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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Asowata EO, Romoli S, Sargeant R, Tan JY, Hoffmann S, Huang MM, Mahbubani KT, Krause FN, Jachimowicz D, Agren R, Koulman A, Jenkins B, Musial B, Griffin JL, Soderberg M, Ling S, Hansen PBL, Saeb-Parsy K, Woollard KJ. Multi-omics and imaging mass cytometry characterization of human kidneys to identify pathways and phenotypes associated with impaired kidney function. Kidney Int 2024:S0085-2538(24)00168-6. [PMID: 38431215 DOI: 10.1016/j.kint.2024.01.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/16/2024] [Accepted: 01/24/2024] [Indexed: 03/05/2024]
Abstract
Despite the recent advances in our understanding of the role of lipids, metabolites, and related enzymes in mediating kidney injury, there is limited integrated multi-omics data identifying potential metabolic pathways driving impaired kidney function. The limited availability of kidney biopsies from living donors with acute kidney injury has remained a major constraint. Here, we validated the use of deceased transplant donor kidneys as a good model to study acute kidney injury in humans and characterized these kidneys using imaging and multi-omics approaches. We noted consistent changes in kidney injury and inflammatory markers in donors with reduced kidney function. Neighborhood and correlation analyses of imaging mass cytometry data showed that subsets of kidney cells (proximal tubular cells and fibroblasts) are associated with the expression profile of kidney immune cells, potentially linking these cells to kidney inflammation. Integrated transcriptomic and metabolomic analysis of human kidneys showed that kidney arachidonic acid metabolism and seven other metabolic pathways were upregulated following diminished kidney function. To validate the arachidonic acid pathway in impaired kidney function we demonstrated increased levels of cytosolic phospholipase A2 protein and related lipid mediators (prostaglandin E2) in the injured kidneys. Further, inhibition of cytosolic phospholipase A2 reduced injury and inflammation in human kidney proximal tubular epithelial cells in vitro. Thus, our study identified cell types and metabolic pathways that may be critical for controlling inflammation associated with impaired kidney function in humans.
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Affiliation(s)
- Evans O Asowata
- Bioscience Renal, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom; Department of Surgery, University of Cambridge and NIHR Biomedical Research Centre, Cambridge, United Kingdom
| | - Simone Romoli
- Bioscience Renal, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Rebecca Sargeant
- Imaging and Data Analytics, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
| | - Jennifer Y Tan
- Imaging and Data Analytics, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
| | - Scott Hoffmann
- Imaging and Data Analytics, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
| | - Margaret M Huang
- Department of Surgery, University of Cambridge and NIHR Biomedical Research Centre, Cambridge, United Kingdom
| | - Krishnaa T Mahbubani
- Department of Surgery, University of Cambridge and NIHR Biomedical Research Centre, Cambridge, United Kingdom
| | - Fynn N Krause
- Bioscience Renal, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom; Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Daniel Jachimowicz
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Rasmus Agren
- Translational Science and Experimental Medicine, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Albert Koulman
- NIHR BRC Core Metabolomics and Lipidomics Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Benjamin Jenkins
- NIHR BRC Core Metabolomics and Lipidomics Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Barbara Musial
- Bioscience Renal, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Julian L Griffin
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Magnus Soderberg
- Department of Pathology, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Stephanie Ling
- Imaging and Data Analytics, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
| | - Pernille B L Hansen
- Bioscience Renal, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge and NIHR Biomedical Research Centre, Cambridge, United Kingdom.
| | - Kevin J Woollard
- Bioscience Renal, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom.
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3
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Jones RE, Gruszczyk AV, Schmidt C, Hammersley DJ, Mach L, Lee M, Wong J, Yang M, Hatipoglu S, Lota AS, Barnett SN, Toscano-Rivalta R, Owen R, Raja S, De Robertis F, Smail H, De-Souza A, Stock U, Kellman P, Griffin J, Dumas ME, Martin JL, Saeb-Parsy K, Vazir A, Cleland JGF, Pennell DJ, Bhudia SK, Halliday BP, Noseda M, Frezza C, Murphy MP, Prasad SK. Assessment of left ventricular tissue mitochondrial bioenergetics in patients with stable coronary artery disease. Nat Cardiovasc Res 2023; 2:733-745. [PMID: 38666037 PMCID: PMC11041759 DOI: 10.1038/s44161-023-00312-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 06/29/2023] [Indexed: 04/28/2024]
Abstract
Recurrent myocardial ischemia can lead to left ventricular (LV) dysfunction in patients with coronary artery disease (CAD). In this observational cohort study, we assessed for chronic metabolomic and transcriptomic adaptations within LV myocardium of patients undergoing coronary artery bypass grafting. During surgery, paired transmural LV biopsies were acquired on the beating heart from regions with and without evidence of inducible ischemia on preoperative stress perfusion cardiovascular magnetic resonance. From 33 patients, 63 biopsies were acquired, compared to analysis of LV samples from 11 donor hearts. The global myocardial adenosine triphosphate (ATP):adenosine diphosphate (ADP) ratio was reduced in patients with CAD as compared to donor LV tissue, with increased expression of oxidative phosphorylation (OXPHOS) genes encoding the electron transport chain complexes across multiple cell types. Paired analyses of biopsies obtained from LV segments with or without inducible ischemia revealed no significant difference in the ATP:ADP ratio, broader metabolic profile or expression of ventricular cardiomyocyte genes implicated in OXPHOS. Differential metabolite analysis suggested dysregulation of several intermediates in patients with reduced LV ejection fraction, including succinate. Overall, our results suggest that viable myocardium in patients with stable CAD has global alterations in bioenergetic and transcriptional profile without large regional differences between areas with or without inducible ischemia.
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Affiliation(s)
- Richard E. Jones
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
- Anglia Ruskin University, Chelmsford, UK
- Essex Cardiothoracic Centre, Basildon, UK
| | - Anja V. Gruszczyk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | | | - Daniel J. Hammersley
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | - Lukas Mach
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | - Michael Lee
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Joyce Wong
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | - Ming Yang
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
- University of Cologne, CECAD, Cologne, Germany
| | - Suzan Hatipoglu
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | - Amrit S. Lota
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | - Sam N. Barnett
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Ruth Owen
- Department of Medical Statistics, London School of Hygiene and Tropical Medicine, London, UK
| | - Shahzad Raja
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | - Fabio De Robertis
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | - Hassiba Smail
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | - Anthony De-Souza
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | - Ulrich Stock
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | - Peter Kellman
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD USA
| | - Julian Griffin
- The Rowett Institute, University of Aberdeen, Aberdeen, UK
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Marc-Emmanuel Dumas
- National Heart and Lung Institute, Imperial College London, London, UK
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- European Genomic Institute of Diabetes, INSERM U1283, CNRS 8199, Institut Pasteur de Lille, Lille University Hospital, University of Lille, Lille, France
- McGill Genome Centre, McGill University, Montréal, QC Canada
| | - Jack L. Martin
- Department of Surgery and Cambridge NIHR Biomedical Research Centre, Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery and Cambridge NIHR Biomedical Research Centre, Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Ali Vazir
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | | | - Dudley J. Pennell
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | - Sunil K. Bhudia
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | - Brian P. Halliday
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | - Michela Noseda
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Michael P. Murphy
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Sanjay K. Prasad
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
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4
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Kanemaru K, Cranley J, Muraro D, Miranda AMA, Ho SY, Wilbrey-Clark A, Patrick Pett J, Polanski K, Richardson L, Litvinukova M, Kumasaka N, Qin Y, Jablonska Z, Semprich CI, Mach L, Dabrowska M, Richoz N, Bolt L, Mamanova L, Kapuge R, Barnett SN, Perera S, Talavera-López C, Mulas I, Mahbubani KT, Tuck L, Wang L, Huang MM, Prete M, Pritchard S, Dark J, Saeb-Parsy K, Patel M, Clatworthy MR, Hübner N, Chowdhury RA, Noseda M, Teichmann SA. Spatially resolved multiomics of human cardiac niches. Nature 2023; 619:801-810. [PMID: 37438528 PMCID: PMC10371870 DOI: 10.1038/s41586-023-06311-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 06/12/2023] [Indexed: 07/14/2023]
Abstract
The function of a cell is defined by its intrinsic characteristics and its niche: the tissue microenvironment in which it dwells. Here we combine single-cell and spatial transcriptomics data to discover cellular niches within eight regions of the human heart. We map cells to microanatomical locations and integrate knowledge-based and unsupervised structural annotations. We also profile the cells of the human cardiac conduction system1. The results revealed their distinctive repertoire of ion channels, G-protein-coupled receptors (GPCRs) and regulatory networks, and implicated FOXP2 in the pacemaker phenotype. We show that the sinoatrial node is compartmentalized, with a core of pacemaker cells, fibroblasts and glial cells supporting glutamatergic signalling. Using a custom CellPhoneDB.org module, we identify trans-synaptic pacemaker cell interactions with glia. We introduce a druggable target prediction tool, drug2cell, which leverages single-cell profiles and drug-target interactions to provide mechanistic insights into the chronotropic effects of drugs, including GLP-1 analogues. In the epicardium, we show enrichment of both IgG+ and IgA+ plasma cells forming immune niches that may contribute to infection defence. Overall, we provide new clarity to cardiac electro-anatomy and immunology, and our suite of computational approaches can be applied to other tissues and organs.
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Affiliation(s)
- Kazumasa Kanemaru
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - James Cranley
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Daniele Muraro
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Siew Yen Ho
- Cardiac Morphology Unit, Royal Brompton Hospital and Imperial College London, London, UK
| | - Anna Wilbrey-Clark
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Jan Patrick Pett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Krzysztof Polanski
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Laura Richardson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Monika Litvinukova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Natsuhiko Kumasaka
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Yue Qin
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Zuzanna Jablonska
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Claudia I Semprich
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Lukas Mach
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton Hospital, London, UK
| | - Monika Dabrowska
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Nathan Richoz
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Liam Bolt
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Lira Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Rakeshlal Kapuge
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Sam N Barnett
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Shani Perera
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Carlos Talavera-López
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Würzburg Institute for Systems Immunology, Max Planck Research Group, Julius-Maximilian-Universität, Würzburg, Germany
| | - Ilaria Mulas
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Krishnaa T Mahbubani
- Department of Surgery, University of Cambridge, and Cambridge Biorepository for Translational Medicine, NIHR Cambridge Biomedical Centre, Cambridge, UK
| | - Liz Tuck
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Lu Wang
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Margaret M Huang
- Department of Surgery, University of Cambridge, and Cambridge Biorepository for Translational Medicine, NIHR Cambridge Biomedical Centre, Cambridge, UK
| | - Martin Prete
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Sophie Pritchard
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - John Dark
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, and Cambridge Biorepository for Translational Medicine, NIHR Cambridge Biomedical Centre, Cambridge, UK
| | - Minal Patel
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Menna R Clatworthy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Norbert Hübner
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité-Universitätsmedizin, Berlin, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
| | | | - Michela Noseda
- National Heart and Lung Institute, Imperial College London, London, UK.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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5
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Stewart BJ, Fergie M, Young MD, Jones C, Sachdeva A, Blain A, Bacon CM, Rand V, Ferdinand JR, James KR, Mahbubani KT, Hook L, Jonas N, Coleman N, Saeb-Parsy K, Collin M, Clatworthy MR, Behjati S, Carey CD. Spatial and molecular profiling of the mononuclear phagocyte network in classic Hodgkin lymphoma. Blood 2023; 141:2343-2358. [PMID: 36758207 DOI: 10.1182/blood.2022015575] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 03/04/2022] [Revised: 12/14/2022] [Accepted: 01/02/2023] [Indexed: 02/11/2023] Open
Abstract
Classic Hodgkin lymphoma (cHL) has a rich immune infiltrate, which is an intrinsic component of the neoplastic process. Malignant Hodgkin Reed-Sternberg cells (HRSCs) create an immunosuppressive microenvironment by the expression of regulatory molecules, preventing T-cell activation. It has also been demonstrated that mononuclear phagocytes (MNPs) in the vicinity of HRSCs express similar regulatory mechanisms in parallel, and their presence in tissue is associated with inferior patient outcomes. MNPs in cHL have hitherto been identified by a small number of canonical markers and are usually described as tumor-associated macrophages. The organization of MNP networks and interactions with HRSCs remains unexplored at high resolution. Here, we defined the global immune-cell composition of cHL and nonlymphoma lymph nodes, integrating data across single-cell RNA sequencing, spatial transcriptomics, and multiplexed immunofluorescence. We observed that MNPs comprise multiple subsets of monocytes, macrophages, and dendritic cells (DCs). Classical monocytes, macrophages and conventional DC2s were enriched in the vicinity of HRSCs, but plasmacytoid DCs and activated DCs were excluded. Unexpectedly, cDCs and monocytes expressed immunoregulatory checkpoints PD-L1, TIM-3, and the tryptophan-catabolizing protein IDO, at the same level as macrophages. Expression of these molecules increased with age. We also found that classical monocytes are important signaling hubs, potentially controlling the retention of cDC2 and ThExh via CCR1-, CCR4-, CCR5-, and CXCR3-dependent signaling. Enrichment of the cDC2-monocyte-macrophage network in diagnostic biopsies is associated with early treatment failure. These results reveal unanticipated complexity and spatial polarization within the MNP compartment, further demonstrating their potential roles in immune evasion by cHL.
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Affiliation(s)
- Benjamin J Stewart
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Martin Fergie
- Division of Informatics, Imaging and Data Sciences, University of Manchester, Manchester, United Kingdom
| | - Matthew D Young
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Claire Jones
- Newcastle upon Tyne NHS Hospitals Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Ashwin Sachdeva
- Genito-urinary Cancer Research Group, Division of Cancer Sciences, Oglesby Cancer Research Building, University of Manchester, Manchester, United Kingdom
- Department of Surgery, The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Alex Blain
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- School of Health and Life Sciences, Teesside University, Middlesbrough, United Kingdom
- National Horizons Centre, Teesside University, Darlington, United Kingdom
| | - Chris M Bacon
- Newcastle upon Tyne NHS Hospitals Foundation Trust, Newcastle upon Tyne, United Kingdom
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Vikki Rand
- School of Health and Life Sciences, Teesside University, Middlesbrough, United Kingdom
- National Horizons Centre, Teesside University, Darlington, United Kingdom
| | - John R Ferdinand
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Kylie R James
- Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW, Australia
| | - Krishnaa T Mahbubani
- Department of Surgery, University of Cambridge, NIHR Cambridge Biomedical Research Centre, Cambridge Biorepository for Translational Medicine, Cambridge, United Kingdom
| | - Liz Hook
- Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Nicolaas Jonas
- Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Nicholas Coleman
- Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, NIHR Cambridge Biomedical Research Centre, Cambridge Biorepository for Translational Medicine, Cambridge, United Kingdom
| | - Matthew Collin
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Menna R Clatworthy
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Sam Behjati
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
- Department of Paediatrics, University of Cambridge, Cambridge, United Kingdom
| | - Christopher D Carey
- Newcastle upon Tyne NHS Hospitals Foundation Trust, Newcastle upon Tyne, United Kingdom
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
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6
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Inaba A, Tuong ZK, Zhao TX, Stewart AP, Mathews R, Truman L, Sriranjan R, Kennet J, Saeb-Parsy K, Wicker L, Waldron-Lynch F, Cheriyan J, Todd JA, Mallat Z, Clatworthy MR. Low-dose IL-2 enhances the generation of IL-10-producing immunoregulatory B cells. Nat Commun 2023; 14:2071. [PMID: 37045832 PMCID: PMC10097719 DOI: 10.1038/s41467-023-37424-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 03/16/2023] [Indexed: 04/14/2023] Open
Abstract
Dysfunction of interleukin-10 producing regulatory B cells has been associated with the pathogenesis of autoimmune diseases, but whether regulatory B cells can be therapeutically induced in humans is currently unknown. Here we demonstrate that a subset of activated B cells expresses CD25, and the addition of low-dose recombinant IL-2 to in vitro stimulated peripheral blood and splenic human B cells augments IL-10 secretion. Administration of low dose IL-2, aldesleukin, to patients increases IL-10-producing B cells. Single-cell RNA sequencing of circulating immune cells isolated from low dose IL2-treated patients reveals an increase in plasmablast and plasma cell populations that are enriched for a regulatory B cell gene signature. The transcriptional repressor BACH2 is significantly down-regulated in plasma cells from IL-2-treated patients, BACH2 binds to the IL-10 gene promoter, and Bach2 depletion or genetic deficiency increases B cell IL-10, implicating BACH2 suppression as an important mechanism by which IL-2 may promote an immunoregulatory phenotype in B cells.
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Affiliation(s)
- Akimichi Inaba
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Zewen Kelvin Tuong
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
- Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Tian X Zhao
- Department of Medicine, Division of Cardiovascular Medicine, University of Cambridge, Cambridge, UK
| | - Andrew P Stewart
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Rebeccah Mathews
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Lucy Truman
- Ear, Nose Throat Department, West Suffolk Hospital, Bury St Edmunds, UK
| | - Rouchelle Sriranjan
- Division of Experimental Medicine and Immunotherapeutics, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Jane Kennet
- Wellcome-MRC Institute of Metabolic Science-Metabolic Research Laboratories and Medical Research Council Metabolic Diseases Unit, University of Cambridge, Cambridge, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, Cambridge, UK
- National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, UK
| | - Linda Wicker
- Medical Sciences Division, University of Oxford, Oxford, UK
| | - Frank Waldron-Lynch
- Novartis Institutes for BioMedical Research, Autoimmunity Transplantation Inflammation, Basel, Switzerland
| | - Joseph Cheriyan
- Division of Experimental Medicine and Immunotherapeutics, Department of Medicine, University of Cambridge, Cambridge, UK
| | - John A Todd
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ziad Mallat
- Department of Medicine, Division of Cardiovascular Medicine, University of Cambridge, Cambridge, UK
- Universite de Paris and INSERM, Paris, France
| | - Menna R Clatworthy
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK.
- Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK.
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7
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Brevini T, Maes M, Webb GJ, John BV, Fuchs CD, Buescher G, Wang L, Griffiths C, Brown ML, Scott WE, Pereyra-Gerber P, Gelson WTH, Brown S, Dillon S, Muraro D, Sharp J, Neary M, Box H, Tatham L, Stewart J, Curley P, Pertinez H, Forrest S, Mlcochova P, Varankar SS, Darvish-Damavandi M, Mulcahy VL, Kuc RE, Williams TL, Heslop JA, Rossetti D, Tysoe OC, Galanakis V, Vila-Gonzalez M, Crozier TWM, Bargehr J, Sinha S, Upponi SS, Fear C, Swift L, Saeb-Parsy K, Davies SE, Wester A, Hagström H, Melum E, Clements D, Humphreys P, Herriott J, Kijak E, Cox H, Bramwell C, Valentijn A, Illingworth CJR, Dahman B, Bastaich DR, Ferreira RD, Marjot T, Barnes E, Moon AM, Barritt AS, Gupta RK, Baker S, Davenport AP, Corbett G, Gorgoulis VG, Buczacki SJA, Lee JH, Matheson NJ, Trauner M, Fisher AJ, Gibbs P, Butler AJ, Watson CJE, Mells GF, Dougan G, Owen A, Lohse AW, Vallier L, Sampaziotis F. FXR inhibition may protect from SARS-CoV-2 infection by reducing ACE2. Nature 2023; 615:134-142. [PMID: 36470304 PMCID: PMC9977684 DOI: 10.1038/s41586-022-05594-0] [Citation(s) in RCA: 93] [Impact Index Per Article: 93.0] [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: 05/03/2021] [Accepted: 11/23/2022] [Indexed: 12/12/2022]
Abstract
Preventing SARS-CoV-2 infection by modulating viral host receptors, such as angiotensin-converting enzyme 2 (ACE2)1, could represent a new chemoprophylactic approach for COVID-19 that complements vaccination2,3. However, the mechanisms that control the expression of ACE2 remain unclear. Here we show that the farnesoid X receptor (FXR) is a direct regulator of ACE2 transcription in several tissues affected by COVID-19, including the gastrointestinal and respiratory systems. We then use the over-the-counter compound z-guggulsterone and the off-patent drug ursodeoxycholic acid (UDCA) to reduce FXR signalling and downregulate ACE2 in human lung, cholangiocyte and intestinal organoids and in the corresponding tissues in mice and hamsters. We show that the UDCA-mediated downregulation of ACE2 reduces susceptibility to SARS-CoV-2 infection in vitro, in vivo and in human lungs and livers perfused ex situ. Furthermore, we reveal that UDCA reduces the expression of ACE2 in the nasal epithelium in humans. Finally, we identify a correlation between UDCA treatment and positive clinical outcomes after SARS-CoV-2 infection using retrospective registry data, and confirm these findings in an independent validation cohort of recipients of liver transplants. In conclusion, we show that FXR has a role in controlling ACE2 expression and provide evidence that modulation of this pathway could be beneficial for reducing SARS-CoV-2 infection, paving the way for future clinical trials.
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Affiliation(s)
- Teresa Brevini
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK.
| | - Mailis Maes
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Gwilym J Webb
- Cambridge Liver Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Binu V John
- Division of Gastroenterology and Hepatology, University of Miami and Miami VA Health System, Miami, FL, USA
| | - Claudia D Fuchs
- Hans Popper Laboratory of Molecular Hepatology, Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Gustav Buescher
- Department of Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Lu Wang
- Transplant and Regenerative Medicine Laboratory, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Chelsea Griffiths
- Transplant and Regenerative Medicine Laboratory, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Marnie L Brown
- Transplant and Regenerative Medicine Laboratory, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - William E Scott
- Transplant and Regenerative Medicine Laboratory, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Pehuén Pereyra-Gerber
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - William T H Gelson
- Cambridge Liver Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | - Scott Dillon
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK
| | | | - Jo Sharp
- Centre of Excellence in Long-acting Therapeutics (CELT), Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Megan Neary
- Centre of Excellence in Long-acting Therapeutics (CELT), Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Helen Box
- Centre of Excellence in Long-acting Therapeutics (CELT), Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Lee Tatham
- Centre of Excellence in Long-acting Therapeutics (CELT), Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - James Stewart
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Paul Curley
- Centre of Excellence in Long-acting Therapeutics (CELT), Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Henry Pertinez
- Centre of Excellence in Long-acting Therapeutics (CELT), Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Sally Forrest
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Petra Mlcochova
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
- Division of Gastroenterology and Hepatology, University of Miami and Miami VA Health System, Miami, FL, USA
| | | | - Mahnaz Darvish-Damavandi
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Victoria L Mulcahy
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Rhoda E Kuc
- Experimental Medicine and Immunotherapeutics, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Thomas L Williams
- Experimental Medicine and Immunotherapeutics, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - James A Heslop
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK
| | | | - Olivia C Tysoe
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | | | | | - Thomas W M Crozier
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Johannes Bargehr
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Division of Cardiovascular Medicine, University of Cambridge, Cambridge, UK
| | - Sanjay Sinha
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Division of Cardiovascular Medicine, University of Cambridge, Cambridge, UK
| | - Sara S Upponi
- Department of Radiology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Corrina Fear
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Lisa Swift
- 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
- Roy Calne Transplant Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Susan E Davies
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Axel Wester
- Department of Medicine, Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Hannes Hagström
- Department of Medicine, Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Espen Melum
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Hybrid Technology Hub Centre of Excellence, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | | | - Jo Herriott
- Centre of Excellence in Long-acting Therapeutics (CELT), Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Edyta Kijak
- Centre of Excellence in Long-acting Therapeutics (CELT), Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Helen Cox
- Centre of Excellence in Long-acting Therapeutics (CELT), Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Chloe Bramwell
- Centre of Excellence in Long-acting Therapeutics (CELT), Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Anthony Valentijn
- Centre of Excellence in Long-acting Therapeutics (CELT), Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Christopher J R Illingworth
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
| | - Bassam Dahman
- Department of Health Behavior and Policy, Virginia Commonwealth University, Richmond, VA, USA
| | - Dustin R Bastaich
- Department of Health Behavior and Policy, Virginia Commonwealth University, Richmond, VA, USA
| | - Raphaella D Ferreira
- Division of Gastroenterology and Hepatology, University of Miami and Miami VA Health System, Miami, FL, USA
| | - Thomas Marjot
- Oxford Liver Unit, Translational Gastroenterology Unit, Oxford University Hospitals NHS Foundation Trust, University of Oxford, Oxford, UK
| | - Eleanor Barnes
- Oxford Liver Unit, Translational Gastroenterology Unit, Oxford University Hospitals NHS Foundation Trust, University of Oxford, Oxford, UK
| | - Andrew M Moon
- Division of Gastroenterology and Hepatology, University of North Carolina, Chapel Hill, NC, USA
| | - Alfred S Barritt
- Division of Gastroenterology and Hepatology, University of North Carolina, Chapel Hill, NC, USA
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Anthony P Davenport
- Experimental Medicine and Immunotherapeutics, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Gareth Corbett
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Vassilis G Gorgoulis
- Department of Histology and Embryology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
- Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
- Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Simon J A Buczacki
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Joo-Hyeon Lee
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Nicholas J Matheson
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Division of Gastroenterology and Hepatology, University of North Carolina, Chapel Hill, NC, USA
- NHS Blood and Transplant, Cambridge, UK
| | - Michael Trauner
- Hans Popper Laboratory of Molecular Hepatology, Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Andrew J Fisher
- Transplant and Regenerative Medicine Laboratory, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Paul Gibbs
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Roy Calne Transplant Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Andrew J Butler
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Roy Calne Transplant Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Christopher J E Watson
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Roy Calne Transplant Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- National Institute of Health Research (NIHR) Cambridge Biomedical Research Centre, and the NIHR Blood and Transplant Research Unit (BTRU) at the University of Cambridge in collaboration with Newcastle University and in partnership with NHS Blood and Transplant (NHSBT), Cambridge, UK
| | - George F Mells
- Cambridge Liver Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Andrew Owen
- Centre of Excellence in Long-acting Therapeutics (CELT), Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Ansgar W Lohse
- Department of Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Ludovic Vallier
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK.
- Wellcome Sanger Institute, Hinxton, UK.
- Berlin Institute of Health (BIH), BIH Centre for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Berlin, Germany.
- Max Planck Institute for Molecular Genetics, Berlin, Germany.
| | - Fotios Sampaziotis
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK.
- Cambridge Liver Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Medicine, University of Cambridge, Cambridge, UK.
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8
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Wang Y, Robinson PS, Coorens THH, Moore L, Lee-Six H, Noorani A, Sanders MA, Jung H, Katainen R, Heuschkel R, Brunton-Sim R, Weston R, Read D, Nobbs B, Fitzgerald RC, Saeb-Parsy K, Martincorena I, Campbell PJ, Rushbrook S, Zilbauer M, Buczacki SJA, Stratton MR. APOBEC mutagenesis is a common process in normal human small intestine. Nat Genet 2023; 55:246-254. [PMID: 36702998 PMCID: PMC9925384 DOI: 10.1038/s41588-022-01296-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [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: 05/08/2022] [Accepted: 12/16/2022] [Indexed: 01/27/2023]
Abstract
APOBEC mutational signatures SBS2 and SBS13 are common in many human cancer types. However, there is an incomplete understanding of its stimulus, when it occurs in the progression from normal to cancer cell and the APOBEC enzymes responsible. Here we whole-genome sequenced 342 microdissected normal epithelial crypts from the small intestines of 39 individuals and found that SBS2/SBS13 mutations were present in 17% of crypts, more frequent than most other normal tissues. Crypts with SBS2/SBS13 often had immediate crypt neighbors without SBS2/SBS13, suggesting that the underlying cause of SBS2/SBS13 is cell-intrinsic. APOBEC mutagenesis occurred in an episodic manner throughout the human lifespan, including in young children. APOBEC1 mRNA levels were very high in the small intestine epithelium, but low in the large intestine epithelium and other tissues. The results suggest that the high levels of SBS2/SBS13 in the small intestine are collateral damage from APOBEC1 fulfilling its physiological function of editing APOB mRNA.
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Affiliation(s)
- Yichen Wang
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK
| | - Philip S Robinson
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Tim H H Coorens
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Luiza Moore
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK
- Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Henry Lee-Six
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK
| | - Ayesha Noorani
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK
| | - Mathijs A Sanders
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK
| | - Hyunchul Jung
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK
| | - Riku Katainen
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Robert Heuschkel
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Addenbrooke's Hospital, Cambridge, UK
| | | | - Robyn Weston
- NIHR Clinical Research Network-East of England, Addenbrooke's Hospital, Cambridge, UK
| | - Debbie Read
- NIHR Clinical Research Network-East of England, Addenbrooke's Hospital, Cambridge, UK
| | - Beverley Nobbs
- NIHR Clinical Research Network-East of England, Addenbrooke's Hospital, Cambridge, UK
| | - Rebecca C Fitzgerald
- The Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery and Cambridge NIHR Biomedical Research Centre, Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Iñigo Martincorena
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK
| | - Peter J Campbell
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK
| | - Simon Rushbrook
- Norfolk and Norwich University Hospital, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Matthias Zilbauer
- Department of Paediatrics, University of Cambridge, Cambridge, UK
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Addenbrooke's Hospital, Cambridge, UK
| | | | - Michael R Stratton
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK.
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9
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Justin AW, Cammarata F, Guy AA, Estevez SR, Burgess S, Davaapil H, Stavropoulou-Tatla A, Ong J, Jacob AG, Saeb-Parsy K, Sinha S, Markaki AE. Densified collagen tubular grafts for human tissue replacement and disease modelling applications. Biomater Adv 2023; 145:213245. [PMID: 36549149 DOI: 10.1016/j.bioadv.2022.213245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022]
Abstract
There is a significant need across multiple indications for an off-the-shelf bioengineered tubular graft which fulfils the mechanical and biological requirements for implantation and function but does not necessarily require cells for manufacture or deployment. Herein, we present a tissue-like tubular construct using a cell-free, materials-based method of manufacture, utilizing densified collagen hydrogel. Our tubular grafts are seamless, mechanically strong, customizable in terms of lumen diameter and wall thickness, and display a uniform fibril density across the wall thickness and along the tube length. While the method enables acellular grafts to be generated rapidly, inexpensively, and to a wide range of specifications, the cell-compatible densification process also enables a high density of cells to be incorporated uniformly into the walls of the tubes, which we show can be maintained under perfusion culture. Additionally, the method enables tubes consisting of distinct cell domains with cellular configurations at the boundaries which may be useful for modelling aortic disease. Further, we demonstrate additional steps which allow for luminal surface patterning. These results highlight the universality of this approach and its potential for developing the next generation of bioengineered grafts.
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Affiliation(s)
- Alexander W Justin
- Department of Engineering, University of Cambridge, Trumpington Street, Cambridge CB2 1PZ, UK.
| | - Federico Cammarata
- Department of Engineering, University of Cambridge, Trumpington Street, Cambridge CB2 1PZ, UK
| | - Andrew A Guy
- Department of Engineering, University of Cambridge, Trumpington Street, Cambridge CB2 1PZ, UK
| | - Silas R Estevez
- Department of Engineering, University of Cambridge, Trumpington Street, Cambridge CB2 1PZ, UK
| | - Sebastian Burgess
- Department of Engineering, University of Cambridge, Trumpington Street, Cambridge CB2 1PZ, UK
| | - Hongorzul Davaapil
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, Division of Cardiovascular Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | | | - John Ong
- Department of Engineering, University of Cambridge, Trumpington Street, Cambridge CB2 1PZ, UK; East of England Gastroenterology Speciality Training Program, Cambridge, UK
| | - Aishwarya G Jacob
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Biochemistry, University of Cambridge, Downing Site, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Sanjay Sinha
- Department of Medicine, Division of Cardiovascular Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Athina E Markaki
- Department of Engineering, University of Cambridge, Trumpington Street, Cambridge CB2 1PZ, UK.
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10
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Albert C, Harris M, DiRito J, Shi A, Edwards C, Harkins L, Lysyy T, Kulkarni S, Mulligan DC, Hosgood SA, Watson CJE, Friend PJ, Nicholson ML, Haakinson D, Saeb-Parsy K, Tietjen GT. Honoring the gift: The transformative potential of transplant-declined human organs. Am J Transplant 2023; 23:165-170. [PMID: 36695696 DOI: 10.1016/j.ajt.2022.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/24/2022] [Accepted: 11/13/2022] [Indexed: 01/09/2023]
Abstract
For decades, transplantation has been a life-saving treatment for those fortunate enough to gain access. Nevertheless, many patients die waiting for an organ and countless more never make it onto the waitlist because of a shortage of donor organs. Concurrently, thousands of donated organs are declined for transplant each year because of concerns about poor outcomes post-transplant. The decline of any donated organ-even if medically justified-is tragic for both the donor family and potential recipients. In this Personal Viewpoint, we discuss the need for a new mindset in how we honor the gift of organ donation. We believe that the use of transplant-declined human organs in translational research has the potential to hasten breakthrough discoveries in a multitude of scientific and medical areas. More importantly, such breakthroughs will allow us to properly value every donated organ. We further discuss the many practical challenges that such research presents and offer some possible solutions based on experiences in our own research laboratories. Finally, we share our perspective on what we believe are the necessary next steps to ensure a future where every donated organ realizes its full potential to impact the lives of current and future patients.
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Affiliation(s)
- Claire Albert
- Yale University, Department of Biomedical Engineering, New Haven, Connecticut, USA
| | - Matthew Harris
- Yale School of Medicine, Department of Surgery, New Haven, Connecticut, USA
| | - Jenna DiRito
- Yale School of Medicine, Department of Surgery, New Haven, Connecticut, USA
| | - Audrey Shi
- Yale School of Medicine, Department of Surgery, New Haven, Connecticut, USA
| | | | - Lauren Harkins
- Yale University, Department of Biomedical Engineering, New Haven, Connecticut, USA
| | - Taras Lysyy
- Yale School of Medicine, Department of Surgery, New Haven, Connecticut, USA
| | - Sanjay Kulkarni
- Yale School of Medicine, Department of Surgery, New Haven, Connecticut, USA
| | - David C Mulligan
- Yale School of Medicine, Department of Surgery, New Haven, Connecticut, USA
| | - Sarah A Hosgood
- Department of Surgery, University of Cambridge, and Cambridge NIHR Biomedical Research Centre, Cambridge, UK
| | - Christopher J E Watson
- Department of Surgery, University of Cambridge, and Cambridge NIHR Biomedical Research Centre, Cambridge, UK
| | - Peter J Friend
- University of Oxford, Nuffield Department of Surgical Sciences and the Oxford Transplant Centre, Oxford, UK
| | - Michael L Nicholson
- Department of Surgery, University of Cambridge, and Cambridge NIHR Biomedical Research Centre, Cambridge, UK
| | - Danielle Haakinson
- Yale School of Medicine, Department of Surgery, New Haven, Connecticut, USA
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, and Cambridge NIHR Biomedical Research Centre, Cambridge, UK.
| | - Gregory T Tietjen
- Yale University, Department of Biomedical Engineering, New Haven, Connecticut, USA; Yale School of Medicine, Department of Surgery, New Haven, Connecticut, USA.
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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. 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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12
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Simon T, Kirk J, Dolezalova N, Guyot M, Panzolini C, Bondue A, Lavergne J, Hugues S, Hypolite N, Saeb-Parsy K, Perkins J, Macia E, Sridhar A, Vervoordeldonk MJ, Glaichenhaus N, Donegá M, Blancou P. The cholinergic anti-inflammatory pathway inhibits inflammation without lymphocyte relay. Front Neurosci 2023; 17:1125492. [PMID: 37123375 PMCID: PMC10140439 DOI: 10.3389/fnins.2023.1125492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/20/2023] [Indexed: 05/02/2023] Open
Abstract
The magnitude of innate inflammatory immune responses is dependent on interactions between peripheral neural and immune cells. In particular, a cholinergic anti-inflammatory pathway (CAP) has been identified in the spleen whereby noradrenaline (NA) released by splenic nerves binds to ß2-adrenergic receptors (β2-AR) on CD4+ T cells which, in turn, release acetylcholine (ACh). The binding of ACh to α7 acetylcholine receptors (α7-AChR) expressed by splenic macrophages inhibits the production of inflammatory cytokines, including tumor necrosis factor (TNF). However, the role of ACh-secreting CD4+ T-cells in the CAP is still controversial and largely based on the absence of this anti-inflammatory pathway in mice lacking T-cells (nude, FoxN1-/-). Using four conscious, non-lymphopenic transgenic mouse models, we found that, rather than acting on CD4+ T-cells, NA released by splenic nerve terminals acts directly onto β2-AR on splenic myeloid cells to exert this anti-inflammatory effect. We also show that, while larger doses of LPS are needed to trigger CAP in nude mouse strain compared to other strains, TNF production can be inhibited in these animals lacking CD4+ T-cell by stimulating either the vagus or the splenic nerve. We demonstrate that CD4+ T-cells are dispensable for the CAP after antibody-mediated CD4+ T-cell depletion in wild type mice. Furthermore, we found that NA-mediated inhibition of in vitro LPS-induced TNF secretion by human or porcine splenocytes does not require α7-AChR signaling. Altogether our data demonstrate that activation of the CAP by stimulation of vagus or splenic nerves in mice is mainly mediated by direct binding of NA to β2-AR on splenic macrophages, and suggest that the same mechanism is at play in larger species.
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Affiliation(s)
- Thomas Simon
- Université Côte d’Azur, CNRS, Molecular and Cellular Pharmacology Institute, Valbonne, France
| | - Joseph Kirk
- The Royal Veterinary College, Hatfield, United Kingdom
| | - Nikola Dolezalova
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Mélanie Guyot
- Université Côte d’Azur, CNRS, Molecular and Cellular Pharmacology Institute, Valbonne, France
| | | | - Alexandre Bondue
- Université Côte d’Azur, CNRS, Molecular and Cellular Pharmacology Institute, Valbonne, France
| | - Julien Lavergne
- Université Côte d’Azur, CNRS, Molecular and Cellular Pharmacology Institute, Valbonne, France
| | | | - Nicolas Hypolite
- Université Côte d’Azur, CNRS, Molecular and Cellular Pharmacology Institute, Valbonne, France
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Justin Perkins
- Galvani Bioelectronics, Translational Sciences, Stevenage, United Kingdom
| | - Eric Macia
- Université Côte d’Azur, CNRS, Molecular and Cellular Pharmacology Institute, Valbonne, France
| | - Arun Sridhar
- Galvani Bioelectronics, Translational Sciences, Stevenage, United Kingdom
| | | | - Nicolas Glaichenhaus
- Université Côte d’Azur, CNRS, Molecular and Cellular Pharmacology Institute, Valbonne, France
| | - Matteo Donegá
- Galvani Bioelectronics, Translational Sciences, Stevenage, United Kingdom
| | - Philippe Blancou
- Université Côte d’Azur, CNRS, Molecular and Cellular Pharmacology Institute, Valbonne, France
- *Correspondence: Philippe Blancou,
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13
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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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14
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Fulton AJP, Saeb-Parsy K, Basu B. Abstract A074: Developing a novel in vivo model of pancreatic ductal adenocarcinoma using primary tumor samples and humanised mouse models. Cancer Res 2022. [DOI: 10.1158/1538-7445.panca22-a074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Abstract
Pancreatic cancer (PDAC) remains one of the most lethal malignancies due to its late diagnosis and poor response to treatment. Preclinical models reflecting the uniquely complex structure of PDAC cells and the surrounding tumor microenvironment (TME) are required to ensure translational results. PDAC organoids, ex vivo 3D models of primary tumor cells, form an exciting preclinical model that reflects the complexity of PDAC. Tumor organoids co-cultured with stromal and immune cells have been previously explored in vitro but have thus far remained limited in any in vivo capacity. We therefore aimed to establish and characterize in vitro co-cultured PDAC organoids using primary human PDAC tumor samples plus autologous peripheral or splenic lymphocytes. Subsequent preliminary in vivo models have been established by engrafting co-cultured PDAC organoids and PDAC cancer associated fibroblasts into immunocompromised mice. The pilot data assessed retention, growth kinetics and metastatic potential and will subsequently form the foundation for comparable experiments using autologous humanized mouse models. This humanized mouse model, consisting of autologous human malignant, stromal and immune compartments, will add to the existing repertoire of preclinical models by more closely representing the entire tumor volume. In vitro and in vivo data compared to other preclinical models. Additional preliminary therapeutic response data may provide translational value and warrant further evaluation.
Citation Format: Alexander J. P. Fulton, Kourosh Saeb-Parsy, Bristi Basu. Developing a novel in vivo model of pancreatic ductal adenocarcinoma using primary tumor samples and humanised mouse models [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr A074.
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Affiliation(s)
| | | | - Bristi Basu
- 1University of Cambridge, Cambridge, United Kingdom
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15
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Wesley BT, Ross ADB, Muraro D, Miao Z, Saxton S, Tomaz RA, Morell CM, Ridley K, Zacharis ED, Petrus-Reurer S, Kraiczy J, Mahbubani KT, Brown S, Garcia-Bernardo J, Alsinet C, Gaffney D, Horsfall D, Tysoe OC, Botting RA, Stephenson E, Popescu DM, MacParland S, Bader G, McGilvray ID, Ortmann D, Sampaziotis F, Saeb-Parsy K, Haniffa M, Stevens KR, Zilbauer M, Teichmann SA, Vallier L. Single-cell atlas of human liver development reveals pathways directing hepatic cell fates. Nat Cell Biol 2022; 24:1487-1498. [PMID: 36109670 DOI: 10.1038/s41556-022-00989-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [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: 10/13/2020] [Accepted: 07/29/2022] [Indexed: 12/14/2022]
Abstract
The liver has been studied extensively due to the broad number of diseases affecting its vital functions. However, therapeutic advances have been hampered by the lack of knowledge concerning human hepatic development. Here, we addressed this limitation by describing the developmental trajectories of different cell types that make up the human liver at single-cell resolution. These transcriptomic analyses revealed that sequential cell-to-cell interactions direct functional maturation of hepatocytes, with non-parenchymal cells playing essential roles during organogenesis. We utilized this information to derive bipotential hepatoblast organoids and then exploited this model system to validate the importance of signalling pathways in hepatocyte and cholangiocyte specification. Further insights into hepatic maturation also enabled the identification of stage-specific transcription factors to improve the functionality of hepatocyte-like cells generated from human pluripotent stem cells. Thus, our study establishes a platform to investigate the basic mechanisms directing human liver development and to produce cell types for clinical applications.
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Affiliation(s)
- Brandon T Wesley
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Alexander D B Ross
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Daniele Muraro
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Zhichao Miao
- Wellcome Sanger Institute, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
| | - Sarah Saxton
- Departments of Bioengineering and Pathology, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Rute A Tomaz
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Carola M Morell
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Katherine Ridley
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Ekaterini D Zacharis
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Sandra Petrus-Reurer
- Department of Surgery, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Judith Kraiczy
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | | | - Stephanie Brown
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | | | | | | | - Dave Horsfall
- Digital Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Olivia C Tysoe
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Rachel A Botting
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Emily Stephenson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | | | - Gary Bader
- University of Toronto, Toronto, Ontario, Canada
| | - Ian D McGilvray
- Multi-Organ Transplant Program, Toronto General Hospital Research Institute, Toronto, Ontario, Canada
| | - Daniel Ortmann
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Fotios Sampaziotis
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge, 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 Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Kelly R Stevens
- Departments of Bioengineering and Pathology, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Matthias Zilbauer
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Hinxton, UK
- Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Ludovic Vallier
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- Department of Surgery, University of Cambridge, Cambridge, UK.
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16
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Tomaz RA, Zacharis ED, Bachinger F, Wurmser A, Yamamoto D, Petrus-Reurer S, Morell CM, Dziedzicka D, Wesley BT, Geti I, Segeritz CP, de Brito MC, Chhatriwala M, Ortmann D, Saeb-Parsy K, Vallier L. Generation of functional hepatocytes by forward programming with nuclear receptors. eLife 2022; 11:71591. [PMID: 35959725 PMCID: PMC9374437 DOI: 10.7554/elife.71591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Production of large quantities of hepatocytes remains a major challenge for a number of clinical applications in the biomedical field. Directed differentiation of human pluripotent stem cells (hPSCs) into hepatocyte-like cells (HLCs) provides an advantageous solution and a number of protocols have been developed for this purpose. However, these methods usually follow different steps of liver development in vitro, which is time consuming and requires complex culture conditions. In addition, HLCs lack the full repertoire of functionalities characterising primary hepatocytes. Here, we explore the interest of forward programming to generate hepatocytes from hPSCs and to bypass these limitations. This approach relies on the overexpression of three hepatocyte nuclear factors (HNF1A, HNF6, and FOXA3) in combination with different nuclear receptors expressed in the adult liver using the OPTi-OX platform. Forward programming allows for the rapid production of hepatocytes (FoP-Heps) with functional characteristics using a simplified process. We also uncovered that the overexpression of nuclear receptors such as RORc can enhance specific functionalities of FoP-Heps thereby validating its role in lipid/glucose metabolism. Together, our results show that forward programming could offer a versatile alternative to direct differentiation for generating hepatocytes in vitro.
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Affiliation(s)
- Rute A Tomaz
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Ekaterini D Zacharis
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Fabian Bachinger
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Annabelle Wurmser
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Daniel Yamamoto
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Sandra Petrus-Reurer
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Carola M Morell
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Dominika Dziedzicka
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Brandon T Wesley
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Imbisaat Geti
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Charis-Patricia Segeritz
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Miguel C de Brito
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Mariya Chhatriwala
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Daniel Ortmann
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Ludovic Vallier
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
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17
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Machado HE, Mitchell E, Øbro NF, Kübler K, Davies M, Leongamornlert D, Cull A, Maura F, Sanders MA, Cagan ATJ, McDonald C, Belmonte M, Shepherd MS, Vieira Braga FA, Osborne RJ, Mahbubani K, Martincorena I, Laurenti E, Green AR, Getz G, Polak P, Saeb-Parsy K, Hodson DJ, Kent DG, Campbell PJ. Diverse mutational landscapes in human lymphocytes. Nature 2022; 608:724-732. [PMID: 35948631 PMCID: PMC9402440 DOI: 10.1038/s41586-022-05072-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [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: 07/20/2021] [Accepted: 07/05/2022] [Indexed: 11/25/2022]
Abstract
The lymphocyte genome is prone to many threats, including programmed mutation during differentiation1, antigen-driven proliferation and residency in diverse microenvironments. Here, after developing protocols for expansion of single-cell lymphocyte cultures, we sequenced whole genomes from 717 normal naive and memory B and T cells and haematopoietic stem cells. All lymphocyte subsets carried more point mutations and structural variants than haematopoietic stem cells, with higher burdens in memory cells than in naive cells, and with T cells accumulating mutations at a higher rate throughout life. Off-target effects of immunological diversification accounted for approximately half of the additional differentiation-associated mutations in lymphocytes. Memory B cells acquired, on average, 18 off-target mutations genome-wide for every on-target IGHV mutation during the germinal centre reaction. Structural variation was 16-fold higher in lymphocytes than in stem cells, with around 15% of deletions being attributable to off-target recombinase-activating gene activity. DNA damage from ultraviolet light exposure and other sporadic mutational processes generated hundreds to thousands of mutations in some memory cells. The mutation burden and signatures of normal B cells were broadly similar to those seen in many B-cell cancers, suggesting that malignant transformation of lymphocytes arises from the same mutational processes that are active across normal ontogeny. The mutational landscape of normal lymphocytes chronicles the off-target effects of programmed genome engineering during immunological diversification and the consequences of differentiation, proliferation and residency in diverse microenvironments.
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Affiliation(s)
| | - Emily Mitchell
- Wellcome Sanger Institute, Hinxton, UK
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Nina F Øbro
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Kirsten Kübler
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Megan Davies
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Cambridge Molecular Diagnostics, Milton Road, Cambridge, United Kingdom
| | | | - Alyssa Cull
- York Biomedical Research Institute, University of York, Wentworth Way, York, United Kingdom
| | | | - Mathijs A Sanders
- Wellcome Sanger Institute, Hinxton, UK
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | | | - Craig McDonald
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- York Biomedical Research Institute, University of York, Wentworth Way, York, United Kingdom
| | - Miriam Belmonte
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- York Biomedical Research Institute, University of York, Wentworth Way, York, United Kingdom
| | - Mairi S Shepherd
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | | | - Robert J Osborne
- Wellcome Sanger Institute, Hinxton, UK
- Biofidelity, 330 Cambridge Science Park, Milton Road, Cambridge, United Kingdom
| | - Krishnaa Mahbubani
- Department of Haematology, University of Cambridge, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, United Kingdom
- NIHR Cambridge Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | | | - Elisa Laurenti
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Anthony R Green
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Paz Polak
- Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, Cambridge, United Kingdom
- NIHR Cambridge Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Daniel J Hodson
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - David G Kent
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
- York Biomedical Research Institute, University of York, Wentworth Way, York, United Kingdom.
| | - Peter J Campbell
- Wellcome Sanger Institute, Hinxton, UK.
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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18
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Robinson PS, Thomas LE, Abascal F, Jung H, Harvey LMR, West HD, Olafsson S, Lee BCH, Coorens THH, Lee-Six H, Butlin L, Lander N, Truscott R, Sanders MA, Lensing SV, Buczacki SJA, Ten Hoopen R, Coleman N, Brunton-Sim R, Rushbrook S, Saeb-Parsy K, Lalloo F, Campbell PJ, Martincorena I, Sampson JR, Stratton MR. Inherited MUTYH mutations cause elevated somatic mutation rates and distinctive mutational signatures in normal human cells. Nat Commun 2022; 13:3949. [PMID: 35803914 PMCID: PMC9270427 DOI: 10.1038/s41467-022-31341-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [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: 10/12/2021] [Accepted: 06/14/2022] [Indexed: 12/21/2022] Open
Abstract
Cellular DNA damage caused by reactive oxygen species is repaired by the base excision repair (BER) pathway which includes the DNA glycosylase MUTYH. Inherited biallelic MUTYH mutations cause predisposition to colorectal adenomas and carcinoma. However, the mechanistic progression from germline MUTYH mutations to MUTYH-Associated Polyposis (MAP) is incompletely understood. Here, we sequence normal tissue DNAs from 10 individuals with MAP. Somatic base substitution mutation rates in intestinal epithelial cells were elevated 2 to 4-fold in all individuals, except for one showing a 31-fold increase, and were also increased in other tissues. The increased mutation burdens were of multiple mutational signatures characterised by C > A changes. Different mutation rates and signatures between individuals are likely due to different MUTYH mutations or additional inherited mutations in other BER pathway genes. The elevated base substitution rate in normal cells likely accounts for the predisposition to neoplasia in MAP. Despite ubiquitously elevated mutation rates, individuals with MAP do not display overt evidence of premature ageing. Thus, accumulation of somatic mutations may not be sufficient to cause the global organismal functional decline of ageing.
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Affiliation(s)
- Philip S Robinson
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Department of Paediatrics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Laura E Thomas
- Institute of Life Science, Swansea University, Swansea, SA28PP, UK
| | - Federico Abascal
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Hyunchul Jung
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Luke M R Harvey
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Hannah D West
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, UK
| | - Sigurgeir Olafsson
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Bernard C H Lee
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Tim H H Coorens
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Henry Lee-Six
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Laura Butlin
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, UK
| | - Nicola Lander
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, UK
| | - Rebekah Truscott
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, UK
| | - Mathijs A Sanders
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Department of Haematology, Erasmus University Medical Centre, 3015 CN, Rotterdam, The Netherlands
| | - Stefanie V Lensing
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Simon J A Buczacki
- Nuffield Department of Surgical Sciences, Medical Sciences Division, University of Oxford, Oxford, UK
| | | | - Nicholas Coleman
- Department of Pathology, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Simon Rushbrook
- Norfolk and Norwich University Hospital, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, Cambridge, UK
- Cambridge NIHR Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Fiona Lalloo
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Oxford Road, Manchester, UK
| | - Peter J Campbell
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Iñigo Martincorena
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Julian R Sampson
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, UK
| | - Michael R Stratton
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK.
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19
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Riding AM, Loudon KW, Guo A, Ferdinand JR, Lok LS, Richoz N, Stewart A, Castro-Dopico T, Tuong ZK, Fiancette R, Bowyer GS, Fleming A, Gillman ES, Suchanek O, Mahbubani KT, Saeb-Parsy K, Withers D, Dougan G, Clare S, Clatworthy MR. Group 3 innate lymphocytes make a distinct contribution to type 17 immunity in bladder defence. iScience 2022; 25:104660. [PMID: 35845169 PMCID: PMC9283510 DOI: 10.1016/j.isci.2022.104660] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 03/08/2022] [Accepted: 06/16/2022] [Indexed: 02/02/2023] Open
Abstract
Bladder infection affects a hundred million people annually, but our understanding of bladder immunity is incomplete. We found type 17 immune response genes among the most up-regulated networks in mouse bladder following uropathogenic Escherichia coli (UPEC) challenge. Intravital imaging revealed submucosal Rorc+ cells responsive to UPEC challenge, and we found increased Il17 and IL22 transcripts in wild-type and Rag2 -/- mice, implicating group 3 innate lymphoid cells (ILC3s) as a source of these cytokines. NCR-positive and negative ILC3 subsets were identified in murine and human bladders, with local proliferation increasing IL17-producing ILC3s post infection. ILC3s made a more limited contribution to bladder IL22, with prominent early induction of IL22 evident in Th17 cells. Single-cell RNA sequencing revealed bladder NCR-negative ILC3s as the source of IL17 and identified putative ILC3-myeloid cell interactions, including via lymphotoxin-β-LTBR. Altogether, our data provide important insights into the orchestration and execution of type 17 immunity in bladder defense.
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Affiliation(s)
- Alexandra M. Riding
- Molecular Immunity Unit, University of Cambridge Department of Medicine MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Kevin W. Loudon
- Molecular Immunity Unit, University of Cambridge Department of Medicine MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Andrew Guo
- Molecular Immunity Unit, University of Cambridge Department of Medicine MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
- Cellular Generics, Wellcome Sanger Institute, Hinxton, UK
| | - John R. Ferdinand
- Molecular Immunity Unit, University of Cambridge Department of Medicine MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Laurence S.C. Lok
- Molecular Immunity Unit, University of Cambridge Department of Medicine MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Nathan Richoz
- Molecular Immunity Unit, University of Cambridge Department of Medicine MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Andrew Stewart
- Molecular Immunity Unit, University of Cambridge Department of Medicine MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Tomas Castro-Dopico
- Molecular Immunity Unit, University of Cambridge Department of Medicine MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Zewen Kelvin Tuong
- Molecular Immunity Unit, University of Cambridge Department of Medicine MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
- Cellular Generics, Wellcome Sanger Institute, Hinxton, UK
| | - Remi Fiancette
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Georgina S. Bowyer
- Molecular Immunity Unit, University of Cambridge Department of Medicine MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Aaron Fleming
- Molecular Immunity Unit, University of Cambridge Department of Medicine MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Eleanor S. Gillman
- Molecular Immunity Unit, University of Cambridge Department of Medicine MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Ondrej Suchanek
- Molecular Immunity Unit, University of Cambridge Department of Medicine MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | | | - Kourosh Saeb-Parsy
- University of Cambridge Department of Surgery, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
| | - David Withers
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Gordan Dougan
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Simon Clare
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Menna R. Clatworthy
- Molecular Immunity Unit, University of Cambridge Department of Medicine MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
- Cellular Generics, Wellcome Sanger Institute, Hinxton, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
- Corresponding author
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20
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Gruszczyk AV, Casey AM, James AM, Prag HA, Burger N, Bates GR, Hall AR, Allen FM, Krieg T, Saeb-Parsy K, Murphy MP. Mitochondrial metabolism and bioenergetic function in an anoxic isolated adult mouse cardiomyocyte model of in vivo cardiac ischemia-reperfusion injury. Redox Biol 2022; 54:102368. [PMID: 35749842 PMCID: PMC9234472 DOI: 10.1016/j.redox.2022.102368] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/07/2022] [Accepted: 06/10/2022] [Indexed: 12/20/2022] Open
Abstract
Cell models of cardiac ischemia-reperfusion (IR) injury are essential to facilitate understanding, but current monolayer cell models poorly replicate the in vivo IR injury that occurs within a three-dimensional tissue. Here we show that this is for two reasons: the residual oxygen present in many cellular hypoxia models sustains mitochondrial oxidative phosphorylation; and the loss of lactate from cells into the incubation medium during ischemia enables cells to sustain glycolysis. To overcome these limitations, we incubated isolated adult mouse cardiomyocytes anoxically while inhibiting lactate efflux. These interventions recapitulated key markers of in vivo ischemia, notably the accumulation of succinate and the loss of adenine nucleotides. Upon reoxygenation after anoxia the succinate that had accumulated during anoxia was rapidly oxidized in association with extensive mitochondrial superoxide/hydrogen peroxide production and cell injury, mimicking reperfusion injury. This cell model will enable key aspects of cardiac IR injury to be assessed in vitro.
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Affiliation(s)
- Anja V Gruszczyk
- MRC Mitochondrial Biology Unit, Biomedical Campus, University of Cambridge, Cambridge, CB2 0XY, UK; Department of Surgery and Cambridge NIHR Biomedical Research Centre, Biomedical Campus, University of Cambridge, Cambridge, CB2 2QQ, UK; NIHR Biomedical Research Centre and NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, Cambridge Biomedical Campus, Cambridge, UK
| | - Alva M Casey
- MRC Mitochondrial Biology Unit, Biomedical Campus, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Andrew M James
- MRC Mitochondrial Biology Unit, Biomedical Campus, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Hiran A Prag
- MRC Mitochondrial Biology Unit, Biomedical Campus, University of Cambridge, Cambridge, CB2 0XY, UK; Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Nils Burger
- MRC Mitochondrial Biology Unit, Biomedical Campus, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Georgina R Bates
- MRC Mitochondrial Biology Unit, Biomedical Campus, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Andrew R Hall
- MRC Mitochondrial Biology Unit, Biomedical Campus, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Fay M Allen
- MRC Mitochondrial Biology Unit, Biomedical Campus, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Thomas Krieg
- Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery and Cambridge NIHR Biomedical Research Centre, Biomedical Campus, University of Cambridge, Cambridge, CB2 2QQ, UK; NIHR Biomedical Research Centre and NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, Cambridge Biomedical Campus, Cambridge, UK
| | - Michael P Murphy
- MRC Mitochondrial Biology Unit, Biomedical Campus, University of Cambridge, Cambridge, CB2 0XY, UK; Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK.
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21
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Coorens TH, Collord G, Jung H, Wang Y, Zumalave S, Leongamornlert D, Moore L, Mahbubani K, Saeb-Parsy K, Leung SY, Stratton MR. Abstract 226: Recurrent trisomies, variable selection and precancerous evolution in the normal gastric epithelium. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Gastric cancer is the third leading cause of cancer-related mortality globally and is often associated with infectious agents such as the bacterium Helicobacter pylori. However, the background mutational landscape in normal gastric epithelium and the first genomic steps towards the formation of gastric cancer remain poorly understood. Here, we use whole-genome sequencing of microdissected gastric glands (n=271) from 30 patients, 18 of whom had gastric cancer. We show that gastric glands are clonal structures and accrue approximately 27 single base substitutions per year. While the mutational signatures in most normal glands reflect age-related mutagenesis, gastric glands sampled close to a tumor showed exposure to a mutagenic process enriched in tumors (COSMIC reference mutational signature SBS17). Phylogenetic analysis shows that acquisition of SBS17 substitutions is closely linked to overt malignant transformation. We also observe widespread trisomies of specific chromosomes, which are recurrently and independently acquired in many gastric glands of the same patient. Mutations in genes encoding epigenetic modifiers and chromatin remodelers showed evidence of positive selection and were highly enriched in some patients. This was confirmed by targeted sequencing of cancer genes in a further 1008 gastric glands. Strikingly, glands that exhibit driver mutations, a recurrent trisomy or elevated mutation loads only overlap minimally, suggesting a highly variable and patient-specific mutation and selection landscape in the normal gastric epithelium. Taken together, these results give novel insights into the preclinical evolution of gastric malignancies.
Citation Format: Tim H. Coorens, Grace Collord, Hyungchul Jung, Yichen Wang, Sonia Zumalave, Daniel Leongamornlert, Luiza Moore, Krishnaa Mahbubani, Kourosh Saeb-Parsy, Suet Yi Leung, Michael R. Stratton. Recurrent trisomies, variable selection and precancerous evolution in the normal gastric epithelium [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 226.
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Affiliation(s)
| | | | | | - Yichen Wang
- 1Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Sonia Zumalave
- 2University of Santiago de Compostela, Santiago de Compostela, Spain
| | | | - Luiza Moore
- 1Wellcome Sanger Institute, Hinxton, United Kingdom
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22
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Mende N, Bastos HP, Santoro A, Mahbubani KT, Ciaurro V, Calderbank EF, Londoño MQ, Sham K, Mantica G, Morishima T, Mitchell E, Lidonnici MR, Meier-Abt F, Hayler D, Jardine L, Curd A, Haniffa M, Ferrari G, Takizawa H, Wilson NK, Göttgens B, Saeb-Parsy K, Frontini M, Laurenti E. Unique molecular and functional features of extramedullary hematopoietic stem and progenitor cell reservoirs in humans. Blood 2022; 139:3387-3401. [PMID: 35073399 PMCID: PMC7612845 DOI: 10.1182/blood.2021013450] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [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: 07/23/2021] [Accepted: 01/05/2022] [Indexed: 02/02/2023] Open
Abstract
Rare hematopoietic stem and progenitor cell (HSPC) pools outside the bone marrow (BM) contribute to blood production in stress and disease but remain ill-defined. Although nonmobilized peripheral blood (PB) is routinely sampled for clinical management, the diagnosis and monitoring potential of PB HSPCs remain untapped, as no healthy PB HSPC baseline has been reported. Here we comprehensively delineate human extramedullary HSPC compartments comparing spleen, PB, and mobilized PB to BM using single-cell RNA-sequencing and/or functional assays. We uncovered HSPC features shared by extramedullary tissues and others unique to PB. First, in contrast to actively dividing BM HSPCs, we found no evidence of substantial ongoing hematopoiesis in extramedullary tissues at steady state but report increased splenic HSPC proliferative output during stress erythropoiesis. Second, extramedullary hematopoietic stem cells/multipotent progenitors (HSCs/MPPs) from spleen, PB, and mobilized PB share a common transcriptional signature and increased abundance of lineage-primed subsets compared with BM. Third, healthy PB HSPCs display a unique bias toward erythroid-megakaryocytic differentiation. At the HSC/MPP level, this is functionally imparted by a subset of phenotypic CD71+ HSCs/MPPs, exclusively producing erythrocytes and megakaryocytes, highly abundant in PB but rare in other adult tissues. Finally, the unique erythroid-megakaryocytic-skewing of PB is perturbed with age in essential thrombocythemia and β-thalassemia. Collectively, we identify extramedullary lineage-primed HSPC reservoirs that are nonproliferative in situ and report involvement of splenic HSPCs during demand-adapted hematopoiesis. Our data also establish aberrant composition and function of circulating HSPCs as potential clinical indicators of BM dysfunction.
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Affiliation(s)
- Nicole Mende
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Hugo P. Bastos
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Antonella Santoro
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Krishnaa T. Mahbubani
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Haematology and Cambridge NIHR Biomedical Research Centre, Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Valerio Ciaurro
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Emily F. Calderbank
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Mariana Quiroga Londoño
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Kendig Sham
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Giovanna Mantica
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Tatsuya Morishima
- Laboratory of Stem Cell Stress, International Research Centre for Medical Sciences, and Centre for Metabolic Regulation of Healthy Aging, Kumamoto University, Kumamoto, Japan
- Laboratory of Hematopoietic Stem Cell Engineering, International Research Center for Medical Sciences, Kumamoto University, 860-0811 Kumamoto, Japan
| | - Emily Mitchell
- Cancer, Ageing and Somatic Mutation Group, Wellcome Sanger Institute, Hinxton, UK
| | - Maria Rosa Lidonnici
- San Raffaele-Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Fabienne Meier-Abt
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
- Institute of Molecular Systems Biology (IMSB), ETH Zurich, Zurich, Switzerland
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Daniel Hayler
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, 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, NE7 7DN, UK
| | - Abbie Curd
- Department of Surgery and Cambridge NIHR Biomedical Research Centre, Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Muzlifah Haniffa
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
| | - Giuliana Ferrari
- San Raffaele-Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Hitoshi Takizawa
- Laboratory of Stem Cell Stress, International Research Centre for Medical Sciences, and Centre for Metabolic Regulation of Healthy Aging, Kumamoto University, Kumamoto, Japan
| | - Nicola K. Wilson
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Berthold Göttgens
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery and Cambridge NIHR Biomedical Research Centre, Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Mattia Frontini
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Institute of Biomedical & Clinical Science, College of Medicine and Health, University of Exeter Medical School, Exeter, UK
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- British Heart Foundation Centre of Excellence, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Elisa Laurenti
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
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23
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Domínguez Conde C, Xu C, Jarvis LB, Rainbow DB, Wells SB, Gomes T, Howlett SK, Suchanek O, Polanski K, King HW, Mamanova L, Huang N, Szabo PA, Richardson L, Bolt L, Fasouli ES, Mahbubani KT, Prete M, Tuck L, Richoz N, Tuong ZK, Campos L, Mousa HS, Needham EJ, Pritchard S, Li T, Elmentaite R, Park J, Rahmani E, Chen D, Menon DK, Bayraktar OA, James LK, Meyer KB, Yosef N, Clatworthy MR, Sims PA, Farber DL, Saeb-Parsy K, Jones JL, Teichmann SA. Cross-tissue immune cell analysis reveals tissue-specific features in humans. Science 2022; 376:eabl5197. [PMID: 35549406 PMCID: PMC7612735 DOI: 10.1126/science.abl5197] [Citation(s) in RCA: 191] [Impact Index Per Article: 95.5] [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] [Indexed: 02/02/2023]
Abstract
Despite their crucial role in health and disease, our knowledge of immune cells within human tissues remains limited. We surveyed the immune compartment of 16 tissues from 12 adult donors by single-cell RNA sequencing and VDJ sequencing generating a dataset of ~360,000 cells. To systematically resolve immune cell heterogeneity across tissues, we developed CellTypist, a machine learning tool for rapid and precise cell type annotation. Using this approach, combined with detailed curation, we determined the tissue distribution of finely phenotyped immune cell types, revealing hitherto unappreciated tissue-specific features and clonal architecture of T and B cells. Our multitissue approach lays the foundation for identifying highly resolved immune cell types by leveraging a common reference dataset, tissue-integrated expression analysis, and antigen receptor sequencing.
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Affiliation(s)
- C Domínguez Conde
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - C Xu
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - LB Jarvis
- Department of Clinical Neurosciences, University of Cambridge
| | - DB Rainbow
- Department of Clinical Neurosciences, University of Cambridge
| | - SB Wells
- Department of Systems Biology, Columbia University Irving Medical Center
| | - T Gomes
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - SK Howlett
- Department of Clinical Neurosciences, University of Cambridge
| | - O Suchanek
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
| | - K Polanski
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - HW King
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London, UK
| | - L Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - N Huang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - PA Szabo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center
| | - L Richardson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - L Bolt
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - ES Fasouli
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - KT Mahbubani
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - M Prete
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - L Tuck
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - N Richoz
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
| | - ZK Tuong
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
| | - L Campos
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- West Suffolk Hospital NHS Trust, Bury Saint Edmunds, UK
| | - HS Mousa
- Department of Clinical Neurosciences, University of Cambridge
| | - EJ Needham
- Department of Clinical Neurosciences, University of Cambridge
| | - S Pritchard
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - T Li
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - R Elmentaite
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - J Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - E Rahmani
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA
| | - D Chen
- Department of Systems Biology, Columbia University Irving Medical Center
| | - DK Menon
- Department of Anaesthesia, University of Cambridge, Cambridge, UK
| | - OA Bayraktar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - LK James
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London, UK
| | - KB Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - N Yosef
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - MR Clatworthy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
| | - PA Sims
- Department of Systems Biology, Columbia University Irving Medical Center
| | - DL Farber
- Department of Microbiology and Immunology, Columbia University Irving Medical Center
| | - K Saeb-Parsy
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - JL Jones
- Department of Clinical Neurosciences, University of Cambridge
| | - SA Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Theory of Condensed Matter, Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Ave, Cambridge CB3 0HE, UK
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24
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Bennett C, Lawrence M, Guerrero JA, Stritt S, Waller AK, Yan Y, Mifsud RW, Ballester-Beltran J, Baig A, Mueller A, Mayer L, Warland J, Penkett CJ, Akbari P, Moreau T, Evans AL, Mookerjee S, Hoffman GJ, Saeb-Parsy K, Adams DJ, Couzens AL, Bender M, Erber WN, Nieswandt B, Read RJ, Ghevaert C. CRLF3 plays a key role in the final stage of platelet genesis and is a potential therapeutic target for thrombocythemia. Blood 2022; 139:2227-2239. [PMID: 35051265 PMCID: PMC7614665 DOI: 10.1182/blood.2021013113] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 06/28/2021] [Accepted: 11/23/2021] [Indexed: 11/20/2022] Open
Abstract
The process of platelet production has so far been understood to be a 2-stage process: megakaryocyte maturation from hematopoietic stem cells followed by proplatelet formation, with each phase regulating the peripheral blood platelet count. Proplatelet formation releases into the bloodstream beads-on-a-string preplatelets, which undergo fission into mature platelets. For the first time, we show that preplatelet maturation is a third, tightly regulated, critical process akin to cytokinesis that regulates platelet count. We show that deficiency in cytokine receptor-like factor 3 (CRLF3) in mice leads to an isolated and sustained 25% to 48% reduction in the platelet count without any effect on other blood cell lineages. We show that Crlf3-/- preplatelets have increased microtubule stability, possibly because of increased microtubule glutamylation via the interaction of CRLF3 with key members of the Hippo pathway. Using a mouse model of JAK2 V617F essential thrombocythemia, we show that a lack of CRLF3 leads to long-term lineage-specific normalization of the platelet count. We thereby postulate that targeting CRLF3 has therapeutic potential for treatment of thrombocythemia.
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Affiliation(s)
- Cavan Bennett
- Department of Haematology, University of Cambridge and NHS Blood and Transplant, Cambridge Blood Centre, Long Road, Cambridge CB2 0PT, UK
| | - Moyra Lawrence
- Department of Haematology, University of Cambridge and NHS Blood and Transplant, Cambridge Blood Centre, Long Road, Cambridge CB2 0PT, UK
- Cambridge Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Jose A. Guerrero
- Department of Haematology, University of Cambridge and NHS Blood and Transplant, Cambridge Blood Centre, Long Road, Cambridge CB2 0PT, UK
| | - Simon Stritt
- Institute of Experimental Biomedicine, University Hospital and University of Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
| | - Amie K. Waller
- Department of Haematology, University of Cambridge and NHS Blood and Transplant, Cambridge Blood Centre, Long Road, Cambridge CB2 0PT, UK
- Cambridge Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Yahui Yan
- Cambridge Institute for Medical Research and Department of Haematology, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, England
| | - Richard W. Mifsud
- Cambridge Institute for Medical Research and Department of Haematology, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, England
| | - Jose Ballester-Beltran
- Department of Haematology, University of Cambridge and NHS Blood and Transplant, Cambridge Blood Centre, Long Road, Cambridge CB2 0PT, UK
| | - Ayesha Baig
- Institute of Experimental Biomedicine, University Hospital and University of Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
| | - Annett Mueller
- Department of Haematology, University of Cambridge and NHS Blood and Transplant, Cambridge Blood Centre, Long Road, Cambridge CB2 0PT, UK
- Cambridge Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Louisa Mayer
- Department of Haematology, University of Cambridge and NHS Blood and Transplant, Cambridge Blood Centre, Long Road, Cambridge CB2 0PT, UK
| | - James Warland
- Department of Haematology, University of Cambridge and NHS Blood and Transplant, Cambridge Blood Centre, Long Road, Cambridge CB2 0PT, UK
- Cambridge Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Christopher J. Penkett
- Department of Haematology, University of Cambridge and NHS Blood and Transplant, Cambridge Blood Centre, Long Road, Cambridge CB2 0PT, UK
| | - Parsa Akbari
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Wort’s Causeway, Cambridge CB1 8RN, UK
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Thomas Moreau
- Department of Haematology, University of Cambridge and NHS Blood and Transplant, Cambridge Blood Centre, Long Road, Cambridge CB2 0PT, UK
| | - Amanda L. Evans
- Department of Haematology, University of Cambridge and NHS Blood and Transplant, Cambridge Blood Centre, Long Road, Cambridge CB2 0PT, UK
- Cambridge Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Souradip Mookerjee
- Department of Haematology, University of Cambridge and NHS Blood and Transplant, Cambridge Blood Centre, Long Road, Cambridge CB2 0PT, UK
- Cambridge Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Gary J. Hoffman
- Medical School, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, WA, 6099, Australia
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - David J. Adams
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1HH, UK
| | - Amber L. Couzens
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, M5G 1X5, Canada
| | - Markus Bender
- Institute of Experimental Biomedicine, University Hospital and University of Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
| | - Wendy N. Erber
- Medical School, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, WA, 6099, Australia
| | - Bernhard Nieswandt
- Institute of Experimental Biomedicine, University Hospital and University of Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
| | - Randy J. Read
- Cambridge Institute for Medical Research and Department of Haematology, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, England
| | - Cedric Ghevaert
- Department of Haematology, University of Cambridge and NHS Blood and Transplant, Cambridge Blood Centre, Long Road, Cambridge CB2 0PT, UK
- Cambridge Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
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25
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Kapetanos K, Light A, Thakare N, Mahbubani K, Saeb-Parsy K, Saeb-Parsy K. Bioengineering solutions for Ureteric disorders: Clinical need, challenges and opportunities. BJU Int 2022; 130:408-419. [PMID: 35388587 PMCID: PMC9544734 DOI: 10.1111/bju.15741] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 02/26/2022] [Accepted: 03/28/2022] [Indexed: 12/01/2022]
Abstract
Objectives To summarise the causes of ureteric damage and the current standard of care, discussing the risks and benefits of available therapeutic options. We then focus on the current and future solutions that can be provided by ureteric bioengineering and provide a description of the ideal characteristics of a bioengineered product. Methods We performed a literature search in February 2021 in: Google Scholar, Medline, and Web of Science. Three searches were conducted, investigating: (a) the epidemiology of ureteric pathology, (b) the current standard of care, and (c) the state of the art in ureteric bioengineering. Results The most‐common causes of ureteric damage are iatrogenic injury and external trauma. Current approaches to treatment include stent placement or surgical reconstruction. Reconstruction can be done using either urological tissue or segments of the gastrointestinal tract. Limitations include scarring, strictures, and infections. Several bioengineered alternatives have been explored in animal studies, with variations in the choice of scaffold material, cellular seeding populations, and pre‐implantation processing. Natural grafts and hybrid material appear to be associated with superior outcomes. Furthermore, seeding of the scaffold material with stem cells or differentiated urothelial cells allows for better function compared to acellular scaffolds. Some studies have attempted to pre‐implant the graft in the omentum prior to reconstruction, but this has yet to prove any definitive benefits. Conclusion There is an unmet clinical need for safer and more effective treatment for ureteric injuries. Urological bioengineering is a promising solution in preclinical studies. However, substantial scientific, logistic, and economic challenges must be addressed to harness its transformative potential in improving outcomes.
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Affiliation(s)
| | - Alexander Light
- Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Niyukta Thakare
- Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Krishnaa Mahbubani
- Cambridge Biorepository for Translational Medicine (CBTM), NIHR Cambridge Biomedical Research Centre, Cambridge, UK.,Department of Haematology, University of Cambridge, Cambridge, UK
| | - Kasra Saeb-Parsy
- Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge and Cambridge NIHR Biomedical Research Centre, Cambridge
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26
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Siu JHY, Pitcher MJ, Tull TJ, Velounias RL, Guesdon W, Montorsi L, Mahbubani KT, Ellis R, Dhami P, Todd K, Kadolsky UD, Kleeman M, D'Cruz DP, Saeb-Parsy K, Bemark M, Pettigrew GJ, Spencer J. Two subsets of human marginal zone B cells resolved by global analysis of lymphoid tissues and blood. Sci Immunol 2022; 7:eabm9060. [PMID: 35302862 DOI: 10.1126/sciimmunol.abm9060] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
B cells generate antibodies that are essential for immune protection, but their subgroups are poorly defined. Here, we perform undirected deep profiling of B cells in matched human lymphoid tissues from deceased transplant organ donors and blood. In addition to identifying unanticipated features of tissue-based B cell differentiation, we resolve two subsets of marginal zone B (MZB) cells differing in cell surface and transcriptomic profiles, clonal relationships to other subsets, enrichment of genes in the NOTCH pathway, distribution bias within splenic marginal zone microenvironment, and immunoglobulin repertoire diversity and hypermutation frequency. Each subset is present in spleen, gut-associated lymphoid tissue, mesenteric lymph nodes, and blood. MZB cells and the lineage from which they are derived are depleted in lupus nephritis. Here, we show that this depletion is of only one MZB subset. The other remains unchanged as a proportion of total B cells compared with health. Thus, it is important to factor MZB cell heterogeneity into studies of human B cell responses and pathology.
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Affiliation(s)
- Jacqueline H Y Siu
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Michael J Pitcher
- School of Immunology and Microbial Sciences, King's College London, Guy's Campus, London SE1 9RT, UK
| | - Thomas J Tull
- School of Immunology and Microbial Sciences, King's College London, Guy's Campus, London SE1 9RT, UK
| | - Rebekah L Velounias
- School of Immunology and Microbial Sciences, King's College London, Guy's Campus, London SE1 9RT, UK
| | - William Guesdon
- School of Immunology and Microbial Sciences, King's College London, Guy's Campus, London SE1 9RT, UK
| | - Lucia Montorsi
- School of Cancer Sciences, King's College London, Guy's Campus, London, UK.,Cancer Systems Biology Laboratory, Francis Crick Institute, London, UK
| | - Krishnaa T Mahbubani
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Richard Ellis
- NIHR Guy's and St Thomas' Biomedical Research Centre, Guy's and St Thomas NHS Foundation Trust, Guy's Hospital, London SE1 9RT, UK
| | - Pawan Dhami
- NIHR Guy's and St Thomas' Biomedical Research Centre, Guy's and St Thomas NHS Foundation Trust, Guy's Hospital, London SE1 9RT, UK
| | - Katrina Todd
- NIHR Guy's and St Thomas' Biomedical Research Centre, Guy's and St Thomas NHS Foundation Trust, Guy's Hospital, London SE1 9RT, UK
| | - Ulrich D Kadolsky
- NIHR Guy's and St Thomas' Biomedical Research Centre, Guy's and St Thomas NHS Foundation Trust, Guy's Hospital, London SE1 9RT, UK
| | - Michelle Kleeman
- NIHR Guy's and St Thomas' Biomedical Research Centre, Guy's and St Thomas NHS Foundation Trust, Guy's Hospital, London SE1 9RT, UK
| | - David P D'Cruz
- School of Immunology and Microbial Sciences, King's College London, Guy's Campus, London SE1 9RT, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Mats Bemark
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE 405 30 Gothenburg, Sweden.,Department of Clinical Immunology and Transfusion Medicine, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Gavin J Pettigrew
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Jo Spencer
- School of Immunology and Microbial Sciences, King's College London, Guy's Campus, London SE1 9RT, UK
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27
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Oxley C, Thankappannair V, Saeb-Parsy K, Lamb B, Shah N, Kastner C, Geoghegan L, Fox H, Gnanapragasam V. 281 Impact of Using Risk Communication Tools in Counselling Patients with Newly Diagnosed Non-Metastatic Prostate Cancer. Br J Surg 2022. [DOI: 10.1093/bjs/znac039.183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Introduction
There have been substantial advances in risk communication tools that help patients understand prognosis associated with prostate cancer and the benefit/gain from treatment. Over the last three years, two tools; Cambridge Prognostic Groups (CPG), and Predict Prostate (https://prostate.predict.nhs.uk), along with decision-making consultations with clinical nurse specialists (CNS) have been integrated into the new diagnosis pathway in our unit.
Method
Treatment decisions for patients with new non-metastatic prostate cancer were audited after (2019–2020) and before (2016–2017) new risk communication tools were implemented. Data were compared between the two time periods and also benchmarked against national level data from the National Prostate Cancer Audit (NPCA) (Parry et al 2020; PMID: 32460859). The main outcome measured was comparison of rates of over and under-treatment of disease.
Results
168 and 95 patients were included in the 2019–2020 and 2016–2017 cohorts, respectively. Following implementation there was a reduction in over-treatment (use of radical surgery/radiotherapy) in patients with low risk/CPG1 (23% to 4%). These rates were also better than the national average from NPCA data (4% vs 11%). In parallel, there was an increase in use of radical treatment (reduced under-treatment) in high risk and very high-risk/CPG4-5 disease (84% vs 73%). Again, these rates were also superior to national level data from the NPCA (84% vs 76%).
Conclusions
Incorporating personalised risk-communication tools and dedicated CNS counselling in our unit has reduced over-treatment of early disease and under-treatment of advanced disease. Wider uptake could enhance risk-appropriate treatment of patients with a new prostate cancer diagnosis.
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Affiliation(s)
- C. Oxley
- University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - V. Thankappannair
- Department of Urology, Cambridge University Hospitals NHS Trust, Cambridge, United Kingdom
| | - K. Saeb-Parsy
- Department of Urology, Cambridge University Hospitals NHS Trust, Cambridge, United Kingdom
| | - B. Lamb
- Department of Urology, Cambridge University Hospitals NHS Trust, Cambridge, United Kingdom
| | - N. Shah
- Department of Urology, Cambridge University Hospitals NHS Trust, Cambridge, United Kingdom
| | - C. Kastner
- Department of Urology, Cambridge University Hospitals NHS Trust, Cambridge, United Kingdom
| | - L. Geoghegan
- Department of Urology, Cambridge University Hospitals NHS Trust, Cambridge, United Kingdom
| | - H. Fox
- Department of Urology, Cambridge University Hospitals NHS Trust, Cambridge, United Kingdom
| | - V. Gnanapragasam
- Department of Urology, Cambridge University Hospitals NHS Trust, Cambridge, United Kingdom
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28
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Prag HA, Pala L, Kula-Alwar D, Mulvey JF, Luping D, Beach TE, Booty LM, Hall AR, Logan A, Sauchanka V, Caldwell ST, Robb EL, James AM, Xu Z, Saeb-Parsy K, Hartley RC, Murphy MP, Krieg T. Ester Prodrugs of Malonate with Enhanced Intracellular Delivery Protect Against Cardiac Ischemia-Reperfusion Injury In Vivo. Cardiovasc Drugs Ther 2022; 36:1-13. [PMID: 32648168 PMCID: PMC8770414 DOI: 10.1007/s10557-020-07033-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/26/2020] [Indexed: 12/01/2022]
Abstract
PURPOSE Mitochondrial reactive oxygen species (ROS) production upon reperfusion of ischemic tissue initiates the ischemia/reperfusion (I/R) injury associated with heart attack. During ischemia, succinate accumulates and its oxidation upon reperfusion by succinate dehydrogenase (SDH) drives ROS production. Inhibition of succinate accumulation and/or oxidation by dimethyl malonate (DMM), a cell permeable prodrug of the SDH inhibitor malonate, can decrease I/R injury. However, DMM is hydrolysed slowly, requiring administration to the heart prior to ischemia, precluding its administration to patients at the point of reperfusion, for example at the same time as unblocking a coronary artery following a heart attack. To accelerate malonate delivery, here we developed more rapidly hydrolysable malonate esters. METHODS We synthesised a series of malonate esters and assessed their uptake and hydrolysis by isolated mitochondria, C2C12 cells and in mice in vivo. In addition, we assessed protection against cardiac I/R injury by the esters using an in vivo mouse model of acute myocardial infarction. RESULTS We found that the diacetoxymethyl malonate diester (MAM) most rapidly delivered large amounts of malonate to cells in vivo. Furthermore, MAM could inhibit mitochondrial ROS production from succinate oxidation and was protective against I/R injury in vivo when added at reperfusion. CONCLUSIONS The rapidly hydrolysed malonate prodrug MAM can protect against cardiac I/R injury in a clinically relevant mouse model.
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Affiliation(s)
- Hiran A Prag
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK
- Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Laura Pala
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | | | - John F Mulvey
- Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Du Luping
- Tianjin Medical University, Tianjin, 300070, China
| | - Timothy E Beach
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
| | - Lee M Booty
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK
| | - Andrew R Hall
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK
| | - Angela Logan
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK
| | - Volha Sauchanka
- Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | | | - Ellen L Robb
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK
| | - Andrew M James
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK
| | - Zhelong Xu
- Tianjin Medical University, Tianjin, 300070, China
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
| | | | - Michael P Murphy
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK.
- Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK.
| | - Thomas Krieg
- Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK.
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29
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Luecken MD, Zaragozi LE, Madissoon E, Sikkema L, Firsova AB, De Domenico E, Kümmerle L, Saglam A, Berg M, Gay ACA, Schniering J, Mayr CH, Abalo XM, Larsson L, Sountoulidis A, Teichmann S, van Eunen K, Koppelman GH, Saeb-Parsy K, Leroy S, Powell P, Sarkans U, Timens W, Lundeberg J, van den Berge M, Nilsson M, Horváth P, Denning J, Papatheodorou I, Schultze J, Schiller HB, Barbry P, Petoukhov I, Misharin AV, Adcock I, von Papen M, Theis FJ, Samakovlis C, Meyer KB, Nawijn MC. The discovAIR project: a roadmap towards the Human Lung Cell Atlas. Eur Respir J 2022; 60:13993003.02057-2021. [PMID: 35086829 PMCID: PMC9386332 DOI: 10.1183/13993003.02057-2021] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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] [Received: 07/26/2021] [Accepted: 12/23/2021] [Indexed: 12/01/2022]
Abstract
The Human Cell Atlas (HCA) consortium aims to establish an atlas of all organs in the healthy human body at single-cell resolution to increase our understanding of basic biological processes that govern development, physiology and anatomy, and to accelerate diagnosis and treatment of disease. The Lung Biological Network of the HCA aims to generate the Human Lung Cell Atlas as a reference for the cellular repertoire, molecular cell states and phenotypes, and cell–cell interactions that characterise normal lung homeostasis in healthy lung tissue. Such a reference atlas of the healthy human lung will facilitate mapping the changes in the cellular landscape in disease. The discovAIR project is one of six pilot actions for the HCA funded by the European Commission in the context of the H2020 framework programme. discovAIR aims to establish the first draft of an integrated Human Lung Cell Atlas, combining single-cell transcriptional and epigenetic profiling with spatially resolving techniques on matched tissue samples, as well as including a number of chronic and infectious diseases of the lung. The integrated Human Lung Cell Atlas will be available as a resource for the wider respiratory community, including basic and translational scientists, clinical medicine, and the private sector, as well as for patients with lung disease and the interested lay public. We anticipate that the Human Lung Cell Atlas will be the founding stone for a more detailed understanding of the pathogenesis of lung diseases, guiding the design of novel diagnostics and preventive or curative interventions. The discovAIR project contributes to the Human Cell Atlas Lung Biological Network by establishing a first draft of the Human Lung Cell Atlas, advancing our insight into the cellular complexity and spatial organisation of the lung in health and diseasehttps://bit.ly/3zX4cad
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Affiliation(s)
- Malte D Luecken
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.,These authors made an equal contribution to this manuscript
| | - Laure-Emmanuelle Zaragozi
- Université Côte d'Azur and CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Sophia Antipolis, France.,These authors made an equal contribution to this manuscript
| | - Elo Madissoon
- Wellcome Sanger Institute, Cambridge, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.,These authors made an equal contribution to this manuscript
| | - Lisa Sikkema
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.,These authors made an equal contribution to this manuscript
| | - Alexandra B Firsova
- Science for Life Laboratory, Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.,These authors made an equal contribution to this manuscript
| | - Elena De Domenico
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,These authors made an equal contribution to this manuscript
| | - Louis Kümmerle
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.,These authors made an equal contribution to this manuscript
| | - Adem Saglam
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,These authors made an equal contribution to this manuscript
| | - Marijn Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,GRIAC research institute at the University Medical Center Groningen, Groningen, the Netherlands.,These authors made an equal contribution to this manuscript
| | - Aurore C A Gay
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,GRIAC research institute at the University Medical Center Groningen, Groningen, the Netherlands.,These authors made an equal contribution to this manuscript
| | - Janine Schniering
- Helmholtz Zentrum München, Institute of Lung Biology and Disease, Comprehensive Pneumology Center, Member of the German Center for Lung Research (DZL), Munich, Germany.,These authors made an equal contribution to this manuscript
| | - Christoph H Mayr
- Helmholtz Zentrum München, Institute of Lung Biology and Disease, Comprehensive Pneumology Center, Member of the German Center for Lung Research (DZL), Munich, Germany.,These authors made an equal contribution to this manuscript
| | - Xesús M Abalo
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.,These authors made an equal contribution to this manuscript
| | - Ludvig Larsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.,These authors made an equal contribution to this manuscript
| | - Alexandros Sountoulidis
- Science for Life Laboratory, Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.,These authors made an equal contribution to this manuscript
| | - Sarah Teichmann
- Wellcome Sanger Institute, Cambridge, UK.,Theory of Condensed Matter, Cavendish Laboratory, Cambridge, UK
| | - Karen van Eunen
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,UMCG Research BV, University Medical Center Groningen, Groningen, The Netherlands
| | - Gerard H Koppelman
- GRIAC research institute at the University Medical Center Groningen, Groningen, the Netherlands.,Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, and Cambridge NIHR Biomedical Research Centre, Cambridge, UK
| | - Sylvie Leroy
- Département de Pneumologie, Université Côte d'Azur and CHU Nice, FHU-OncoAge, Nice, France
| | | | - Ugis Sarkans
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Wim Timens
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,GRIAC research institute at the University Medical Center Groningen, Groningen, the Netherlands
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden
| | - Maarten van den Berge
- GRIAC research institute at the University Medical Center Groningen, Groningen, the Netherlands.,Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Peter Horváth
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
| | | | - Irene Papatheodorou
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Joachim Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,PRECISE Platform for Single Cell Genomics and Epigenomics, Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) and the University of Bonn, Bonn, Germany.,Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Herbert B Schiller
- Helmholtz Zentrum München, Institute of Lung Biology and Disease, Comprehensive Pneumology Center, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Pascal Barbry
- Université Côte d'Azur and CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Sophia Antipolis, France
| | - Ilya Petoukhov
- A Beta World (former Principal at MIcompany), Amsterdam, the Netherlands
| | - Alexander V Misharin
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, USA
| | - Ian Adcock
- Airway Disease Section, National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, UK
| | | | - Fabian J Theis
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.,Institute of Computational Biology, Helmholtz Center Munich (HMGU), Neuherberg, Germany
| | - Christos Samakovlis
- Science for Life Laboratory, Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | | | - Martijn C Nawijn
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands .,GRIAC research institute at the University Medical Center Groningen, Groningen, the Netherlands
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30
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Ghazaly M, Sethi P, Kathirvel M, Tiwari NA, Thillai M, Gaurav R, Surendrakumar V, Ayorinde JOO, Allison M, Upponi S, Watson CJ, Praseedom RK, Gibbs P, Saeb-Parsy K. OUP accepted manuscript. BJS Open 2022; 6:6526445. [PMID: 35143624 PMCID: PMC8830758 DOI: 10.1093/bjsopen/zrab146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/18/2021] [Accepted: 12/21/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Mohamed Ghazaly
- Transplant Unit, Addenbrooke’s Hospital, Cambridge, UK
- Department of Surgery, Tanta University, Tanta, Gharbia, Egypt
| | - Pulkit Sethi
- Transplant Unit, Addenbrooke’s Hospital, Cambridge, UK
| | | | | | - Manoj Thillai
- Transplant Unit, Addenbrooke’s Hospital, Cambridge, UK
| | - Rohit Gaurav
- Transplant Unit, Addenbrooke’s Hospital, Cambridge, UK
| | | | | | - Michael Allison
- Department of Hepatology, Cambridge Biomedical Research Centre, Addenbrooke’s Hospital, Cambridge, UK
| | - Sara Upponi
- Department of Radiology, Addenbrooke’s Hospital, Cambridge, UK
| | - Christopher J. Watson
- Transplant Unit, Addenbrooke’s Hospital, Cambridge, UK
- Department of Surgery, University of Cambridge, and Cambridge NIHR Biomedical Centre, Cambridge, UK
| | | | - Paul Gibbs
- Transplant Unit, Addenbrooke’s Hospital, Cambridge, UK
| | - Kourosh Saeb-Parsy
- Transplant Unit, Addenbrooke’s Hospital, Cambridge, UK
- Department of Surgery, University of Cambridge, and Cambridge NIHR Biomedical Centre, Cambridge, UK
- Correspondence to: Kourosh Saeb-Parsy, Department of Surgery, Addenbrooke’s Hospital, Hills Road, Box 202, Cambridge CB2 0QQ, UK (e-mail: )
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31
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Jarvis LB, Rainbow DB, Coppard V, Howlett SK, Georgieva Z, Davies JL, Mullay HK, Hester J, Ashmore T, Van Den Bosch A, Grist JT, Coles AJ, Mousa HS, Pluchino S, Mahbubani KT, Griffin JL, Saeb-Parsy K, Issa F, Peruzzotti-Jametti L, Wicker LS, Jones JL. Therapeutically expanded human regulatory T-cells are super-suppressive due to HIF1A induced expression of CD73. Commun Biol 2021; 4:1186. [PMID: 34650224 PMCID: PMC8516976 DOI: 10.1038/s42003-021-02721-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 09/27/2021] [Indexed: 12/14/2022] Open
Abstract
The adoptive transfer of regulatory T-cells (Tregs) is a promising therapeutic approach in transplantation and autoimmunity. However, because large cell numbers are needed to achieve a therapeutic effect, in vitro expansion is required. By comparing their function, phenotype and transcriptomic profile against ex vivo Tregs, we demonstrate that expanded human Tregs switch their metabolism to aerobic glycolysis and show enhanced suppressive function through hypoxia-inducible factor 1-alpha (HIF1A) driven acquisition of CD73 expression. In conjunction with CD39, CD73 expression enables expanded Tregs to convert ATP to immunosuppressive adenosine. We conclude that for maximum therapeutic benefit, Treg expansion protocols should be optimised for CD39/CD73 co-expression.
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Affiliation(s)
- Lorna B Jarvis
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Daniel B Rainbow
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Valerie Coppard
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Sarah K Howlett
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Zoya Georgieva
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Jessica L Davies
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | | | - Joanna Hester
- Department of Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Tom Ashmore
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | | | - James T Grist
- Department of Radiology, University of Cambridge, Cambridge, UK
| | - Alasdair J Coles
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Hani S Mousa
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Stefano Pluchino
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | | | - Julian L Griffin
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
- Imperial College London Dementia Research Institute & Section of Biomolecular Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | | | - Fadi Issa
- Department of Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | | | - Linda S Wicker
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Joanne L Jones
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK.
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32
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Colom B, Herms A, Hall MWJ, Dentro SC, King C, Sood RK, Alcolea MP, Piedrafita G, Fernandez-Antoran D, Ong SH, Fowler JC, Mahbubani KT, Saeb-Parsy K, Gerstung M, Hall BA, Jones PH. Mutant clones in normal epithelium outcompete and eliminate emerging tumours. Nature 2021; 598:510-514. [PMID: 34646013 PMCID: PMC7612642 DOI: 10.1038/s41586-021-03965-7] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [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: 08/03/2020] [Accepted: 08/26/2021] [Indexed: 02/08/2023]
Abstract
Human epithelial tissues accumulate cancer-driver mutations with age1-9, yet tumour formation remains rare. The positive selection of these mutations suggests that they alter the behaviour and fitness of proliferating cells10-12. Thus, normal adult tissues become a patchwork of mutant clones competing for space and survival, with the fittest clones expanding by eliminating their less competitive neighbours11-14. However, little is known about how such dynamic competition in normal epithelia influences early tumorigenesis. Here we show that the majority of newly formed oesophageal tumours are eliminated through competition with mutant clones in the adjacent normal epithelium. We followed the fate of nascent, microscopic, pre-malignant tumours in a mouse model of oesophageal carcinogenesis and found that most were rapidly lost with no indication of tumour cell death, decreased proliferation or an anti-tumour immune response. However, deep sequencing of ten-day-old and one-year-old tumours showed evidence of selection on the surviving neoplasms. Induction of highly competitive clones in transgenic mice increased early tumour removal, whereas pharmacological inhibition of clonal competition reduced tumour loss. These results support a model in which survival of early neoplasms depends on their competitive fitness relative to that of mutant clones in the surrounding normal tissue. Mutant clones in normal epithelium have an unexpected anti-tumorigenic role in purging early tumours through cell competition, thereby preserving tissue integrity.
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Affiliation(s)
- B Colom
- Wellcome Sanger Institute, Hinxton, UK
| | - A Herms
- Wellcome Sanger Institute, Hinxton, UK
| | - M W J Hall
- Wellcome Sanger Institute, Hinxton, UK
- MRC Cancer Unit, University of Cambridge, Hutchison-MRC Research Centre, Cambridge, UK
| | - S C Dentro
- Wellcome Sanger Institute, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - C King
- Wellcome Sanger Institute, Hinxton, UK
| | - R K Sood
- Wellcome Sanger Institute, Hinxton, UK
| | - M P Alcolea
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Hutchison-MRC Research Centre, Cambridge, UK
| | - G Piedrafita
- Wellcome Sanger Institute, Hinxton, UK
- Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - D Fernandez-Antoran
- Wellcome Sanger Institute, Hinxton, UK
- Wellcome Trust-Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
| | - S H Ong
- Wellcome Sanger Institute, Hinxton, UK
| | | | - K T Mahbubani
- Department of Surgery and Cambridge NIHR Biomedical Research Centre, Cambridge, UK
| | - K Saeb-Parsy
- Department of Surgery and Cambridge NIHR Biomedical Research Centre, Cambridge, UK
| | - M Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - B A Hall
- Department of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom
| | - P H Jones
- Wellcome Sanger Institute, Hinxton, UK.
- MRC Cancer Unit, University of Cambridge, Hutchison-MRC Research Centre, Cambridge, UK.
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33
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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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Georgiades F, Silva ANS, Purohit K, King S, Torpey N, Saeb-Parsy K, Pettigrew GJ, Rouhani FJ. Outpatient ureteric stent removal following kidney transplantation. Br J Surg 2021; 109:152-154. [PMID: 34435203 PMCID: PMC10364773 DOI: 10.1093/bjs/znab223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/18/2021] [Indexed: 11/13/2022]
Abstract
Lay Summary
During a kidney transplant, a plastic tube (stent) is placed in the ureter, connecting the new kidney to the bladder, in order to keep the new join open during the initial phase of transplantation. The stent is then removed after a few weeks via a camera procedure (cystoscopy), as it is no longer needed. The present study compared performing this in the operating theatre or in clinic for transplanted patients using a new single-use type of camera with an integrated grasper system. The results have shown that it is safe and cost-effective to do this in clinic, despite patients being susceptible to infection after transplantation.
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Affiliation(s)
- F Georgiades
- Department of Surgery, University of Cambridge, and Cambridge National Institute for Health Research Biomedical Research Centre, Cambridge, UK
| | - A N S Silva
- Department of Surgery, University of Cambridge, and Cambridge National Institute for Health Research Biomedical Research Centre, Cambridge, UK
| | - K Purohit
- Department of Surgery, University of Cambridge, and Cambridge National Institute for Health Research Biomedical Research Centre, Cambridge, UK
| | - S King
- Transplant Unit, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - N Torpey
- Transplant Unit, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - K Saeb-Parsy
- Department of Surgery, University of Cambridge, and Cambridge National Institute for Health Research Biomedical Research Centre, Cambridge, UK
| | - G J Pettigrew
- Department of Surgery, University of Cambridge, and Cambridge National Institute for Health Research Biomedical Research Centre, Cambridge, UK
| | - F J Rouhani
- Department of Surgery, University of Cambridge, and Cambridge National Institute for Health Research Biomedical Research Centre, Cambridge, UK
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35
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Nowicki-Osuch K, Zhuang L, Jammula S, Bleaney CW, Mahbubani KT, Devonshire G, Katz-Summercorn A, Eling N, Wilbrey-Clark A, Madissoon E, Gamble J, Di Pietro M, O'Donovan M, Meyer KB, Saeb-Parsy K, Sharrocks AD, Teichmann SA, Marioni JC, Fitzgerald RC. Molecular phenotyping reveals the identity of Barrett's esophagus and its malignant transition. Science 2021; 373:760-767. [PMID: 34385390 DOI: 10.1126/science.abd1449] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [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: 06/11/2020] [Revised: 01/26/2021] [Accepted: 06/07/2021] [Indexed: 12/12/2022]
Abstract
The origin of human metaplastic states and their propensity for cancer is poorly understood. Barrett's esophagus is a common metaplastic condition that increases the risk for esophageal adenocarcinoma, and its cellular origin is enigmatic. To address this, we harvested tissues spanning the gastroesophageal junction from healthy and diseased donors, including isolation of esophageal submucosal glands. A combination of single-cell transcriptomic profiling, in silico lineage tracing from methylation, open chromatin and somatic mutation analyses, and functional studies in organoid models showed that Barrett's esophagus originates from gastric cardia through c-MYC and HNF4A-driven transcriptional programs. Furthermore, our data indicate that esophageal adenocarcinoma likely arises from undifferentiated Barrett's esophagus cell types even in the absence of a pathologically identifiable metaplastic precursor, illuminating early detection strategies.
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Affiliation(s)
- Karol Nowicki-Osuch
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge CB2 0X2, UK
| | - Lizhe Zhuang
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge CB2 0X2, UK
| | - Sriganesh Jammula
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Christopher W Bleaney
- Faculty of Biology, Medicine and Health, Michael Smith Building, Oxford Road, University of Manchester, Manchester, UK
| | - Krishnaa T Mahbubani
- Cambridge Biorepository for Translational Medicine (CBTM), NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Ginny Devonshire
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Annalise Katz-Summercorn
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge CB2 0X2, UK
| | - Nils Eling
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Anna Wilbrey-Clark
- Wellcome Sanger Institute, Welcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Elo Madissoon
- Wellcome Sanger Institute, Welcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - John Gamble
- Cambridge Biorepository for Translational Medicine (CBTM), NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Massimiliano Di Pietro
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge CB2 0X2, UK
| | - Maria O'Donovan
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge CB2 0X2, UK
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Welcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Kourosh Saeb-Parsy
- Cambridge Biorepository for Translational Medicine (CBTM), NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Andrew D Sharrocks
- Faculty of Biology, Medicine and Health, Michael Smith Building, Oxford Road, University of Manchester, Manchester, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Welcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
| | - John C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- Wellcome Sanger Institute, Welcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Rebecca C Fitzgerald
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge CB2 0X2, UK.
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36
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Petrus-Reurer S, Romano M, Howlett S, Jones JL, Lombardi G, Saeb-Parsy K. Immunological considerations and challenges for regenerative cellular therapies. Commun Biol 2021; 4:798. [PMID: 34172826 PMCID: PMC8233383 DOI: 10.1038/s42003-021-02237-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [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: 11/09/2020] [Accepted: 05/17/2021] [Indexed: 02/06/2023] Open
Abstract
The central goal of regenerative medicine is to replace damaged or diseased tissue with cells that integrate and function optimally. The capacity of pluripotent stem cells to produce unlimited numbers of differentiated cells is of considerable therapeutic interest, with several clinical trials underway. However, the host immune response represents an important barrier to clinical translation. Here we describe the role of the host innate and adaptive immune responses as triggers of allogeneic graft rejection. We discuss how the immune response is determined by the cellular therapy. Additionally, we describe the range of available in vitro and in vivo experimental approaches to examine the immunogenicity of cellular therapies, and finally we review potential strategies to ameliorate immune rejection. In conclusion, we advocate establishment of platforms that bring together the multidisciplinary expertise and infrastructure necessary to comprehensively investigate the immunogenicity of cellular therapies to ensure their clinical safety and efficacy.
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Affiliation(s)
- Sandra Petrus-Reurer
- Department of Surgery, University of Cambridge, and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom.
| | - Marco Romano
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, Guy's Hospital, London, United Kingdom
| | - Sarah Howlett
- Department of Clinical Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Joanne Louise Jones
- Department of Clinical Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Giovanna Lombardi
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, Guy's Hospital, London, United Kingdom
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom.
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37
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Thakare N, Tanase F, Saeb-Parsy K, Atassi N, Endriss R, Kamphuis G, Pérez-Fentes D, Hasan M, Brehmer M, Osther P, Jung H, Turney B, Finch W, Burgess N, Irving S, Dragos L, Liatsikos E, Knoll T, Cauni V, Wiseman O. Stone clearance using the EMS Swiss LithoClast® Trilogy: Results of the European multicentre prospective study in comparison to the BAUS national PCNL outcomes on behalf of European Society of UroTechnology. Eur Urol 2021. [DOI: 10.1016/s0302-2838(21)00665-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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38
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Thakare N, Tanase F, Saeb-Parsy K, Atassi N, Endriss R, Kamphuis G, Pérez-Fentes D, Hasan M, Brehmer M, Osther P, Jung H, Turney B, Finch W, Burgess N, Irving S, Dragos L, Liatsikos E, Knoll T, Cauni V, Wiseman O. Efficacy and safety of the EMS Swiss LithoClast® Trilogy for PCNL: results of the European multicentre prospective study on behalf of European Section of UroTechnology. World J Urol 2021; 39:4247-4253. [PMID: 33991214 PMCID: PMC8122211 DOI: 10.1007/s00345-021-03710-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 01/06/2021] [Accepted: 04/19/2021] [Indexed: 11/28/2022] Open
Abstract
Purpose PCNL requires a lithotrite to efficiently break stones, and some devices include active suction to remove the fragments. We set out to determine the efficacy and safety of the Swiss LithoClast® Trilogy, in a prospective European multicentre evaluation and compared it to published stone clearance rates for Trilogy based on surface area (68.9 mm2/min) and using the 3D calculated stone volume (526.7 mm3/min). Methods Ten European centres participated in this prospective non-randomized study of Trilogy for PCNL. Objective measures of stone clearance rate, device malfunction, complications and stone-free rates were assessed. Each surgeon subjectively evaluated ergonomic and device effectiveness, on a 1–10 scale (10 = extremely ergonomic/effective) and compared to their usual lithotrite on a 1–10 scale (10 = extremely effective). Results One hundred and fifty seven PCNLs using Trilogy were included (53% male, 47% female; mean age 55 years, range 13–84 years). Mean stone clearance rate was 65.55 mm2/min or 945 mm3/min based on calculated 3D volume. Stone-free rate on fluoroscopy screening at the end of the procedure was 83%. Feedback for suction effectiveness was 9.0 with 9.1 for combination and 9.0 for overall effectiveness compared to lithotrite used previously. Ergonomic score was 8.1, the least satisfactory element. Complications included 13 (8.2%) Clavien–Dindo Grade II and 2 (1.3%) Grade III. Probe breakage was seen in 9 (5.7%), none required using a different lithotrite. Conclusions We have demonstrated that Trilogy is highly effective at stone removal. From a user perspective, the device was perceived by surgeons to be highly effective overall and compared to the most commonly used previous lithotrite, with an excellent safety profile.
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Affiliation(s)
- N Thakare
- Department of Urology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Trust, Hills Road, Cambridge, CB2 0QQ, UK.
| | - F Tanase
- Department of Urology, Colentina Clinical Hospital, Șoseaua Ștefan cel Mare 19-21, Bucharest, Romania
| | - K Saeb-Parsy
- Department of Urology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Trust, Hills Road, Cambridge, CB2 0QQ, UK
| | - N Atassi
- Department of Urology, Sindelfingen-Boblingen Medical Center, Sindelfingen, Baden-Wurttemberg, Germany
| | - R Endriss
- Department of Urology, Sindelfingen-Boblingen Medical Center, Sindelfingen, Baden-Wurttemberg, Germany
| | - G Kamphuis
- Amsterdam UMC Locatie AMC, Department of Urology, Amsterdam University Medical Center, Meibergdreef, 91105 AZ, Amsterdam, The Netherlands
| | - D Pérez-Fentes
- Department of Urology, University Hospital Complex of Santiago de Compostela, 15706, Santiago de Compostela, Spain
| | - M Hasan
- Department of Urology, Danderyd University Hospital, Stockholm, Sweden
| | - M Brehmer
- Department of Urology, Danderyd University Hospital, Stockholm, Sweden
| | - P Osther
- Lillebaelt Hospital, Department of Urology, University of Southern Denmark, Beriderbakken 4, Vejle, Denmark
| | - H Jung
- Lillebaelt Hospital, Department of Urology, University of Southern Denmark, Beriderbakken 4, Vejle, Denmark
| | - B Turney
- The Churchill Hospital, Oxford, OX3 7LJ, UK
| | - W Finch
- Department of Urology, Norfolk and Norwich University Hospitals NHS Foundation Trust, Colney Ln, Norwich, NR4 7UY, UK
| | - N Burgess
- Department of Urology, Norfolk and Norwich University Hospitals NHS Foundation Trust, Colney Ln, Norwich, NR4 7UY, UK
| | - S Irving
- Department of Urology, Norfolk and Norwich University Hospitals NHS Foundation Trust, Colney Ln, Norwich, NR4 7UY, UK
| | - L Dragos
- Department of Urology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Trust, Hills Road, Cambridge, CB2 0QQ, UK
| | - E Liatsikos
- Department of Urology, University Hospital, University of Patras, Rio, 26500, Patras, Greece
| | - T Knoll
- Department of Urology, Sindelfingen-Boblingen Medical Center, Sindelfingen, Baden-Wurttemberg, Germany
| | - V Cauni
- Department of Urology, Colentina Clinical Hospital, Șoseaua Ștefan cel Mare 19-21, Bucharest, Romania
| | - O Wiseman
- Department of Urology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Trust, Hills Road, Cambridge, CB2 0QQ, UK
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Hamed M, Logan A, Gruszczyk AV, Beach TE, James AM, Dare AJ, Barlow A, Martin J, Georgakopoulos N, Gane AM, Crick K, Fouto D, Fear C, Thiru S, Dolezalova N, Ferdinand JR, Clatworthy MR, Hosgood SA, Nicholson ML, Murphy MP, Saeb-Parsy K. Mitochondria-targeted antioxidant MitoQ ameliorates ischaemia-reperfusion injury in kidney transplantation models. Br J Surg 2021; 108:1072-1081. [PMID: 33963377 DOI: 10.1093/bjs/znab108] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 02/28/2021] [Indexed: 11/12/2022]
Abstract
BACKGROUND Ischaemia-reperfusion (IR) injury makes a major contribution to graft damage during kidney transplantation. Oxidative damage to mitochondria is an early event in IR injury. Therefore, the uptake, safety, and efficacy of the mitochondria-targeted antioxidant MitoQ were investigated in models of transplant IR injury. METHODS MitoQ uptake by warm and cooled pairs of pig and declined human kidneys was measured when preserved in cold static storage or by hypothermic machine perfusion. Pairs of pigs' kidneys were exposed to defined periods of warm and cold ischaemia, flushed and stored at 4°C with or without MitoQ (50 nmol/l to 250 µmol/l), followed by reperfusion with oxygenated autologous blood in an ex vivo normothermic perfusion (EVNP). Pairs of declined human kidneys were flushed and stored with or without MitoQ (5-100 µmol/l) at 4°C for 6 h and underwent EVNP with ABO group-matched blood. RESULTS Stable and concentration-dependent uptake of MitoQ was demonstrated for up to 24 h in pig and human kidneys. Total blood flow and urine output were significantly greater in pig kidneys treated with 50 µmol/l MitoQ compared with controls (P = 0.006 and P = 0.007 respectively). In proof-of-concept experiments, blood flow after 1 h of EVNP was significantly greater in human kidneys treated with 50 µmol/l MitoQ than in controls (P ≤ 0.001). Total urine output was numerically higher in the 50-µmol/l MitoQ group compared with the control, but the difference did not reach statistical significance (P = 0.054). CONCLUSION Mitochondria-targeted antioxidant MitoQ can be administered to ischaemic kidneys simply and effectively during cold storage, and may improve outcomes after transplantation.
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Affiliation(s)
- M Hamed
- Department of Surgery, University of Cambridge, Cambridge, UK.,MRC Mitochondrial Biology Unit, Cambridge, UK.,Cambridge National Institute for Health Research (NIHR) Biomedical Research Centre and NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, Cambridge, UK
| | - A Logan
- MRC Mitochondrial Biology Unit, Cambridge, UK
| | - A V Gruszczyk
- Department of Surgery, University of Cambridge, Cambridge, UK.,MRC Mitochondrial Biology Unit, Cambridge, UK.,Cambridge National Institute for Health Research (NIHR) Biomedical Research Centre and NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, Cambridge, UK
| | - T E Beach
- Department of Surgery, University of Cambridge, Cambridge, UK.,MRC Mitochondrial Biology Unit, Cambridge, UK.,Cambridge National Institute for Health Research (NIHR) Biomedical Research Centre and NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, Cambridge, UK
| | - A M James
- MRC Mitochondrial Biology Unit, Cambridge, UK
| | - A J Dare
- Department of Surgery, University of Cambridge, Cambridge, UK.,MRC Mitochondrial Biology Unit, Cambridge, UK
| | - A Barlow
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - J Martin
- Department of Surgery, University of Cambridge, Cambridge, UK.,MRC Mitochondrial Biology Unit, Cambridge, UK.,Cambridge National Institute for Health Research (NIHR) Biomedical Research Centre and NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, Cambridge, UK
| | - N Georgakopoulos
- Department of Surgery, University of Cambridge, Cambridge, UK.,Cambridge National Institute for Health Research (NIHR) Biomedical Research Centre and NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, Cambridge, UK
| | - A M Gane
- Department of Surgery, University of Cambridge, Cambridge, UK.,MRC Mitochondrial Biology Unit, Cambridge, UK
| | - K Crick
- Department of Surgery, University of Cambridge, Cambridge, UK.,Cambridge National Institute for Health Research (NIHR) Biomedical Research Centre and NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, Cambridge, UK
| | - D Fouto
- Department of Surgery, University of Cambridge, Cambridge, UK.,Cambridge National Institute for Health Research (NIHR) Biomedical Research Centre and NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, Cambridge, UK
| | - C Fear
- Department of Surgery, University of Cambridge, Cambridge, UK.,Cambridge National Institute for Health Research (NIHR) Biomedical Research Centre and NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, Cambridge, UK
| | - S Thiru
- Department of Pathology, Cambridge University Hospitals NHS Trust, Addenbrooke's Hospital, Cambridge, UK
| | - N Dolezalova
- Department of Surgery, University of Cambridge, Cambridge, UK.,Cambridge National Institute for Health Research (NIHR) Biomedical Research Centre and NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, Cambridge, UK
| | - J R Ferdinand
- Cambridge National Institute for Health Research (NIHR) Biomedical Research Centre and NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, Cambridge, UK.,Department of Medicine, University of Cambridge, Cambridge, UK
| | - M R Clatworthy
- Cambridge National Institute for Health Research (NIHR) Biomedical Research Centre and NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, Cambridge, UK.,Department of Medicine, University of Cambridge, Cambridge, UK
| | - S A Hosgood
- Department of Surgery, University of Cambridge, Cambridge, UK.,Cambridge National Institute for Health Research (NIHR) Biomedical Research Centre and NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, Cambridge, UK
| | - M L Nicholson
- Department of Surgery, University of Cambridge, Cambridge, UK.,Cambridge National Institute for Health Research (NIHR) Biomedical Research Centre and NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, Cambridge, UK
| | - M P Murphy
- MRC Mitochondrial Biology Unit, Cambridge, UK.,Department of Medicine, University of Cambridge, Cambridge, UK
| | - K Saeb-Parsy
- Department of Surgery, University of Cambridge, Cambridge, UK.,Cambridge National Institute for Health Research (NIHR) Biomedical Research Centre and NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, Cambridge, UK
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Abascal F, Harvey LMR, Mitchell E, Lawson ARJ, Lensing SV, Ellis P, Russell AJC, Alcantara RE, Baez-Ortega A, Wang Y, Kwa EJ, Lee-Six H, Cagan A, Coorens THH, Chapman MS, Olafsson S, Leonard S, Jones D, Machado HE, Davies M, Øbro NF, Mahubani KT, Allinson K, Gerstung M, Saeb-Parsy K, Kent DG, Laurenti E, Stratton MR, Rahbari R, Campbell PJ, Osborne RJ, Martincorena I. Somatic mutation landscapes at single-molecule resolution. Nature 2021; 593:405-410. [PMID: 33911282 DOI: 10.1038/s41586-021-03477-4] [Citation(s) in RCA: 187] [Impact Index Per Article: 62.3] [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: 11/13/2020] [Accepted: 03/22/2021] [Indexed: 02/02/2023]
Abstract
Somatic mutations drive the development of cancer and may contribute to ageing and other diseases1,2. Despite their importance, the difficulty of detecting mutations that are only present in single cells or small clones has limited our knowledge of somatic mutagenesis to a minority of tissues. Here, to overcome these limitations, we developed nanorate sequencing (NanoSeq), a duplex sequencing protocol with error rates of less than five errors per billion base pairs in single DNA molecules from cell populations. This rate is two orders of magnitude lower than typical somatic mutation loads, enabling the study of somatic mutations in any tissue independently of clonality. We used this single-molecule sensitivity to study somatic mutations in non-dividing cells across several tissues, comparing stem cells to differentiated cells and studying mutagenesis in the absence of cell division. Differentiated cells in blood and colon displayed remarkably similar mutation loads and signatures to their corresponding stem cells, despite mature blood cells having undergone considerably more divisions. We then characterized the mutational landscape of post-mitotic neurons and polyclonal smooth muscle, confirming that neurons accumulate somatic mutations at a constant rate throughout life without cell division, with similar rates to mitotically active tissues. Together, our results suggest that mutational processes that are independent of cell division are important contributors to somatic mutagenesis. We anticipate that the ability to reliably detect mutations in single DNA molecules could transform our understanding of somatic mutagenesis and enable non-invasive studies on large-scale cohorts.
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Affiliation(s)
| | | | - Emily Mitchell
- Wellcome Sanger Institute, Hinxton, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
| | | | | | - Peter Ellis
- Wellcome Sanger Institute, Hinxton, UK
- Inivata, Babraham Research Campus, Cambridge, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Megan Davies
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
| | - Nina F Øbro
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Krishnaa T Mahubani
- Department of Haematology, University of Cambridge, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Kieren Allinson
- Cambridge Brain Bank, Division of the Human Research Tissue Bank, Addenbrooke's Hospital, Cambridge, UK
| | - Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - David G Kent
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
- York Biomedical Research Institute, Department of Biology, University of York, York, UK
| | - Elisa Laurenti
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | | | | | - Peter J Campbell
- Wellcome Sanger Institute, Hinxton, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Robert J Osborne
- Wellcome Sanger Institute, Hinxton, UK.
- Biofidelity, Cambridge Science Park, Cambridge, UK.
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Hamed MO, Barlow AD, Dolezalova N, Khosla S, Sagar A, Gribble FM, Davies S, Murphy MP, Hosgood SA, Nicholson ML, Saeb-Parsy K. Ex vivo normothermic perfusion of isolated segmental porcine bowel: a novel functional model of the small intestine. BJS Open 2021; 5:6220254. [PMID: 33839750 PMCID: PMC8038264 DOI: 10.1093/bjsopen/zrab009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/26/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND There is an unmet need for suitable ex vivo large animal models in experimental gastroenterology and intestinal transplantation. This study details a reliable and effective technique for ex vivo normothermic perfusion (EVNP) of segmental porcine small intestine. METHODS Segments of small intestine, 1.5-3.0 m in length, were retrieved from terminally anaesthetized pigs. After a period of cold ischaemia, EVNP was performed for 2 h at 37°C with a mean pressure of 80 mmHg using oxygenated autologous blood diluted with Ringer's solution. The duration of EVNP was extended to 4 h for a second set of experiments in which two segments of proximal to mid-ileum (1.5-3.0 m) were retrieved from each animal and reperfused with whole blood (control) or leucocyte-depleted blood to examine the impact of leucocyte depletion on reperfusion injury. RESULTS After a mean cold ischaemia time of 5 h and 20 min, EVNP was performed in an initial group of four pigs. In the second set of experiments, five pigs were used in each group. In all experiments bowel segments were well perfused and exhibited peristalsis during EVNP. Venous glucose levels significantly increased following luminal glucose stimulation (mean(s.e.m.) basal level 1.8(0.6) mmol/l versus peak 15.5(5.8) mmol/l; P < 0.001) and glucagon-like peptide 1 (GLP-1) levels increased in all experiments, demonstrating intact absorptive and secretory intestinal functions. There were no significant differences between control and leucocyte-depleted animals regarding blood flow, venous glucose, GLP-1 levels or histopathology at the end of 4 h of EVNP. CONCLUSIONS This novel model is suitable for the investigation of gastrointestinal physiology, pathology and ischaemia reperfusion injury, along with evaluation of potential therapeutic interventions.
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Affiliation(s)
- M O Hamed
- Correspondence to: Department of Surgery, Addenbrookes Hospital, Hills Road, Cambridge, CB2 0QQ, UK (e-mail:)
| | - A D Barlow
- Department of Surgery, University of Cambridge, and NIHR Cambridge Biomedical Research Campus, Cambridge, UK
| | - N Dolezalova
- Department of Surgery, University of Cambridge, and NIHR Cambridge Biomedical Research Campus, Cambridge, UK
| | - S Khosla
- Wellcome Trust – MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - A Sagar
- Wellcome Trust – MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - F M Gribble
- Department of Histopathology, University of Cambridge, Cambridge, UK
| | - S Davies
- Department of Histopathology, University of Cambridge, Cambridge, UK
| | - M P Murphy
- MRC Mitochondrial Biology Unit, Cambridge, UK
| | - S A Hosgood
- Department of Surgery, University of Cambridge, and NIHR Cambridge Biomedical Research Campus, Cambridge, UK
| | - M L Nicholson
- Department of Surgery, University of Cambridge, and NIHR Cambridge Biomedical Research Campus, Cambridge, UK
| | - K Saeb-Parsy
- Department of Surgery, University of Cambridge, and NIHR Cambridge Biomedical Research Campus, Cambridge, UK
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42
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Prag HA, Gruszczyk AV, Huang MM, Beach TE, Young T, Tronci L, Nikitopoulou E, Mulvey JF, Ascione R, Hadjihambi A, Shattock MJ, Pellerin L, Saeb-Parsy K, Frezza C, James AM, Krieg T, Murphy MP, Aksentijević D. Mechanism of succinate efflux upon reperfusion of the ischaemic heart. Cardiovasc Res 2021; 117:1188-1201. [PMID: 32766828 PMCID: PMC7983001 DOI: 10.1093/cvr/cvaa148] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/13/2020] [Accepted: 07/28/2020] [Indexed: 12/15/2022] Open
Abstract
AIMS Succinate accumulates several-fold in the ischaemic heart and is then rapidly oxidized upon reperfusion, contributing to reactive oxygen species production by mitochondria. In addition, a significant amount of the accumulated succinate is released from the heart into the circulation at reperfusion, potentially activating the G-protein-coupled succinate receptor (SUCNR1). However, the factors that determine the proportion of succinate oxidation or release, and the mechanism of this release, are not known. METHODS AND RESULTS To address these questions, we assessed the fate of accumulated succinate upon reperfusion of anoxic cardiomyocytes, and of the ischaemic heart both ex vivo and in vivo. The release of accumulated succinate was selective and was enhanced by acidification of the intracellular milieu. Furthermore, pharmacological inhibition, or haploinsufficiency of the monocarboxylate transporter 1 (MCT1) significantly decreased succinate efflux from the reperfused heart. CONCLUSION Succinate release upon reperfusion of the ischaemic heart is mediated by MCT1 and is facilitated by the acidification of the myocardium during ischaemia. These findings will allow the signalling interaction between succinate released from reperfused ischaemic myocardium and SUCNR1 to be explored.
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Affiliation(s)
- Hiran A Prag
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - Anja V Gruszczyk
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
- Department of Surgery, University of Cambridge, Cambridge NIHR Biomedical Research Centre, Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK
| | - Margaret M Huang
- Department of Surgery, University of Cambridge, Cambridge NIHR Biomedical Research Centre, Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK
| | - Timothy E Beach
- Department of Surgery, University of Cambridge, Cambridge NIHR Biomedical Research Centre, Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK
| | - Timothy Young
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Hills Road, Cambridge CB2 0QQ, UK
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, PO Box 197, Cambridge CB2 0XZ, UK
| | - Laura Tronci
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, PO Box 197, Cambridge CB2 0XZ, UK
| | - Efterpi Nikitopoulou
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, PO Box 197, Cambridge CB2 0XZ, UK
| | - John F Mulvey
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - Raimondo Ascione
- Bristol Medical School and Translational Biomedical Research Centre, Faculty of Health Science, University of Bristol, Level 7, Bristol Royal Infirmary, Upper Maudlin Street, Bristol BS2 8HW, UK
| | - Anna Hadjihambi
- Département de Physiologie, Université de Lausanne, 7 Rue du Bugnon, 1005 Lausanne, Switzerland
| | - Michael J Shattock
- King’s College London, British Heart Foundation Centre of Excellence, The Rayne Institute, St Thomas’ Hospital, Lambeth Palace Road, London SE1 7EH, UK
| | - Luc Pellerin
- Département de Physiologie, Université de Lausanne, 7 Rue du Bugnon, 1005 Lausanne, Switzerland
- Centre de Résonance Magnétique des Systèmes Biologiques, UMR5536 CNRS, LabEx TRAIL-IBIO, Université de Bordeaux, 146 Rue Leo Saignat, Bordeaux 33076, France
- Inserm U1082, Université de Poitiers, 2 Rue de la Miletrie, Poitiers 86021, France
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, Cambridge NIHR Biomedical Research Centre, Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK
| | - Christian Frezza
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, PO Box 197, Cambridge CB2 0XZ, UK
| | - Andrew M James
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Thomas Krieg
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - Michael P Murphy
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - Dunja Aksentijević
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, UK
- Centre for inflammation and Therapeutic Innovation, Queen Mary University of London, Charterhouse Square, London, UK
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Sampaziotis F, Muraro D, Tysoe OC, Sawiak S, Beach TE, Godfrey EM, Upponi SS, Brevini T, Wesley BT, Garcia-Bernardo J, Mahbubani K, Canu G, Gieseck R, Berntsen NL, Mulcahy VL, Crick K, Fear C, Robinson S, Swift L, Gambardella L, Bargehr J, Ortmann D, Brown SE, Osnato A, Murphy MP, Corbett G, Gelson WTH, Mells GF, Humphreys P, Davies SE, Amin I, Gibbs P, Sinha S, Teichmann SA, Butler AJ, See TC, Melum E, Watson CJE, Saeb-Parsy K, Vallier L. Cholangiocyte organoids can repair bile ducts after transplantation in the human liver. Science 2021; 371:839-846. [PMID: 33602855 PMCID: PMC7610478 DOI: 10.1126/science.aaz6964] [Citation(s) in RCA: 135] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 05/01/2020] [Accepted: 12/09/2020] [Indexed: 02/02/2023]
Abstract
Organoid technology holds great promise for regenerative medicine but has not yet been applied to humans. We address this challenge using cholangiocyte organoids in the context of cholangiopathies, which represent a key reason for liver transplantation. Using single-cell RNA sequencing, we show that primary human cholangiocytes display transcriptional diversity that is lost in organoid culture. However, cholangiocyte organoids remain plastic and resume their in vivo signatures when transplanted back in the biliary tree. We then utilize a model of cell engraftment in human livers undergoing ex vivo normothermic perfusion to demonstrate that this property allows extrahepatic organoids to repair human intrahepatic ducts after transplantation. Our results provide proof of principle that cholangiocyte organoids can be used to repair human biliary epithelium.
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Affiliation(s)
- Fotios Sampaziotis
- Wellcome and MRC Cambridge Stem Cell Institute,Department of Medicine, University of Cambridge,Cambridge Liver Unit, Cambridge University Hospitals NHS Foundation Trust,Correspondence to: Fotios Sampaziotis, ; Ludovic Vallier,
| | | | - Olivia C. Tysoe
- Wellcome and MRC Cambridge Stem Cell Institute,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research centre, Cambridge, UK
| | - Stephen Sawiak
- University of Cambridge, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Timothy E. Beach
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research centre, Cambridge, UK
| | - Edmund M. Godfrey
- Department of Radiology, Cambridge University Hospitals NHS Foundation Trust
| | - Sara S. Upponi
- Department of Radiology, Cambridge University Hospitals NHS Foundation Trust
| | | | | | - Jose Garcia-Bernardo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Krishnaa Mahbubani
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research centre, Cambridge, UK
| | | | - Richard Gieseck
- Immunopathogenesis Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20852, USA
| | - Natalie L. Berntsen
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway,Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Victoria L. Mulcahy
- Department of Medicine, University of Cambridge,Academic Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Keziah Crick
- Department of Surgery, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Corrina Fear
- Department of Surgery, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Sharayne Robinson
- Department of Surgery, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Lisa Swift
- Department of Surgery, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Laure Gambardella
- Wellcome and MRC Cambridge Stem Cell Institute,Department of Medicine, University of Cambridge
| | - Johannes Bargehr
- Wellcome and MRC Cambridge Stem Cell Institute,Department of Medicine, University of Cambridge,Division of Cardiovascular Medicine, University of Cambridge, ACCI Level 6, Box 110, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | | | | | - Anna Osnato
- Wellcome and MRC Cambridge Stem Cell Institute
| | - Michael P. Murphy
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | | | - William T. H. Gelson
- Department of Medicine, University of Cambridge,Cambridge Liver Unit, Cambridge University Hospitals NHS Foundation Trust
| | - George F. Mells
- Department of Medicine, University of Cambridge,Cambridge Liver Unit, Cambridge University Hospitals NHS Foundation Trust,Academic Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | | | - Susan E. Davies
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Irum Amin
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research centre, Cambridge, UK,Department of Surgery, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Paul Gibbs
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research centre, Cambridge, UK,Department of Surgery, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Sanjay Sinha
- Wellcome and MRC Cambridge Stem Cell Institute,Department of Medicine, University of Cambridge
| | - Sarah A. Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK,Cavendish Laboratory, JJ Thomson Ave, Cambridge CB3 0HE, UK
| | - Andrew J Butler
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research centre, Cambridge, UK,Department of Surgery, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Teik Choon See
- Department of Radiology, Cambridge University Hospitals NHS Foundation Trust
| | - Espen Melum
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway,Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway,Section for Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway,Hybrid Technology Hub-Centre of Excellence, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Christopher J. E. Watson
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research centre, Cambridge, UK,Department of Surgery, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK,National Institute of Health Research (NIHR) Cambridge Biomedical Research Centre, and the NIHR Blood and Transplant Research Unit (BTRU) at the,University of Cambridge in collaboration with Newcastle University and in partnership with NHS Blood and Transplant (NHSBT), Cambridge, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research centre, Cambridge, UK,Department of Surgery, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Ludovic Vallier
- Wellcome and MRC Cambridge Stem Cell Institute,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research centre, Cambridge, UK,Correspondence to: Fotios Sampaziotis, ; Ludovic Vallier,
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44
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Fowler JC, King C, Bryant C, Hall MWJ, Sood R, Ong SH, Earp E, Fernandez-Antoran D, Koeppel J, Dentro SC, Shorthouse D, Durrani A, Fife K, Rytina E, Milne D, Roshan A, Mahububani K, Saeb-Parsy K, Hall BA, Gerstung M, Jones PH. Selection of Oncogenic Mutant Clones in Normal Human Skin Varies with Body Site. Cancer Discov 2021; 11:340-361. [PMID: 33087317 PMCID: PMC7116717 DOI: 10.1158/2159-8290.cd-20-1092] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [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: 07/23/2020] [Revised: 09/24/2020] [Accepted: 10/15/2020] [Indexed: 11/16/2022]
Abstract
Skin cancer risk varies substantially across the body, yet how this relates to the mutations found in normal skin is unknown. Here we mapped mutant clones in skin from high- and low-risk sites. The density of mutations varied by location. The prevalence of NOTCH1 and FAT1 mutations in forearm, trunk, and leg skin was similar to that in keratinocyte cancers. Most mutations were caused by ultraviolet light, but mutational signature analysis suggested differences in DNA-repair processes between sites. Eleven mutant genes were under positive selection, with TP53 preferentially selected in the head and FAT1 in the leg. Fine-scale mapping revealed 10% of clones had copy-number alterations. Analysis of hair follicles showed mutations in the upper follicle resembled adjacent skin, but the lower follicle was sparsely mutated. Normal skin is a dense patchwork of mutant clones arising from competitive selection that varies by location. SIGNIFICANCE: Mapping mutant clones across the body reveals normal skin is a dense patchwork of mutant cells. The variation in cancer risk between sites substantially exceeds that in mutant clone density. More generally, mutant genes cannot be assigned as cancer drivers until their prevalence in normal tissue is known.See related commentary by De Dominici and DeGregori, p. 227.This article is highlighted in the In This Issue feature, p. 211.
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Affiliation(s)
| | | | | | - Michael W J Hall
- Wellcome Sanger Institute, Hinxton, United Kingdom
- MRC Cancer Unit, University of Cambridge, Hutchison-MRC Research Centre, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Roshan Sood
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Swee Hoe Ong
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Eleanor Earp
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | | | | | - Stefan C Dentro
- Wellcome Sanger Institute, Hinxton, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
| | - David Shorthouse
- MRC Cancer Unit, University of Cambridge, Hutchison-MRC Research Centre, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Amer Durrani
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Kate Fife
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Edward Rytina
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Doreen Milne
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Amit Roshan
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Krishnaa Mahububani
- Department of Surgery and Cambridge NIHR Biomedical Research Centre, Biomedical Campus, Cambridge, United Kingdom
| | - Kourosh Saeb-Parsy
- Department of Surgery and Cambridge NIHR Biomedical Research Centre, Biomedical Campus, Cambridge, United Kingdom
| | - Benjamin A Hall
- Department of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom
| | - Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Philip H Jones
- Wellcome Sanger Institute, Hinxton, United Kingdom.
- MRC Cancer Unit, University of Cambridge, Hutchison-MRC Research Centre, Cambridge Biomedical Campus, Cambridge, United Kingdom
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45
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Yu J, Liu Z, Li C, Wei Q, Zheng S, Saeb-Parsy K, Xu X. Regulatory T Cell Therapy Following Liver Transplantation. Liver Transpl 2021; 27:264-280. [PMID: 37160016 DOI: 10.1002/lt.25948] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/25/2020] [Accepted: 10/31/2020] [Indexed: 12/17/2022]
Abstract
Liver transplantation (LT) is considered the gold standard of curative treatment for patients with end-stage liver disease or nonresectable hepatic malignant tumors. Rejection after LT is the main nontechnical factor affecting the prognosis of recipients. Medical and surgical advances, combined with improved immunosuppression with drugs such as calcineurin inhibitors (CNIs), have contributed to an increase in 1-year graft survival to around 80%. However, medium- and long-term improvements in LT outcomes have lagged behind. Importantly, CNIs and other classical immunosuppressive drugs are associated with significant adverse effects, including malignancies, cardiovascular disease, and severe renal dysfunction. Immunomodulation using regulatory T cells (Tregs) is emerging as a promising alternative to classical immunosuppression. Since their discovery, the immunomodulatory effects of Tregs have been demonstrated in a range of diseases. This has rejuvenated the interest in using Tregs as a therapeutic strategy to induce immune tolerance after LT. In this review, we first summarize the discovery and development of Tregs. We then review the preclinical data supporting their production, mechanism of action, and therapeutic efficacy followed by a summary of relevant clinical trials. Finally, we discuss the outstanding challenges of Treg therapy and its future prospects for routine use in LT.
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Affiliation(s)
- Jiongjie Yu
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,National Health and Family Planning Commission (NHFPC) Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China
| | - Zhikun Liu
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,National Health and Family Planning Commission (NHFPC) Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China
| | - Changbiao Li
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,National Health and Family Planning Commission (NHFPC) Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China
| | - Qiang Wei
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,National Health and Family Planning Commission (NHFPC) Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China
| | - Shusen Zheng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,National Health and Family Planning Commission (NHFPC) Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China.,Department of Hepatobiliary and Pancreatic Surgery, Shulan (Hangzhou) Hospital, Hangzhou, China
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, Cambridge, UK.,Cambridge National Institute of Health Research Biomedical Research Centre, Cambridge, UK
| | - Xiao Xu
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,National Health and Family Planning Commission (NHFPC) Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China
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46
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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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47
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Youk J, Kim T, Evans KV, Jeong YI, Hur Y, Hong SP, Kim JH, Yi K, Kim SY, Na KJ, Bleazard T, Kim HM, Fellows M, Mahbubani KT, Saeb-Parsy K, Kim SY, Kim YT, Koh GY, Choi BS, Ju YS, Lee JH. Three-Dimensional Human Alveolar Stem Cell Culture Models Reveal Infection Response to SARS-CoV-2. Cell Stem Cell 2020; 27:905-919.e10. [PMID: 33142113 PMCID: PMC7577700 DOI: 10.1016/j.stem.2020.10.004] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [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: 06/10/2020] [Revised: 08/27/2020] [Accepted: 10/13/2020] [Indexed: 01/22/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the cause of a present pandemic, infects human lung alveolar type 2 (hAT2) cells. Characterizing pathogenesis is crucial for developing vaccines and therapeutics. However, the lack of models mirroring the cellular physiology and pathology of hAT2 cells limits the study. Here, we develop a feeder-free, long-term, three-dimensional (3D) culture technique for hAT2 cells derived from primary human lung tissue and investigate infection response to SARS-CoV-2. By imaging-based analysis and single-cell transcriptome profiling, we reveal rapid viral replication and the increased expression of interferon-associated genes and proinflammatory genes in infected hAT2 cells, indicating a robust endogenous innate immune response. Further tracing of viral mutations acquired during transmission identifies full infection of individual cells effectively from a single viral entry. Our study provides deep insights into the pathogenesis of SARS-CoV-2 and the application of defined 3D hAT2 cultures as models for respiratory diseases.
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Affiliation(s)
- Jeonghwan Youk
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea; GENOME INSIGHT, Inc., Daejeon 34051, Republic of Korea
| | - Taewoo Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Kelly V Evans
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 A0W, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EL, UK
| | - Young-Il Jeong
- Division of Viral Disease Research, Center for Infectious Diseases Research, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Cheongju 28159, Republic of Korea
| | - Yongsuk Hur
- BioMedical Research Center, Korea Advanced institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Seon Pyo Hong
- Center for Vascular Research, Institute for Basic Science, Daejeon 34126, Republic of Korea
| | - Je Hyoung Kim
- Division of Viral Disease Research, Center for Infectious Diseases Research, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Cheongju 28159, Republic of Korea
| | - Kijong Yi
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Su Yeon Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Kwon Joong Na
- Department of Thoracic and Cardiovascular Surgery, Seoul National University Hospital, Seoul National University Cancer Research Institute, Seoul 03080, Republic of Korea
| | - Thomas Bleazard
- The National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK
| | - Ho Min Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea; Center for Biomolecular and Cellular Structure, Institute for Basic Science, Daejeon 34126, Republic of Korea
| | - Mick Fellows
- Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Krishnaa T Mahbubani
- Department of Surgery and Cambridge NIHR Biomedical Research Centre, Biomedical Campus, University of Cambridge, Cambridge CB2 2QQ, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery and Cambridge NIHR Biomedical Research Centre, Biomedical Campus, University of Cambridge, Cambridge CB2 2QQ, UK
| | - Seon Young Kim
- Department of Laboratory Medicine, Chungnam National University College of Medicine, Daejeon 35015, Republic of Korea
| | - Young Tae Kim
- Department of Thoracic and Cardiovascular Surgery, Seoul National University Hospital, Seoul National University Cancer Research Institute, Seoul 03080, Republic of Korea.
| | - Gou Young Koh
- Center for Vascular Research, Institute for Basic Science, Daejeon 34126, Republic of Korea.
| | - Byeong-Sun Choi
- Division of Viral Disease Research, Center for Infectious Diseases Research, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Cheongju 28159, Republic of Korea.
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea; GENOME INSIGHT, Inc., Daejeon 34051, Republic of Korea.
| | - Joo-Hyeon Lee
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 A0W, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EL, UK.
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48
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Lawson ARJ, Abascal F, Coorens THH, Hooks Y, O'Neill L, Latimer C, Raine K, Sanders MA, Warren AY, Mahbubani KTA, Bareham B, Butler TM, Harvey LMR, Cagan A, Menzies A, Moore L, Colquhoun AJ, Turner W, Thomas B, Gnanapragasam V, Williams N, Rassl DM, Vöhringer H, Zumalave S, Nangalia J, Tubío JMC, Gerstung M, Saeb-Parsy K, Stratton MR, Campbell PJ, Mitchell TJ, Martincorena I. Extensive heterogeneity in somatic mutation and selection in the human bladder. Science 2020; 370:75-82. [PMID: 33004514 DOI: 10.1126/science.aba8347] [Citation(s) in RCA: 149] [Impact Index Per Article: 37.3] [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: 01/09/2020] [Accepted: 08/05/2020] [Indexed: 12/17/2022]
Abstract
The extent of somatic mutation and clonal selection in the human bladder remains unknown. We sequenced 2097 bladder microbiopsies from 20 individuals using targeted (n = 1914 microbiopsies), whole-exome (n = 655), and whole-genome (n = 88) sequencing. We found widespread positive selection in 17 genes. Chromatin remodeling genes were frequently mutated, whereas mutations were absent in several major bladder cancer genes. There was extensive interindividual variation in selection, with different driver genes dominating the clonal landscape across individuals. Mutational signatures were heterogeneous across clones and individuals, which suggests differential exposure to mutagens in the urine. Evidence of APOBEC mutagenesis was found in 22% of the microbiopsies. Sequencing multiple microbiopsies from five patients with bladder cancer enabled comparisons with cancer-free individuals and across histological features. This study reveals a rich landscape of mutational processes and selection in normal urothelium with large heterogeneity across clones and individuals.
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Affiliation(s)
- Andrew R J Lawson
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Federico Abascal
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Tim H H Coorens
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Yvette Hooks
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Laura O'Neill
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Calli Latimer
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Keiran Raine
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Mathijs A Sanders
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Department of Hematology, Erasmus University Medical Center, Rotterdam 3015 GD, Netherlands
| | - Anne Y Warren
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Krishnaa T A Mahbubani
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Bethany Bareham
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Timothy M Butler
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Luke M R Harvey
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Alex Cagan
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Andrew Menzies
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Luiza Moore
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Alexandra J Colquhoun
- Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - William Turner
- Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Benjamin Thomas
- The Royal Melbourne Hospital, Parkville, Victoria 3010, Australia
- Department of Surgery, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Vincent Gnanapragasam
- Academic Urology Group, Department of Surgery and Oncology, University of Cambridge, Cambridge CB2 0QQ, UK
- Cambridge Urology Translational Research and Clinical Trials Office, University of Cambridge CB2 0QQ, UK
| | - Nicholas Williams
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Doris M Rassl
- Department of Pathology, Royal Papworth Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0AY, UK
| | - Harald Vöhringer
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Sonia Zumalave
- Mobile Genomes and Disease, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain
| | - Jyoti Nangalia
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - José M C Tubío
- Mobile Genomes and Disease, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain
- The Biomedical Research Centre (CINBIO), University of Vigo, Vigo 36310, Spain
| | - Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Michael R Stratton
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Peter J Campbell
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Department of Haematology, University of Cambridge, Cambridge CB2 2XY, UK
| | - Thomas J Mitchell
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Iñigo Martincorena
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK.
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49
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Litviňuková M, Talavera-López C, Maatz H, Reichart D, Worth CL, Lindberg EL, Kanda M, Polanski K, Heinig M, Lee M, Nadelmann ER, Roberts K, Tuck L, Fasouli ES, DeLaughter DM, McDonough B, Wakimoto H, Gorham JM, Samari S, Mahbubani KT, Saeb-Parsy K, Patone G, Boyle JJ, Zhang H, Zhang H, Viveiros A, Oudit GY, Bayraktar OA, Seidman JG, Seidman CE, Noseda M, Hubner N, Teichmann SA. Cells of the adult human heart. Nature 2020; 588:466-472. [PMID: 32971526 PMCID: PMC7681775 DOI: 10.1038/s41586-020-2797-4] [Citation(s) in RCA: 670] [Impact Index Per Article: 167.5] [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] [Received: 02/10/2020] [Accepted: 09/18/2020] [Indexed: 12/15/2022]
Abstract
Cardiovascular disease is the leading cause of death worldwide. Advanced insights into disease mechanisms and therapeutic strategies require a deeper understanding of the molecular processes involved in the healthy heart. Knowledge of the full repertoire of cardiac cells and their gene expression profiles is a fundamental first step in this endeavour. Here, using state-of-the-art analyses of large-scale single-cell and single-nucleus transcriptomes, we characterize six anatomical adult heart regions. Our results highlight the cellular heterogeneity of cardiomyocytes, pericytes and fibroblasts, and reveal distinct atrial and ventricular subsets of cells with diverse developmental origins and specialized properties. We define the complexity of the cardiac vasculature and its changes along the arterio-venous axis. In the immune compartment, we identify cardiac-resident macrophages with inflammatory and protective transcriptional signatures. Furthermore, analyses of cell-to-cell interactions highlight different networks of macrophages, fibroblasts and cardiomyocytes between atria and ventricles that are distinct from those of skeletal muscle. Our human cardiac cell atlas improves our understanding of the human heart and provides a valuable reference for future studies.
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Affiliation(s)
- Monika Litviňuková
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.,Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Carlos Talavera-López
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.,EMBL - EBI, Wellcome Genome Campus, Hinxton, UK
| | - Henrike Maatz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Daniel Reichart
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Department of Cardiology, University Heart & Vascular Center, University of Hamburg, Hamburg, Germany
| | - Catherine L Worth
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Eric L Lindberg
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Masatoshi Kanda
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.,Department of Rheumatology and Clinical Immunology, Sapporo Medical University, Sapporo, Japan
| | - Krzysztof Polanski
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Matthias Heinig
- Institute of Computational Biology (ICB), HMGU, Neuherberg, Germany.,Department of Informatics, Technische Universitaet Muenchen (TUM), Munich, Germany
| | - Michael Lee
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Kenny Roberts
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Liz Tuck
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Eirini S Fasouli
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Barbara McDonough
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Cardiovascular Division, Brigham and Women's Hospital, Boston, MA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Hiroko Wakimoto
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Joshua M Gorham
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Sara Samari
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Krishnaa T Mahbubani
- Department of Surgery, University of Cambridge, NIHR Cambridge Biomedical Centre, Cambridge Biorepository for Translational Medicine, Cambridge, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, NIHR Cambridge Biomedical Centre, Cambridge Biorepository for Translational Medicine, Cambridge, UK
| | - Giannino Patone
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Joseph J Boyle
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Hongbo Zhang
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.,Department of Histology and Embryology of Zhongshan School of Medicine, Sun-Yat Sen University, Guangzhou, China
| | - Hao Zhang
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada.,Mazankowski Alberta Heart Institute, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Anissa Viveiros
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada.,Mazankowski Alberta Heart Institute, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Gavin Y Oudit
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada.,Mazankowski Alberta Heart Institute, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Omer Ali Bayraktar
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - J G Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA. .,Cardiovascular Division, Brigham and Women's Hospital, Boston, MA, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Michela Noseda
- National Heart and Lung Institute, Imperial College London, London, UK. .,British Heart Foundation Centre of Regenerative Medicine, British Heart Foundation Centre of Research Excellence, Imperial College London, London, UK.
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany. .,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany. .,Charité-Universitätsmedizin, Berlin, Germany. .,Berlin Institute of Health (BIH), Berlin, Germany.
| | - Sarah A Teichmann
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK. .,Deptartment of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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50
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Saeb-Parsy K, Martin JL, Summers DM, Watson CJE, Krieg T, Murphy MP. Mitochondria as Therapeutic Targets in Transplantation. Trends Mol Med 2020; 27:185-198. [PMID: 32952044 DOI: 10.1016/j.molmed.2020.08.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/09/2020] [Accepted: 08/03/2020] [Indexed: 12/23/2022]
Abstract
Advances in surgical procedures, technology, and immune suppression have transformed organ transplantation. However, the metabolic changes that occur during organ retrieval, storage, and implantation have been relatively neglected since the developments many decades ago of cold storage organ preservation solutions. In this review we discuss how the metabolic changes that occur within the organ during transplantation, particularly those associated with mitochondria, may contribute to the outcome. We show how a better understanding of these processes can lead to changes in surgical practice and the development of new drug classes to improve the function and longevity of transplanted grafts, while increasing the pool of organs available for transplantation.
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Affiliation(s)
- Kourosh Saeb-Parsy
- Department of Surgery and Cambridge National Institute for Health Research (NIHR) Biomedical Research Centre, Biomedical Campus, University of Cambridge, Cambridge, CB2 2QQ, UK; NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, Cambridge Biomedical Campus, Cambridge, UK
| | - Jack L Martin
- Department of Surgery and Cambridge National Institute for Health Research (NIHR) Biomedical Research Centre, Biomedical Campus, University of Cambridge, Cambridge, CB2 2QQ, UK; NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, Cambridge Biomedical Campus, Cambridge, UK
| | - Dominic M Summers
- Department of Surgery and Cambridge National Institute for Health Research (NIHR) Biomedical Research Centre, Biomedical Campus, University of Cambridge, Cambridge, CB2 2QQ, UK; NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, Cambridge Biomedical Campus, Cambridge, UK
| | - Christopher J E Watson
- Department of Surgery and Cambridge National Institute for Health Research (NIHR) Biomedical Research Centre, Biomedical Campus, University of Cambridge, Cambridge, CB2 2QQ, UK; NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, Cambridge Biomedical Campus, Cambridge, UK
| | - Thomas Krieg
- Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Michael P Murphy
- Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK; Medical Research Council (MRC) Mitochondrial Biology Unit, Biomedical Campus, University of Cambridge, Cambridge CB2 0XY, UK.
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