma Dann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Chenqu Suo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Sarah J. Kinston
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell
Institute, CB2 0AW, UK
| | - Jong-eun Park
- Korea Advanced Institute of Science and Technology, Daejeon, South
Korea
| | - Krzysztof Polanski
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - John Marioni
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- EMBL-EBI, Wellcome Genome Campus, Cambridge, UK
- CRUK Cambridge Institute, University of Cambridge, Cambridge,
UK
| | - Stijn van Dongen
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Kerstin B. Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Marella de Bruijn
- MRC Molecular Haematology Unit, MRC Weatherall Institute of
Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS,
UK
| | - James Palis
- Department of Pediatrics, University of Rochester Medical Center,
Rochester, 14642, NY, USA
| | - Sam Behjati
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Department of Paediatrics, University of Cambridge, Cambridge,
UK
| | - Elisa Laurenti
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell
Institute, CB2 0AW, UK
| | - Nicola K. Wilson
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell
Institute, CB2 0AW, UK
| | - Roser Vento-Tormo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Alain Chédotal
- Sorbonne Université, INSERM, CNRS, Institut de la Vision,
Paris, France
| | - Omer Bayraktar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Irene Roberts
- Department of Paediatrics, University of Oxford, OX3 9DS, UK
| | - Laura Jardine
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | - Berthold Göttgens
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell
Institute, CB2 0AW, UK
| | - Sarah A. Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Theory of Condensed Matter Group, Cavendish Laboratory/Department
of Physics, University of Cambridge, Cambridge, UK
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research
Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE1 4LP,
UK
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3
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Garcia-Alonso L, Lorenzi V, Mazzeo CI, Alves-Lopes JP, Roberts K, Sancho-Serra C, Engelbert J, Marečková M, Gruhn WH, Botting RA, Li T, Crespo B, van Dongen S, Kiselev VY, Prigmore E, Herbert M, Moffett A, Chédotal A, Bayraktar OA, Surani A, Haniffa M, Vento-Tormo R. Single-cell roadmap of human gonadal development. Nature 2022; 607:540-547. [PMID: 35794482 PMCID: PMC9300467 DOI: 10.1038/s41586-022-04918-4] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [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: 05/05/2021] [Accepted: 05/30/2022] [Indexed: 01/09/2023]
Abstract
Gonadal development is a complex process that involves sex determination followed by divergent maturation into either testes or ovaries1. Historically, limited tissue accessibility, a lack of reliable in vitro models and critical differences between humans and mice have hampered our knowledge of human gonadogenesis, despite its importance in gonadal conditions and infertility. Here, we generated a comprehensive map of first- and second-trimester human gonads using a combination of single-cell and spatial transcriptomics, chromatin accessibility assays and fluorescent microscopy. We extracted human-specific regulatory programmes that control the development of germline and somatic cell lineages by profiling equivalent developmental stages in mice. In both species, we define the somatic cell states present at the time of sex specification, including the bipotent early supporting population that, in males, upregulates the testis-determining factor SRY and sPAX8s, a gonadal lineage located at the gonadal-mesonephric interface. In females, we resolve the cellular and molecular events that give rise to the first and second waves of granulosa cells that compartmentalize the developing ovary to modulate germ cell differentiation. In males, we identify human SIGLEC15+ and TREM2+ fetal testicular macrophages, which signal to somatic cells outside and inside the developing testis cords, respectively. This study provides a comprehensive spatiotemporal map of human and mouse gonadal differentiation, which can guide in vitro gonadogenesis.
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Affiliation(s)
| | | | | | - João Pedro Alves-Lopes
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge, UK
| | | | | | - Justin Engelbert
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Magda Marečková
- Wellcome Sanger Institute, Cambridge, UK
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, UK
| | - Wolfram H Gruhn
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge, UK
| | - Rachel A Botting
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Tong Li
- Wellcome Sanger Institute, Cambridge, UK
| | - Berta Crespo
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | | | | | | | - Mary Herbert
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Ashley Moffett
- University of Cambridge Centre for Trophoblast Research, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Alain Chédotal
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | | | - Azim Surani
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Cambridge, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
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4
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Suo C, Dann E, Goh I, Jardine L, Kleshchevnikov V, Park JE, Botting RA, Stephenson E, Engelbert J, Tuong ZK, Polanski K, Yayon N, Xu C, Suchanek O, Elmentaite R, Domínguez Conde C, He P, Pritchard S, Miah M, Moldovan C, Steemers AS, Mazin P, Prete M, Horsfall D, Marioni JC, Clatworthy MR, Haniffa M, Teichmann SA. Mapping the developing human immune system across organs. Science 2022; 376:eabo0510. [PMID: 35549310 PMCID: PMC7612819 DOI: 10.1126/science.abo0510] [Citation(s) in RCA: 87] [Impact Index Per Article: 43.5] [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] [Indexed: 12/13/2022]
Abstract
Single-cell genomics studies have decoded the immune-cell composition of several human prenatal organs but were limited in understanding the developing immune system as a distributed network across tissues. We profiled nine prenatal tissues combining single-cell RNA sequencing, antigen-receptor sequencing, and spatial transcriptomics to reconstruct the developing human immune system. This revealed the late acquisition of immune effector functions by myeloid and lymphoid cell subsets and the maturation of monocytes and T cells prior to peripheral tissue seeding. Moreover, we uncovered system-wide blood and immune cell development beyond primary hematopoietic organs, characterized human prenatal B1 cells, and shed light on the origin of unconventional T cells. Our atlas provides both valuable data resources and biological insights that will facilitate cell engineering, regenerative medicine, and disease understanding.
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Affiliation(s)
- Chenqu Suo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,Department of Paediatrics, Cambridge University Hospitals, Hills Road, Cambridge, UK
| | - Emma Dann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Issac Goh
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Laura Jardine
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.,Haematology Department, Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | - Jong-Eun Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Rachel A Botting
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Emily Stephenson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Justin Engelbert
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Zewen Kelvin Tuong
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Krzysztof Polanski
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Nadav Yayon
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,European Molecular Biology Laboratory European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Chuan Xu
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ondrej Suchanek
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Rasa Elmentaite
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Peng He
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,European Molecular Biology Laboratory European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Sophie Pritchard
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Mohi Miah
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Corina Moldovan
- Department of Cellular Pathology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | - Pavel Mazin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Martin Prete
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Dave Horsfall
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - John C Marioni
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,European Molecular Biology Laboratory European Bioinformatics Institute, Hinxton, Cambridge, UK.,Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Menna R Clatworthy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.,Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,Theory of Condensed Matter, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
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5
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Khabirova E, Jardine L, Coorens THH, Webb S, Treger TD, Engelbert J, Porter T, Prigmore E, Collord G, Piapi A, Teichmann SA, Inglott S, Williams O, Heidenreich O, Young MD, Straathof K, Bomken S, Bartram J, Haniffa M, Behjati S. Single-cell transcriptomics reveals a distinct developmental state of KMT2A-rearranged infant B-cell acute lymphoblastic leukemia. Nat Med 2022; 28:743-751. [PMID: 35288693 PMCID: PMC9018413 DOI: 10.1038/s41591-022-01720-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [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: 08/03/2021] [Accepted: 01/27/2022] [Indexed: 12/23/2022]
Abstract
KMT2A-rearranged infant ALL is an aggressive childhood leukemia with poor prognosis. Here, we investigated the developmental state of KMT2A-rearranged infant B-cell acute lymphoblastic leukemia (B-ALL) using bulk messenger RNA (mRNA) meta-analysis and examination of single lymphoblast transcriptomes against a developing bone marrow reference. KMT2A-rearranged infant B-ALL was uniquely dominated by an early lymphocyte precursor (ELP) state, whereas less adverse NUTM1-rearranged infant ALL demonstrated signals of later developing B cells, in line with most other childhood B-ALLs. We compared infant lymphoblasts with ELP cells and revealed that the cancer harbored hybrid myeloid-lymphoid features, including nonphysiological antigen combinations potentially targetable to achieve cancer specificity. We validated surface coexpression of exemplar combinations by flow cytometry. Through analysis of shared mutations in separate leukemias from a child with infant KMT2A-rearranged B-ALL relapsing as AML, we established that KMT2A rearrangement occurred in very early development, before hematopoietic specification, emphasizing that cell of origin cannot be inferred from the transcriptional state.
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Affiliation(s)
| | - Laura Jardine
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- Haematology Department, Freeman Hospital, Newcastle-upon-Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | - Simone Webb
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Taryn D Treger
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Justin Engelbert
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | | | - Grace Collord
- Wellcome Sanger Institute, Hinxton, UK
- Department of Haematology, University College London Hospital, London, UK
- Department of Haematology, University College London Cancer Institute, London, UK
| | - Alice Piapi
- Great Ormond Street Hospital for Children NHS Foundation Trust and NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK
| | | | - Sarah Inglott
- Great Ormond Street Hospital for Children NHS Foundation Trust and NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK
| | - Owen Williams
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Olaf Heidenreich
- Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | - Karin Straathof
- Great Ormond Street Hospital for Children NHS Foundation Trust and NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Simon Bomken
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.
- The Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
| | - Jack Bartram
- Great Ormond Street Hospital for Children NHS Foundation Trust and NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK.
- UCL Great Ormond Street Institute of Child Health, London, UK.
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Hinxton, UK.
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, UK.
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6
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Mather MW, Verdon B, Botting RA, Engelbert J, Delpiano L, Xu X, Hatton C, Davey T, Lisgo S, Yates P, Dawe N, Bingle CD, Haniffa M, Powell J, Ward C. Development of a physiological model of human middle ear epithelium. Laryngoscope Investig Otolaryngol 2021; 6:1167-1174. [PMID: 34667862 PMCID: PMC8513425 DOI: 10.1002/lio2.661] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 12/16/2022] Open
Abstract
INTRODUCTION Otitis media is an umbrella term for middle ear inflammation; ranging from acute infection to chronic mucosal disease. It is a leading cause of antimicrobial therapy prescriptions and surgery in children. Despite this, treatments have changed little in over 50 years. Research has been limited by the lack of physiological models of middle ear epithelium. METHODS We develop a novel human middle ear epithelial culture using an air-liquid interface (ALI) system; akin to the healthy ventilated middle ear in vivo. We validate this using immunohistochemistry, immunofluorescence, scanning and transmission electron microscopy, and membrane conductance studies. We also utilize this model to perform a pilot challenge of middle ear epithelial cells with SARS-CoV-2. RESULTS We demonstrate that human middle ear epithelial cells cultured at an ALI undergo mucociliary differentiation to produce diverse epithelial subtypes including basal (p63+), goblet (MUC5AC+, MUC5B+), and ciliated (FOXJ1+) cells. Mature ciliagenesis is visualized and tight junction formation is shown with electron microscopy, and confirmed by membrane conductance. Together, these demonstrate this model reflects the complex epithelial cell types which exist in vivo. Following SARS-CoV-2 challenge, human middle ear epithelium shows positive viral uptake, as measured by polymerase chain reaction and immunohistochemistry. CONCLUSION We describe a novel physiological system to study the human middle ear. This can be utilized for translational research into middle ear diseases. We also demonstrate, for the first time under controlled conditions, that human middle ear epithelium is susceptible to SARS-CoV-2 infection, which has important clinical implications for safe otological surgery. LEVEL OF EVIDENCE NA.
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Affiliation(s)
- Michael William Mather
- Faculty of Medical SciencesBiosciences Institute, Newcastle UniversityNewcastle‐upon‐TyneUK
- Department of OtolaryngologyFreeman HospitalNewcastle‐upon‐TyneUK
| | - Bernard Verdon
- Faculty of Medical SciencesBiosciences Institute, Newcastle UniversityNewcastle‐upon‐TyneUK
| | - Rachel Anne Botting
- Faculty of Medical SciencesBiosciences Institute, Newcastle UniversityNewcastle‐upon‐TyneUK
| | - Justin Engelbert
- Faculty of Medical SciencesBiosciences Institute, Newcastle UniversityNewcastle‐upon‐TyneUK
| | - Livia Delpiano
- Faculty of Medical SciencesBiosciences Institute, Newcastle UniversityNewcastle‐upon‐TyneUK
| | - Xin Xu
- Newcastle Biobank, Faculty of Medical SciencesNewcastle UniversityNewcastle‐upon‐TyneUK
| | - Catherine Hatton
- Faculty of Medical SciencesTranslational and Clinical Research Institute, Newcastle UniversityNewcastle‐upon‐TyneUK
| | - Tracey Davey
- Electron Microscopy Research Services, Faculty of Medical SciencesNewcastle UniversityNewcastle‐upon‐TyneUK
| | - Steven Lisgo
- Faculty of Medical SciencesBiosciences Institute, Newcastle UniversityNewcastle‐upon‐TyneUK
| | - Philip Yates
- Department of OtolaryngologyFreeman HospitalNewcastle‐upon‐TyneUK
| | - Nicholas Dawe
- Department of OtolaryngologyFreeman HospitalNewcastle‐upon‐TyneUK
| | - Colin D. Bingle
- Department of Infection, Immunity and Cardiovascular DiseaseThe Medical SchoolSheffieldUK
| | - Muzlifah Haniffa
- Faculty of Medical SciencesBiosciences Institute, Newcastle UniversityNewcastle‐upon‐TyneUK
| | - Jason Powell
- Department of OtolaryngologyFreeman HospitalNewcastle‐upon‐TyneUK
- Faculty of Medical SciencesTranslational and Clinical Research Institute, Newcastle UniversityNewcastle‐upon‐TyneUK
| | - Chris Ward
- Faculty of Medical SciencesTranslational and Clinical Research Institute, Newcastle UniversityNewcastle‐upon‐TyneUK
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7
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Elmentaite R, Kumasaka N, Roberts K, Fleming A, Dann E, King HW, Kleshchevnikov V, Dabrowska M, Pritchard S, Bolt L, Vieira SF, Mamanova L, Huang N, Perrone F, Goh Kai'En I, Lisgo SN, Katan M, Leonard S, Oliver TRW, Hook CE, Nayak K, Campos LS, Domínguez Conde C, Stephenson E, Engelbert J, Botting RA, Polanski K, van Dongen S, Patel M, Morgan MD, Marioni JC, Bayraktar OA, Meyer KB, He X, Barker RA, Uhlig HH, Mahbubani KT, Saeb-Parsy K, Zilbauer M, Clatworthy MR, Haniffa M, James KR, Teichmann SA. Cells of the human intestinal tract mapped across space and time. Nature 2021; 597:250-255. [PMID: 34497389 PMCID: PMC8426186 DOI: 10.1038/s41586-021-03852-1] [Citation(s) in RCA: 219] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 07/26/2021] [Indexed: 12/12/2022]
Abstract
The cellular landscape of the human intestinal tract is dynamic throughout life, developing in utero and changing in response to functional requirements and environmental exposures. Here, to comprehensively map cell lineages, we use single-cell RNA sequencing and antigen receptor analysis of almost half a million cells from up to 5 anatomical regions in the developing and up to 11 distinct anatomical regions in the healthy paediatric and adult human gut. This reveals the existence of transcriptionally distinct BEST4 epithelial cells throughout the human intestinal tract. Furthermore, we implicate IgG sensing as a function of intestinal tuft cells. We describe neural cell populations in the developing enteric nervous system, and predict cell-type-specific expression of genes associated with Hirschsprung's disease. Finally, using a systems approach, we identify key cell players that drive the formation of secondary lymphoid tissue in early human development. We show that these programs are adopted in inflammatory bowel disease to recruit and retain immune cells at the site of inflammation. This catalogue of intestinal cells will provide new insights into cellular programs in development, homeostasis and disease.
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Affiliation(s)
- Rasa Elmentaite
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Kenny Roberts
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Aaron Fleming
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Emma Dann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Hamish W King
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London, UK
| | | | | | | | - Liam Bolt
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Sara F Vieira
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Lira Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Ni Huang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Issac Goh Kai'En
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Steven N Lisgo
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Matilda Katan
- Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Steven Leonard
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Thomas R W Oliver
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - C Elizabeth Hook
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Komal Nayak
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Lia S Campos
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Emily Stephenson
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Justin Engelbert
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Rachel A Botting
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | | | | | - Minal Patel
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Michael D Morgan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - John C Marioni
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Xiaoling He
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences and Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Roger A Barker
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences and Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Holm H Uhlig
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Krishnaa T Mahbubani
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Matthias Zilbauer
- Department of Paediatrics, University of Cambridge, Cambridge, UK
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals Trust, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, UK
| | - Menna R Clatworthy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Kylie R James
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
- Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
- Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge, UK.
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8
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Stephenson E, Reynolds G, Botting RA, Calero-Nieto FJ, Morgan MD, Tuong ZK, Bach K, Sungnak W, Worlock KB, Yoshida M, Kumasaka N, Kania K, Engelbert J, Olabi B, Spegarova JS, Wilson NK, Mende N, Jardine L, Gardner LCS, Goh I, Horsfall D, McGrath J, Webb S, Mather MW, Lindeboom RGH, Dann E, Huang N, Polanski K, Prigmore E, Gothe F, Scott J, Payne RP, Baker KF, Hanrath AT, Schim van der Loeff ICD, Barr AS, Sanchez-Gonzalez A, Bergamaschi L, Mescia F, Barnes JL, Kilich E, de Wilton A, Saigal A, Saleh A, Janes SM, Smith CM, Gopee N, Wilson C, Coupland P, Coxhead JM, Kiselev VY, van Dongen S, Bacardit J, King HW, Rostron AJ, Simpson AJ, Hambleton S, Laurenti E, Lyons PA, Meyer KB, Nikolić MZ, Duncan CJA, Smith KGC, Teichmann SA, Clatworthy MR, Marioni JC, Göttgens B, Haniffa M. Single-cell multi-omics analysis of the immune response in COVID-19. Nat Med 2021; 27:904-916. [PMID: 33879890 PMCID: PMC8121667 DOI: 10.1038/s41591-021-01329-2] [Citation(s) in RCA: 321] [Impact Index Per Article: 107.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/23/2021] [Indexed: 02/07/2023]
Abstract
Analysis of human blood immune cells provides insights into the coordinated response to viral infections such as severe acute respiratory syndrome coronavirus 2, which causes coronavirus disease 2019 (COVID-19). We performed single-cell transcriptome, surface proteome and T and B lymphocyte antigen receptor analyses of over 780,000 peripheral blood mononuclear cells from a cross-sectional cohort of 130 patients with varying severities of COVID-19. We identified expansion of nonclassical monocytes expressing complement transcripts (CD16+C1QA/B/C+) that sequester platelets and were predicted to replenish the alveolar macrophage pool in COVID-19. Early, uncommitted CD34+ hematopoietic stem/progenitor cells were primed toward megakaryopoiesis, accompanied by expanded megakaryocyte-committed progenitors and increased platelet activation. Clonally expanded CD8+ T cells and an increased ratio of CD8+ effector T cells to effector memory T cells characterized severe disease, while circulating follicular helper T cells accompanied mild disease. We observed a relative loss of IgA2 in symptomatic disease despite an overall expansion of plasmablasts and plasma cells. Our study highlights the coordinated immune response that contributes to COVID-19 pathogenesis and reveals discrete cellular components that can be targeted for therapy.
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Affiliation(s)
- Emily Stephenson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Gary Reynolds
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Rachel A Botting
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | - Michael D Morgan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Zewen Kelvin Tuong
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Karsten Bach
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Waradon Sungnak
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Kaylee B Worlock
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Masahiro Yoshida
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | | | - Katarzyna Kania
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Justin Engelbert
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Bayanne Olabi
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | - Nicola K Wilson
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Nicole Mende
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Laura Jardine
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Louis C S Gardner
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Issac Goh
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Dave Horsfall
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Jim McGrath
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Simone Webb
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Michael W Mather
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | - Emma Dann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Ni Huang
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Florian Gothe
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Jonathan Scott
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Rebecca P Payne
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Kenneth F Baker
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Aidan T Hanrath
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Infection and Tropical Medicine, Newcastle upon Tyne Hospitals NHS Foundation, Newcastle upon Tyne, UK
| | | | - Andrew S Barr
- Department of Infection and Tropical Medicine, Newcastle upon Tyne Hospitals NHS Foundation, Newcastle upon Tyne, UK
| | - Amada Sanchez-Gonzalez
- Department of Infection and Tropical Medicine, Newcastle upon Tyne Hospitals NHS Foundation, Newcastle upon Tyne, UK
| | - Laura Bergamaschi
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Federica Mescia
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Josephine L Barnes
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Eliz Kilich
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Angus de Wilton
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Anita Saigal
- Royal Free Hospital NHS Foundation Trust, London, UK
| | - Aarash Saleh
- Royal Free Hospital NHS Foundation Trust, London, UK
| | - Sam M Janes
- UCL Respiratory, Division of Medicine, University College London, London, UK
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Claire M Smith
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Nusayhah Gopee
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Dermatology, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Caroline Wilson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- The Innovation Lab Integrated COVID Hub North East, Newcastle Upon Tyne, UK
| | - Paul Coupland
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | | | - Stijn van Dongen
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Jaume Bacardit
- School of Computing, Newcastle University, Newcastle Upon Tyne, UK
| | - Hamish W King
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London, UK
| | - Anthony J Rostron
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Integrated Critical Care Unit, Sunderland Royal Hospital, South Tyneside and Sunderland NHS Foundation Trust, Sunderland, UK
| | - A John Simpson
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Sophie Hambleton
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Elisa Laurenti
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Paul A Lyons
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Marko Z Nikolić
- UCL Respiratory, Division of Medicine, University College London, London, UK
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Christopher J A Duncan
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Infection and Tropical Medicine, Newcastle upon Tyne Hospitals NHS Foundation, Newcastle upon Tyne, UK
| | - Kenneth G C Smith
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge, UK.
| | - Menna R Clatworthy
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Cambridge Biomedical Campus, Cambridge, UK.
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK.
| | - John C Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK.
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
| | - Berthold Göttgens
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
| | - Muzlifah Haniffa
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
- Department of Dermatology, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
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9
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Reynolds G, Vegh P, Fletcher J, Poyner EFM, Stephenson E, Goh I, Botting RA, Huang N, Olabi B, Dubois A, Dixon D, Green K, Maunder D, Engelbert J, Efremova M, Polański K, Jardine L, Jones C, Ness T, Horsfall D, McGrath J, Carey C, Popescu DM, Webb S, Wang XN, Sayer B, Park JE, Negri VA, Belokhvostova D, Lynch MD, McDonald D, Filby A, Hagai T, Meyer KB, Husain A, Coxhead J, Vento-Tormo R, Behjati S, Lisgo S, Villani AC, Bacardit J, Jones PH, O'Toole EA, Ogg GS, Rajan N, Reynolds NJ, Teichmann SA, Watt FM, Haniffa M. Developmental cell programs are co-opted in inflammatory skin disease. Science 2021; 371:eaba6500. [PMID: 33479125 PMCID: PMC7611557 DOI: 10.1126/science.aba6500] [Citation(s) in RCA: 232] [Impact Index Per Article: 77.3] [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: 12/21/2019] [Revised: 09/03/2020] [Accepted: 12/01/2020] [Indexed: 12/16/2022]
Abstract
The skin confers biophysical and immunological protection through a complex cellular network established early in embryonic development. We profiled the transcriptomes of more than 500,000 single cells from developing human fetal skin, healthy adult skin, and adult skin with atopic dermatitis and psoriasis. We leveraged these datasets to compare cell states across development, homeostasis, and disease. Our analysis revealed an enrichment of innate immune cells in skin during the first trimester and clonal expansion of disease-associated lymphocytes in atopic dermatitis and psoriasis. We uncovered and validated in situ a reemergence of prenatal vascular endothelial cell and macrophage cellular programs in atopic dermatitis and psoriasis lesional skin. These data illustrate the dynamism of cutaneous immunity and provide opportunities for targeting pathological developmental programs in inflammatory skin diseases.
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Affiliation(s)
- Gary Reynolds
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Peter Vegh
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - James Fletcher
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Elizabeth F M Poyner
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
| | - Emily Stephenson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Issac Goh
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Rachel A Botting
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Ni Huang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Bayanne Olabi
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Department of Dermatology, NHS Lothian, Lauriston Building, Edinburgh EH3 9EN, UK
| | - Anna Dubois
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
| | - David Dixon
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Kile Green
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Daniel Maunder
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Justin Engelbert
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Mirjana Efremova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Krzysztof Polański
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Laura Jardine
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Claire Jones
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Thomas Ness
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Dave Horsfall
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Jim McGrath
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Christopher Carey
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Dorin-Mirel Popescu
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Simone Webb
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Xiao-Nong Wang
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Ben Sayer
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Jong-Eun Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Victor A Negri
- Centre for Stem Cells and Regenerative Medicine, King's College London, Guy's Hospital Campus, London SE1 9RT, UK
| | - Daria Belokhvostova
- Centre for Stem Cells and Regenerative Medicine, King's College London, Guy's Hospital Campus, London SE1 9RT, UK
| | - Magnus D Lynch
- Centre for Stem Cells and Regenerative Medicine, King's College London, Guy's Hospital Campus, London SE1 9RT, UK
| | - David McDonald
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Andrew Filby
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Tzachi Hagai
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Akhtar Husain
- Department of Pathology, Royal Victoria Infirmary, Newcastle upon Tyne NE1 4LP, UK
| | - Jonathan Coxhead
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Roser Vento-Tormo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Sam Behjati
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0SP, UK
| | - Steven Lisgo
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Alexandra-Chloé Villani
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Jaume Bacardit
- School of Computing, Newcastle University, Newcastle upon Tyne NE4 5TG, UK
| | - Philip H Jones
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Edel A O'Toole
- Centre for Cell Biology and Cutaneous Research, Blizard Institute, Queen Mary University of London, London, UK
| | - Graham S Ogg
- MRC Human Immunology Unit, Oxford Biomedical Research Centre, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Neil Rajan
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
| | - Nick J Reynolds
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
- Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge CB3 0HE, UK
| | - Fiona M Watt
- Centre for Stem Cells and Regenerative Medicine, King's College London, Guy's Hospital Campus, London SE1 9RT, UK.
| | - Muzlifah Haniffa
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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Engelbert J. [Pediatric clinical study on the trimethoprim-sulfamethoxazole assoication]. Brux Med 1971; 51:899-902. [PMID: 5143373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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