1
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Kedlian VR, Wang Y, Liu T, Chen X, Bolt L, Tudor C, Shen Z, Fasouli ES, Prigmore E, Kleshchevnikov V, Pett JP, Li T, Lawrence JEG, Perera S, Prete M, Huang N, Guo Q, Zeng X, Yang L, Polański K, Chipampe NJ, Dabrowska M, Li X, Bayraktar OA, Patel M, Kumasaka N, Mahbubani KT, Xiang AP, Meyer KB, Saeb-Parsy K, Teichmann SA, Zhang H. Human skeletal muscle aging atlas. Nat Aging 2024:10.1038/s43587-024-00613-3. [PMID: 38622407 DOI: 10.1038/s43587-024-00613-3] [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] [Received: 11/20/2023] [Accepted: 03/19/2024] [Indexed: 04/17/2024]
Abstract
Skeletal muscle aging is a key contributor to age-related frailty and sarcopenia with substantial implications for global health. Here we profiled 90,902 single cells and 92,259 single nuclei from 17 donors to map the aging process in the adult human intercostal muscle, identifying cellular changes in each muscle compartment. We found that distinct subsets of muscle stem cells exhibit decreased ribosome biogenesis genes and increased CCL2 expression, causing different aging phenotypes. Our atlas also highlights an expansion of nuclei associated with the neuromuscular junction, which may reflect re-innervation, and outlines how the loss of fast-twitch myofibers is mitigated through regeneration and upregulation of fast-type markers in slow-twitch myofibers with age. Furthermore, we document the function of aging muscle microenvironment in immune cell attraction. Overall, we present a comprehensive human skeletal muscle aging resource ( https://www.muscleageingcellatlas.org/ ) together with an in-house mouse muscle atlas to study common features of muscle aging across species.
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Affiliation(s)
- Veronika R Kedlian
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Yaning Wang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Tianliang Liu
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xiaoping Chen
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Liam Bolt
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Catherine Tudor
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Zhuojian Shen
- Department of Thoracic Surgery, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Eirini S Fasouli
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Jan Patrick Pett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Tong Li
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - John E G Lawrence
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Shani Perera
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Martin Prete
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ni Huang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Qin Guo
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xinrui Zeng
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Lu Yang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Krzysztof Polański
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Nana-Jane Chipampe
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Monika Dabrowska
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Xiaobo Li
- Core Facilities for Medical Science, Sun Yat-sen University, Guangzhou, China
| | - Omer Ali Bayraktar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Minal Patel
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Natsuhiko Kumasaka
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Krishnaa T Mahbubani
- Department of Surgery, University of Cambridge, Cambridge, UK
- Collaborative Biorepository for Translational Medicine (CBTM), NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Andy Peng Xiang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, Cambridge, UK.
- Collaborative Biorepository for Translational Medicine (CBTM), NIHR Cambridge Biomedical Research Centre, Cambridge, UK.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
| | - Hongbo Zhang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
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2
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Zhang B, He P, Lawrence JEG, Wang S, Tuck E, Williams BA, Roberts K, Kleshchevnikov V, Mamanova L, Bolt L, Polanski K, Li T, Elmentaite R, Fasouli ES, Prete M, He X, Yayon N, Fu Y, Yang H, Liang C, Zhang H, Blain R, Chedotal A, FitzPatrick DR, Firth H, Dean A, Bayraktar OA, Marioni JC, Barker RA, Storer MA, Wold BJ, Zhang H, Teichmann SA. A human embryonic limb cell atlas resolved in space and time. Nature 2023:10.1038/s41586-023-06806-x. [PMID: 38057666 DOI: 10.1038/s41586-023-06806-x] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 10/31/2023] [Indexed: 12/08/2023]
Abstract
Human limbs emerge during the fourth post-conception week as mesenchymal buds, which develop into fully formed limbs over the subsequent months1. This process is orchestrated by numerous temporally and spatially restricted gene expression programmes, making congenital alterations in phenotype common2. Decades of work with model organisms have defined the fundamental mechanisms underlying vertebrate limb development, but an in-depth characterization of this process in humans has yet to be performed. Here we detail human embryonic limb development across space and time using single-cell and spatial transcriptomics. We demonstrate extensive diversification of cells from a few multipotent progenitors to myriad differentiated cell states, including several novel cell populations. We uncover two waves of human muscle development, each characterized by different cell states regulated by separate gene expression programmes, and identify musculin (MSC) as a key transcriptional repressor maintaining muscle stem cell identity. Through assembly of multiple anatomically continuous spatial transcriptomic samples using VisiumStitcher, we map cells across a sagittal section of a whole fetal hindlimb. We reveal a clear anatomical segregation between genes linked to brachydactyly and polysyndactyly, and uncover transcriptionally and spatially distinct populations of the mesenchyme in the autopod. Finally, we perform single-cell RNA sequencing on mouse embryonic limbs to facilitate cross-species developmental comparison, finding substantial homology between the two species.
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Affiliation(s)
- Bao Zhang
- The Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Peng He
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - John E G Lawrence
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Department of Trauma and Orthopaedics, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, UK
| | - Shuaiyu Wang
- The Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Obstetrics, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Elizabeth Tuck
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Brian A Williams
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Kenny Roberts
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Lira Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Enhanc3D Genomics Ltd, Cambridge, UK
| | - Liam Bolt
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Genomics England, London, UK
| | | | - Tong Li
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Rasa Elmentaite
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Eirini S Fasouli
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Basic Research Center, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Martin Prete
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Xiaoling He
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Nadav Yayon
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Yixi Fu
- The Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Hao Yang
- The Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Chen Liang
- The Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Hui Zhang
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Raphael Blain
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Alain Chedotal
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
- Institut de pathologie, groupe hospitalier Est, hospices civils de Lyon, Lyon, France
- University Claude Bernard Lyon 1, MeLiS, CNRS UMR5284, INSERM U1314, Lyon, France
| | | | - Helen Firth
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Andrew Dean
- Department of Clinical Neurosciences, Cambridge University Hospitals NHS Foundation, Cambridge, UK
| | | | - John C Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Roger A Barker
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Mekayla A Storer
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Barbara J Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Hongbo Zhang
- The Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
- Advanced Medical Technology Center, the First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
- Theory of Condensed Matter Group, Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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3
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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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4
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Garcia-Alonso L, Handfield LF, Roberts K, Nikolakopoulou K, Fernando RC, Gardner L, Woodhams B, Arutyunyan A, Polanski K, Hoo R, Sancho-Serra C, Li T, Kwakwa K, Tuck E, Lorenzi V, Massalha H, Prete M, Kleshchevnikov V, Tarkowska A, Porter T, Mazzeo CI, van Dongen S, Dabrowska M, Vaskivskyi V, Mahbubani KT, Park JE, Jimenez-Linan M, Campos L, Kiselev VY, Lindskog C, Ayuk P, Prigmore E, Stratton MR, Saeb-Parsy K, Moffett A, Moore L, Bayraktar OA, Teichmann SA, Turco MY, Vento-Tormo R. Author Correction: Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro. Nat Genet 2023; 55:165. [PMID: 36539619 PMCID: PMC9839447 DOI: 10.1038/s41588-022-01287-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Luz Garcia-Alonso
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | | | - Kenny Roberts
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | - Konstantina Nikolakopoulou
- grid.5335.00000000121885934Centre for Trophoblast Research, University of Cambridge, Cambridge, UK ,grid.5335.00000000121885934Department of Pathology, University of Cambridge, Cambridge, UK ,grid.482245.d0000 0001 2110 3787Present Address: Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Ridma C. Fernando
- grid.5335.00000000121885934Centre for Trophoblast Research, University of Cambridge, Cambridge, UK ,grid.5335.00000000121885934Department of Pathology, University of Cambridge, Cambridge, UK ,grid.482245.d0000 0001 2110 3787Present Address: Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Lucy Gardner
- grid.5335.00000000121885934Centre for Trophoblast Research, University of Cambridge, Cambridge, UK ,grid.5335.00000000121885934Department of Pathology, University of Cambridge, Cambridge, UK
| | - Benjamin Woodhams
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Anna Arutyunyan
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Krzysztof Polanski
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | - Regina Hoo
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | | | - Tong Li
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | | | - Elizabeth Tuck
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | - Valentina Lorenzi
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | - Hassan Massalha
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Martin Prete
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | | | | | - Tarryn Porter
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | | | - Stijn van Dongen
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | - Monika Dabrowska
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | - Vasyl Vaskivskyi
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | - Krishnaa T. Mahbubani
- grid.5335.00000000121885934Department of Haematology, University of Cambridge, Cambridge, UK ,grid.454369.9Cambridge Biorepository for Translational Medicine (CBTM), NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Jong-eun Park
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | - Mercedes Jimenez-Linan
- grid.24029.3d0000 0004 0383 8386Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Lia Campos
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | | | - Cecilia Lindskog
- grid.8993.b0000 0004 1936 9457Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Paul Ayuk
- grid.420004.20000 0004 0444 2244Department of Women’s Services, Newcastle-upon-Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Elena Prigmore
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | | | - Kourosh Saeb-Parsy
- grid.454369.9Cambridge Biorepository for Translational Medicine (CBTM), NIHR Cambridge Biomedical Research Centre, Cambridge, UK ,grid.5335.00000000121885934Department of Surgery, University of Cambridge, Cambridge, UK
| | - Ashley Moffett
- grid.5335.00000000121885934Centre for Trophoblast Research, University of Cambridge, Cambridge, UK ,grid.5335.00000000121885934Department of Pathology, University of Cambridge, Cambridge, UK
| | - Luiza Moore
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.24029.3d0000 0004 0383 8386Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Omer A. Bayraktar
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | - Sarah A. Teichmann
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Margherita Y. Turco
- grid.5335.00000000121885934Centre for Trophoblast Research, University of Cambridge, Cambridge, UK ,grid.5335.00000000121885934Department of Pathology, University of Cambridge, Cambridge, UK ,grid.482245.d0000 0001 2110 3787Present Address: Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Roser Vento-Tormo
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
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5
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Madissoon E, Oliver AJ, Kleshchevnikov V, Wilbrey-Clark A, Polanski K, Richoz N, Ribeiro Orsi A, Mamanova L, Bolt L, Elmentaite R, Pett JP, Huang N, Xu C, He P, Dabrowska M, Pritchard S, Tuck L, Prigmore E, Perera S, Knights A, Oszlanczi A, Hunter A, Vieira SF, Patel M, Lindeboom RGH, Campos LS, Matsuo K, Nakayama T, Yoshida M, Worlock KB, Nikolić MZ, Georgakopoulos N, Mahbubani KT, Saeb-Parsy K, Bayraktar OA, Clatworthy MR, Stegle O, Kumasaka N, Teichmann SA, Meyer KB. A spatially resolved atlas of the human lung characterizes a gland-associated immune niche. Nat Genet 2023; 55:66-77. [PMID: 36543915 PMCID: PMC9839452 DOI: 10.1038/s41588-022-01243-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/25/2022] [Indexed: 12/24/2022]
Abstract
Single-cell transcriptomics has allowed unprecedented resolution of cell types/states in the human lung, but their spatial context is less well defined. To (re)define tissue architecture of lung and airways, we profiled five proximal-to-distal locations of healthy human lungs in depth using multi-omic single cell/nuclei and spatial transcriptomics (queryable at lungcellatlas.org ). Using computational data integration and analysis, we extend beyond the suspension cell paradigm and discover macro and micro-anatomical tissue compartments including previously unannotated cell types in the epithelial, vascular, stromal and nerve bundle micro-environments. We identify and implicate peribronchial fibroblasts in lung disease. Importantly, we discover and validate a survival niche for IgA plasma cells in the airway submucosal glands (SMG). We show that gland epithelial cells recruit B cells and IgA plasma cells, and promote longevity and antibody secretion locally through expression of CCL28, APRIL and IL-6. This new 'gland-associated immune niche' has implications for respiratory health.
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Affiliation(s)
- Elo Madissoon
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK
| | - Amanda J Oliver
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | | | | | - Nathan Richoz
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Francis Crick Ave, Cambridge, UK
| | - Ana Ribeiro Orsi
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Lira Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Liam Bolt
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Rasa Elmentaite
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - J Patrick Pett
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Ni Huang
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Chuan Xu
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Peng He
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK
| | - Monika Dabrowska
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Sophie Pritchard
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Liz Tuck
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Shani Perera
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Andrew Knights
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Agnes Oszlanczi
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Adam Hunter
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Sara F Vieira
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Minal Patel
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | - Lia S Campos
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | | | - Masahiro Yoshida
- UCL Respiratory, Division of Medicine, University College London Hospitals NHS Foundation Trust, London, UK
| | - Kaylee B Worlock
- UCL Respiratory, Division of Medicine, University College London Hospitals NHS Foundation Trust, London, UK
| | - Marko Z Nikolić
- UCL Respiratory, Division of Medicine, University College London Hospitals NHS Foundation Trust, London, UK
| | - Nikitas Georgakopoulos
- Department of Surgery, University of Cambridge, and Cambridge NIHR Biomedical Research Centre, Cambridge, UK
| | - Krishnaa T Mahbubani
- Department of Surgery, University of Cambridge, and Cambridge NIHR Biomedical Research Centre, Cambridge, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, and Cambridge NIHR Biomedical Research Centre, Cambridge, UK
| | | | - Menna R Clatworthy
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Francis Crick Ave, Cambridge, UK
| | - Oliver Stegle
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | | | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Theory of Condensed Matter, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge, UK.
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
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6
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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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7
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Wadie B, Kleshchevnikov V, Sandaltzopoulou E, Benz C, Petsalaki E. Use of viral motif mimicry improves the proteome-wide discovery of human linear motifs. Cell Rep 2022; 39:110764. [PMID: 35508127 DOI: 10.1016/j.celrep.2022.110764] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 02/09/2022] [Accepted: 04/08/2022] [Indexed: 12/16/2022] Open
Abstract
Linear motifs have an integral role in dynamic cell functions, including cell signaling. However, due to their small size, low complexity, and frequent mutations, identifying novel functional motifs poses a challenge. Viruses rely extensively on the molecular mimicry of cellular linear motifs. In this study, we apply systematic motif prediction combined with functional filters to identify human linear motifs convergently evolved also in viral proteins. We observe an increase in the sensitivity of motif prediction and improved enrichment in known instances. We identify >7,300 non-redundant motif instances at various confidence levels, 99 of which are supported by all functional and structural filters. Overall, we provide a pipeline to improve the identification of functional linear motifs from interactomics datasets and a comprehensive catalog of putative human motifs that can contribute to our understanding of the human domain-linear motif code and the associated mechanisms of viral interference.
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Affiliation(s)
- Bishoy Wadie
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Vitalii Kleshchevnikov
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Elissavet Sandaltzopoulou
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Caroline Benz
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Evangelia Petsalaki
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK.
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8
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Gayoso A, Lopez R, Xing G, Boyeau P, Valiollah Pour Amiri V, Hong J, Wu K, Jayasuriya M, Mehlman E, Langevin M, Liu Y, Samaran J, Misrachi G, Nazaret A, Clivio O, Xu C, Ashuach T, Gabitto M, Lotfollahi M, Svensson V, da Veiga Beltrame E, Kleshchevnikov V, Talavera-López C, Pachter L, Theis FJ, Streets A, Jordan MI, Regier J, Yosef N. A Python library for probabilistic analysis of single-cell omics data. Nat Biotechnol 2022; 40:163-166. [DOI: 10.1038/s41587-021-01206-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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9
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Kleshchevnikov V, Shmatko A, Dann E, Aivazidis A, King HW, Li T, Elmentaite R, Lomakin A, Kedlian V, Gayoso A, Jain MS, Park JS, Ramona L, Tuck E, Arutyunyan A, Vento-Tormo R, Gerstung M, James L, Stegle O, Bayraktar OA. Cell2location maps fine-grained cell types in spatial transcriptomics. Nat Biotechnol 2022; 40:661-671. [PMID: 35027729 DOI: 10.1038/s41587-021-01139-4] [Citation(s) in RCA: 208] [Impact Index Per Article: 104.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 10/28/2021] [Indexed: 12/11/2022]
Abstract
Spatial transcriptomic technologies promise to resolve cellular wiring diagrams of tissues in health and disease, but comprehensive mapping of cell types in situ remains a challenge. Here we present сell2location, a Bayesian model that can resolve fine-grained cell types in spatial transcriptomic data and create comprehensive cellular maps of diverse tissues. Cell2location accounts for technical sources of variation and borrows statistical strength across locations, thereby enabling the integration of single-cell and spatial transcriptomics with higher sensitivity and resolution than existing tools. We assessed cell2location in three different tissues and show improved mapping of fine-grained cell types. In the mouse brain, we discovered fine regional astrocyte subtypes across the thalamus and hypothalamus. In the human lymph node, we spatially mapped a rare pre-germinal center B cell population. In the human gut, we resolved fine immune cell populations in lymphoid follicles. Collectively, our results present сell2location as a versatile analysis tool for mapping tissue architectures in a comprehensive manner.
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Affiliation(s)
| | - Artem Shmatko
- Wellcome Sanger Institute, Hinxton, Cambridge, UK.,Moscow State University, Leninskie Gory, Moscow, Russia
| | - Emma Dann
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | | | - Hamish W King
- Wellcome Sanger Institute, Hinxton, Cambridge, UK.,Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London, UK
| | - Tong Li
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | | | - Artem Lomakin
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK.,European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | | | - Adam Gayoso
- Center for Computational Biology, University of California, Berkeley, Berkeley CA, USA
| | - Mika Sarkin Jain
- Wellcome Sanger Institute, Hinxton, Cambridge, UK.,Theory of Condensed Matter, Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Jun Sung Park
- Wellcome Sanger Institute, Hinxton, Cambridge, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Lauma Ramona
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | | | | | | | - Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK.,European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Louisa James
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London, UK
| | - Oliver Stegle
- Wellcome Sanger Institute, Hinxton, Cambridge, UK. .,European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany. .,Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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10
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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: 213] [Impact Index Per Article: 71.0] [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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11
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Garcia-Alonso L, Handfield LF, Roberts K, Nikolakopoulou K, Fernando RC, Gardner L, Woodhams B, Arutyunyan A, Polanski K, Hoo R, Sancho-Serra C, Li T, Kwakwa K, Tuck E, Lorenzi V, Massalha H, Prete M, Kleshchevnikov V, Tarkowska A, Porter T, Mazzeo CI, van Dongen S, Dabrowska M, Vaskivskyi V, Mahbubani KT, Park JE, Jimenez-Linan M, Campos L, Kiselev VY, Lindskog C, Ayuk P, Prigmore E, Stratton MR, Saeb-Parsy K, Moffett A, Moore L, Bayraktar OA, Teichmann SA, Turco MY, Vento-Tormo R. Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro. Nat Genet 2021; 53:1698-1711. [PMID: 34857954 PMCID: PMC8648563 DOI: 10.1038/s41588-021-00972-2] [Citation(s) in RCA: 173] [Impact Index Per Article: 57.7] [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: 02/13/2021] [Accepted: 10/18/2021] [Indexed: 12/24/2022]
Abstract
The endometrium, the mucosal lining of the uterus, undergoes dynamic changes throughout the menstrual cycle in response to ovarian hormones. We have generated dense single-cell and spatial reference maps of the human uterus and three-dimensional endometrial organoid cultures. We dissect the signaling pathways that determine cell fate of the epithelial lineages in the lumenal and glandular microenvironments. Our benchmark of the endometrial organoids reveals the pathways and cell states regulating differentiation of the secretory and ciliated lineages both in vivo and in vitro. In vitro downregulation of WNT or NOTCH pathways increases the differentiation efficiency along the secretory and ciliated lineages, respectively. We utilize our cellular maps to deconvolute bulk data from endometrial cancers and endometriotic lesions, illuminating the cell types dominating in each of these disorders. These mechanistic insights provide a platform for future development of treatments for common conditions including endometriosis and endometrial carcinoma.
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Affiliation(s)
- Luz Garcia-Alonso
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | | | - Kenny Roberts
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | - Konstantina Nikolakopoulou
- grid.5335.00000000121885934Centre for Trophoblast Research, University of Cambridge, Cambridge, UK ,grid.5335.00000000121885934Department of Pathology, University of Cambridge, Cambridge, UK ,grid.482245.d0000 0001 2110 3787Present Address: Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Ridma C. Fernando
- grid.5335.00000000121885934Centre for Trophoblast Research, University of Cambridge, Cambridge, UK ,grid.5335.00000000121885934Department of Pathology, University of Cambridge, Cambridge, UK ,grid.482245.d0000 0001 2110 3787Present Address: Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Lucy Gardner
- grid.5335.00000000121885934Centre for Trophoblast Research, University of Cambridge, Cambridge, UK ,grid.5335.00000000121885934Department of Pathology, University of Cambridge, Cambridge, UK
| | - Benjamin Woodhams
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Anna Arutyunyan
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Krzysztof Polanski
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | - Regina Hoo
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | | | - Tong Li
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | | | - Elizabeth Tuck
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | - Valentina Lorenzi
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | - Hassan Massalha
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Martin Prete
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | | | | | - Tarryn Porter
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | | | - Stijn van Dongen
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | - Monika Dabrowska
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | - Vasyl Vaskivskyi
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | - Krishnaa T. Mahbubani
- grid.5335.00000000121885934Department of Haematology, University of Cambridge, Cambridge, UK ,grid.454369.9Cambridge Biorepository for Translational Medicine (CBTM), NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Jong-eun Park
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | - Mercedes Jimenez-Linan
- grid.24029.3d0000 0004 0383 8386Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Lia Campos
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | | | - Cecilia Lindskog
- grid.8993.b0000 0004 1936 9457Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Paul Ayuk
- grid.420004.20000 0004 0444 2244Department of Women’s Services, Newcastle-upon-Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Elena Prigmore
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | | | - Kourosh Saeb-Parsy
- grid.454369.9Cambridge Biorepository for Translational Medicine (CBTM), NIHR Cambridge Biomedical Research Centre, Cambridge, UK ,grid.5335.00000000121885934Department of Surgery, University of Cambridge, Cambridge, UK
| | - Ashley Moffett
- grid.5335.00000000121885934Centre for Trophoblast Research, University of Cambridge, Cambridge, UK ,grid.5335.00000000121885934Department of Pathology, University of Cambridge, Cambridge, UK
| | - Luiza Moore
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.24029.3d0000 0004 0383 8386Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Omer A. Bayraktar
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | - Sarah A. Teichmann
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Margherita Y. Turco
- grid.5335.00000000121885934Centre for Trophoblast Research, University of Cambridge, Cambridge, UK ,grid.5335.00000000121885934Department of Pathology, University of Cambridge, Cambridge, UK ,grid.482245.d0000 0001 2110 3787Present Address: Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Roser Vento-Tormo
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
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12
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Bayraktar OA, Bartels T, Holmqvist S, Kleshchevnikov V, Martirosyan A, Polioudakis D, Ben Haim L, Young AMH, Batiuk MY, Prakash K, Brown A, Roberts K, Paredes MF, Kawaguchi R, Stockley JH, Sabeur K, Chang SM, Huang E, Hutchinson P, Ullian EM, Hemberg M, Coppola G, Holt MG, Geschwind DH, Rowitch DH. Astrocyte layers in the mammalian cerebral cortex revealed by a single-cell in situ transcriptomic map. Nat Neurosci 2020; 23:500-509. [PMID: 32203496 PMCID: PMC7116562 DOI: 10.1038/s41593-020-0602-1] [Citation(s) in RCA: 240] [Impact Index Per Article: 60.0] [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: 09/19/2018] [Accepted: 01/28/2020] [Indexed: 11/09/2022]
Abstract
Although the cerebral cortex is organized into six excitatory neuronal layers, it is unclear whether glial cells show distinct layering. In the present study, we developed a high-content pipeline, the large-area spatial transcriptomic (LaST) map, which can quantify single-cell gene expression in situ. Screening 46 candidate genes for astrocyte diversity across the mouse cortex, we identified superficial, mid and deep astrocyte identities in gradient layer patterns that were distinct from those of neurons. Astrocyte layer features, established in the early postnatal cortex, mostly persisted in adult mouse and human cortex. Single-cell RNA sequencing and spatial reconstruction analysis further confirmed the presence of astrocyte layers in the adult cortex. Satb2 and Reeler mutations that shifted neuronal post-mitotic development were sufficient to alter glial layering, indicating an instructive role for neuronal cues. Finally, astrocyte layer patterns diverged between mouse cortical regions. These findings indicate that excitatory neurons and astrocytes are organized into distinct lineage-associated laminae.
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Affiliation(s)
- Omer Ali Bayraktar
- Department of Paediatrics, Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- Departments of Pediatrics and Neurosurgery, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA.
- Wellcome Sanger Institute, Hinxton, UK.
| | - Theresa Bartels
- Department of Paediatrics, Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Staffan Holmqvist
- Department of Paediatrics, Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | | | - Araks Martirosyan
- Laboratory of Glia Biology, VIB-KU Leuven Center for Brain and Disease Research, KU Leuven Department of Neuroscience, Leuven, Belgium
| | - Damon Polioudakis
- Departments of Neurology and Human Genetics, University of California Los Angeles, Los Angeles, CA, USA
- Center for Autism Research and Treatment, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Lucile Ben Haim
- Department of Paediatrics, Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Adam M H Young
- Division of Academic Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Mykhailo Y Batiuk
- Laboratory of Glia Biology, VIB-KU Leuven Center for Brain and Disease Research, KU Leuven Department of Neuroscience, Leuven, Belgium
| | - Kirti Prakash
- Department of Paediatrics, Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Alexander Brown
- Sainsbury Wellcome Centre, University College London, London, UK
| | | | - Mercedes F Paredes
- Departments of Pediatrics and Neurosurgery, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Riki Kawaguchi
- Department of Psychiatry, University of California Los Angeles, Los Angeles, CA, USA
| | - John H Stockley
- Department of Paediatrics, Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Khalida Sabeur
- Department of Paediatrics, Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Departments of Pediatrics and Neurosurgery, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Sandra M Chang
- Department of Paediatrics, Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Departments of Pediatrics and Neurosurgery, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Eric Huang
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Peter Hutchinson
- Division of Academic Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Erik M Ullian
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA, USA
| | | | - Giovanni Coppola
- Departments of Neurology and Human Genetics, University of California Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry, University of California Los Angeles, Los Angeles, CA, USA
| | - Matthew G Holt
- Laboratory of Glia Biology, VIB-KU Leuven Center for Brain and Disease Research, KU Leuven Department of Neuroscience, Leuven, Belgium
| | - Daniel H Geschwind
- Departments of Neurology and Human Genetics, University of California Los Angeles, Los Angeles, CA, USA
- Center for Autism Research and Treatment, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - David H Rowitch
- Department of Paediatrics, Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- Departments of Pediatrics and Neurosurgery, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA.
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13
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Allen F, Crepaldi L, Alsinet C, Strong AJ, Kleshchevnikov V, De Angeli P, Palenikova P, Khodak A, Kiselev V, Kosicki M, Bassett AR, Harding H, Galanty Y, Muñoz-Martínez F, Metzakopian E, Jackson SP, Parts L. Predicting the mutations generated by repair of Cas9-induced double-strand breaks. Nat Biotechnol 2018; 37:nbt.4317. [PMID: 30480667 PMCID: PMC6949135 DOI: 10.1038/nbt.4317] [Citation(s) in RCA: 275] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/12/2018] [Indexed: 12/15/2022]
Abstract
The DNA mutation produced by cellular repair of a CRISPR-Cas9-generated double-strand break determines its phenotypic effect. It is known that the mutational outcomes are not random, but depend on DNA sequence at the targeted location. Here we systematically study the influence of flanking DNA sequence on repair outcome by measuring the edits generated by >40,000 guide RNAs (gRNAs) in synthetic constructs. We performed the experiments in a range of genetic backgrounds and using alternative CRISPR-Cas9 reagents. In total, we gathered data for >109 mutational outcomes. The majority of reproducible mutations are insertions of a single base, short deletions or longer microhomology-mediated deletions. Each gRNA has an individual cell-line-dependent bias toward particular outcomes. We uncover sequence determinants of the mutations produced and use these to derive a predictor of Cas9 editing outcomes. Improved understanding of sequence repair will allow better design of gene editing experiments.
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Affiliation(s)
| | | | | | | | | | | | | | - Anton Khodak
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | | | | | | | - Heather Harding
- Cambridge Institute of Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Yaron Galanty
- The Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Francisco Muñoz-Martínez
- The Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Emmanouil Metzakopian
- Wellcome Sanger Institute, Hinxton, United Kingdom
- UK Dementia Research Institute, Cambridge, United Kingdom
| | - Stephen P. Jackson
- The Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Leopold Parts
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Department of Computer Science, University of Tartu, Tartu, Estonia
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