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Griffith S, Muir L, Suchanek O, Hope J, Pade C, Gibbons JM, Tuong ZK, Fung A, Touizer E, Rees-Spear C, Nans A, Roustan C, Alguel Y, Fink D, Orkin C, Deayton J, Anderson J, Gupta RK, Doores KJ, Cherepanov P, McKnight Á, Clatworthy M, McCoy LE. Preservation of memory B cell homeostasis in an individual producing broadly neutralising antibodies against HIV-1. bioRxiv 2024:2024.02.05.578789. [PMID: 38370662 PMCID: PMC10871235 DOI: 10.1101/2024.02.05.578789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Immunological determinants favouring emergence of broadly neutralising antibodies are crucial to the development of HIV-1 vaccination strategies. Here, we combined RNAseq and B cell cloning approaches to isolate a broadly neutralising antibody (bnAb) ELC07 from an individual living with untreated HIV-1. Using single particle cryogenic electron microscopy (cryo-EM), we show that the antibody recognises a conformational epitope at the gp120-gp41 interface. ELC07 binds the closed state of the viral glycoprotein causing considerable perturbations to the gp41 trimer core structure. Phenotypic analysis of memory B cell subsets from the ELC07 bnAb donor revealed a lack of expected HIV-1-associated dysfunction, specifically no increase in CD21-/CD27- cells was observed whilst the resting memory (CD21+/CD27+) population appeared preserved despite uncontrolled HIV-1 viraemia. Moreover, single cell transcriptomes of memory B cells from this bnAb donor showed a resting memory phenotype irrespective of the epitope they targeted or their ability to neutralise diverse strains of HIV-1. Strikingly, single memory B cells from the ELC07 bnAb donor were transcriptionally similar to memory B cells from HIV-negative individuals. Our results demonstrate that potent bnAbs can arise without the HIV-1-induced dysregulation of the memory B cell compartment and suggest that sufficient levels of antigenic stimulation with a strategically designed immunogen could be effective in HIV-negative vaccine recipients.
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Affiliation(s)
- Sarah Griffith
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
| | - Luke Muir
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
| | - Ondrej Suchanek
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Joshua Hope
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Corinna Pade
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, UK
| | - Joseph M Gibbons
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, UK
| | - Zewen Kelvin Tuong
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK
- Cellular Genetics, Wellcome Sanger Institute, Cambridge, UK
- Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Audrey Fung
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
| | - Emma Touizer
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
| | - Chloe Rees-Spear
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
| | - Andrea Nans
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
| | - Chloe Roustan
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
| | - Yilmaz Alguel
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Douglas Fink
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
| | - Chloe Orkin
- SHARE collaborative, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Jane Deayton
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, UK
| | - Jane Anderson
- Homerton University Hospital NHS Foundation, London, UK
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Katie J Doores
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
- Department of Infectious Disease, St-Mary's Campus, Imperial College London, London, UK
| | - Áine McKnight
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, UK
| | - Menna Clatworthy
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Cellular Genetics, Wellcome Sanger Institute, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Cambridge, UK
| | - Laura E McCoy
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
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2
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Aguiar R, Bourmpaki E, Bunce C, Coker B, Delaney F, de Jongh L, Oliveira G, Weir A, Higgins F, Spiridou A, Hasan S, Smith J, Mulla A, Glampson B, Mercuri L, Montero R, Hernandez-Fuentes M, Roufosse CA, Simmonds N, Clatworthy M, McLean A, Ploeg R, Davies J, Várnai KA, Woods K, Lord G, Pruthi R, Breen C, Chowdhury P. Incidence, Risk Factors, and Effect on Allograft Survival of Glomerulonephritis Post-transplantation in a United Kingdom Population: Cohort Study. Front Nephrol 2022; 2:923813. [PMID: 37675026 PMCID: PMC10479671 DOI: 10.3389/fneph.2022.923813] [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] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/17/2022] [Indexed: 09/08/2023]
Abstract
Background Post-transplant glomerulonephritis (PTGN) has been associated with inferior long-term allograft survival, and its incidence varies widely in the literature. Methods This is a cohort study of 7,623 patients transplanted between 2005 and 2016 at four major transplant UK centres. The diagnosis of glomerulonephritis (GN) in the allograft was extracted from histology reports aided by the use of text-mining software. The incidence of the four most common GN post-transplantation was calculated, and the risk factors for disease and allograft outcomes were analyzed. Results In total, 214 patients (2.8%) presented with PTGN. IgA nephropathy (IgAN), focal segmental glomerulosclerosis (FSGS), membranous nephropathy (MN), and membranoproliferative/mesangiocapillary GN (MPGN/MCGN) were the four most common forms of post-transplant GN. Living donation, HLA DR match, mixed race, and other ethnic minority groups were associated with an increased risk of developing a PTGN. Patients with PTGN showed a similar allograft survival to those without in the first 8 years of post-transplantation, but the results suggest that they do less well after that timepoint. IgAN was associated with the best allograft survival and FSGS with the worst allograft survival. Conclusions PTGN has an important impact on long-term allograft survival. Significant challenges can be encountered when attempting to analyze large-scale data involving unstructured or complex data points, and the use of computational analysis can assist.
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Affiliation(s)
- Rute Aguiar
- Department of Transplantation and Renal Medicine, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Elli Bourmpaki
- School of Population Health and Environmental Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Catey Bunce
- School of Population Health and Environmental Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Bola Coker
- National Institute for Health and Care Research (NIHR) Biomedical Research Centre, Guy’s & St Thomas’ National Health Service (NHS) Foundation Trust and King’s College London, London, United Kingdom
| | - Florence Delaney
- National Institute for Health and Care Research (NIHR) Biomedical Research Centre, Guy’s & St Thomas’ National Health Service (NHS) Foundation Trust and King’s College London, London, United Kingdom
| | - Leonardo de Jongh
- National Institute for Health and Care Research (NIHR) Biomedical Research Centre, Guy’s & St Thomas’ National Health Service (NHS) Foundation Trust and King’s College London, London, United Kingdom
| | - Giovani Oliveira
- National Institute for Health and Care Research (NIHR) Biomedical Research Centre, Guy’s & St Thomas’ National Health Service (NHS) Foundation Trust and King’s College London, London, United Kingdom
| | - Alistair Weir
- National Institute for Health and Care Research (NIHR) Biomedical Research Centre, Guy’s & St Thomas’ National Health Service (NHS) Foundation Trust and King’s College London, London, United Kingdom
| | - Finola Higgins
- National Institute for Health and Care Research (NIHR) Biomedical Research Centre, Guy’s & St Thomas’ National Health Service (NHS) Foundation Trust and King’s College London, London, United Kingdom
| | - Anastasia Spiridou
- Data Research, Innovation and Virtual Environments Unit (DRIVE), Great Ormond Street Hospital for Children National Health Service (NHS) Foundation Trust, London, United Kingdom
| | - Syed Hasan
- National Institute for Health and Care Research (NIHR) Biomedical Research Centre, Guy’s & St Thomas’ National Health Service (NHS) Foundation Trust and King’s College London, London, United Kingdom
| | - Jonathan Smith
- National Institute for Health and Care Research (NIHR) Biomedical Research Centre, Guy’s & St Thomas’ National Health Service (NHS) Foundation Trust and King’s College London, London, United Kingdom
| | - Abdulrahim Mulla
- National Institute for Health and Care Research (NIHR) Imperial Biomedical Research Centre, Imperial College London and Imperial College Healthcare National Health Service (NHS) Trust, Hammersmith Hospital, London, United Kingdom
| | - Ben Glampson
- Research Informatics Team, Imperial College Healthcare National Health Service (NHS) Trust, London, United Kingdom
| | - Luca Mercuri
- National Institute for Health and Care Research (NIHR) Imperial Biomedical Research Centre, Imperial College London and Imperial College Healthcare National Health Service (NHS) Trust, Hammersmith Hospital, London, United Kingdom
| | - Rosa Montero
- National Institute for Health and Care Research (NIHR) Biomedical Research Centre, Guy’s & St Thomas’ National Health Service (NHS) Foundation Trust and King’s College London, London, United Kingdom
| | | | - Candice A. Roufosse
- Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Naomi Simmonds
- Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Menna Clatworthy
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Adam McLean
- Renal Section, Department of Medicine, Hammersmith Hospital Campus, Imperial College London, London, United Kingdom
| | - Rutger Ploeg
- Nuffield Department of Surgical Sciences, Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Jim Davies
- National Institute for Health and Care Research (NIHR) Oxford Biomedical Research Centre, Big Data Institute, University of Oxford, Oxford, Oxfordshire, United Kingdom
- Department of Computer Science, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Kinga Anna Várnai
- National Institute for Health and Care Research (NIHR) Oxford Biomedical Research Centre, Big Data Institute, University of Oxford, Oxford, Oxfordshire, United Kingdom
- Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, Oxfordshire, United Kingdom
| | - Kerrie Woods
- National Institute for Health and Care Research (NIHR) Oxford Biomedical Research Centre, Big Data Institute, University of Oxford, Oxford, Oxfordshire, United Kingdom
- Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, Oxfordshire, United Kingdom
| | - Graham Lord
- Faculty of Biology Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Rishi Pruthi
- Department of Transplantation and Renal Medicine, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Cormac Breen
- Department of Transplantation and Renal Medicine, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Paramit Chowdhury
- Department of Transplantation and Renal Medicine, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
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3
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Wlodek E, Kirkpatrick RB, Andrews S, Noble R, Schroyer R, Scott J, Watson CJE, Clatworthy M, Harrison EM, Wigmore SJ, Stevenson K, Kingsmore D, Sheerin NS, Bestard O, Stirnadel-Farrant HA, Abberley L, Busz M, DeWall S, Birchler M, Krull D, Thorneloe KS, Weber A, Devey L. A pilot study evaluating GSK1070806 inhibition of interleukin-18 in renal transplant delayed graft function. PLoS One 2021; 16:e0247972. [PMID: 33684160 PMCID: PMC7939287 DOI: 10.1371/journal.pone.0247972] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 12/11/2020] [Indexed: 01/08/2023] Open
Abstract
INTRODUCTION Delayed graft function (DGF) following renal transplantation is a manifestation of acute kidney injury (AKI) leading to poor long-term outcome. Current treatments have limited effectiveness in preventing DGF. Interleukin-18 (IL18), a biomarker of AKI, induces interferon-γ expression and immune activation. GSK1070806, an anti-IL18 monoclonal antibody, neutralizes activated (mature) IL18 released from damaged cells following inflammasome activation. This phase IIa, single-arm trial assessed the effect of a single dose of GSK1070806 on DGF occurrence post donation after circulatory death (DCD) kidney transplantation. METHODS The 3 mg/kg intravenous dose was selected based on prior studies and physiologically based pharmacokinetic (PBPK) modeling, indicating the high likelihood of a rapid and high level of IL18 target engagement when administered prior to kidney allograft reperfusion. Utilization of a Bayesian sequential design with a background standard-of-care DGF rate of 50% based on literature, and confirmed via extensive registry data analyses, enabled a statistical efficacy assessment with a minimal sample size. The primary endpoint was DGF frequency, defined as dialysis requirement ≤7 days post transplantation (except for hyperkalemia). Secondary endpoints included safety, pharmacokinetics and pharmacodynamic biomarkers. RESULTS GSK1070806 administration was associated with IL18-GSK1070806 complex detection and increased total serum IL18 levels due to IL18 half-life prolongation induced by GSK1070806 binding. Interferon-γ-induced chemokine levels declined or remained unchanged in most patients. Although the study was concluded prior to the Bayesian-defined stopping point, 4/7 enrolled patients (57%) had DGF, exceeding the 50% standard-of-care rate, and an additional two patients, although not reaching the protocol-defined DGF definition, demonstrated poor graft function. Six of seven patients experienced serious adverse events (SAEs), including two treatment-related SAEs. CONCLUSION Overall, using a Bayesian design and extensive PBPK dose modeling with only a small sample size, it was deemed unlikely that GSK1070806 would be efficacious in preventing DGF in the enrolled DCD transplant population. TRIAL REGISTRATION NCT02723786.
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Affiliation(s)
- E. Wlodek
- GlaxoSmithKline, Clinical Unit Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - R. B. Kirkpatrick
- GlaxoSmithKline, Philadelphia, Pennsylvania, United States of America
| | - S. Andrews
- GlaxoSmithKline, Philadelphia, Pennsylvania, United States of America
| | - R. Noble
- GlaxoSmithKline, Philadelphia, Pennsylvania, United States of America
| | - R. Schroyer
- GlaxoSmithKline, Philadelphia, Pennsylvania, United States of America
| | - J. Scott
- JMS Statistics Ltd, Pinner, United Kingdom
| | - C. J. E. Watson
- University of Cambridge and the NIHR Cambridge Biomedical Research Centre and the NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation at the University of Cambridge, Cambridge, United Kingdom
| | - M. Clatworthy
- University of Cambridge and the NIHR Cambridge Biomedical Research Centre and the NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation at the University of Cambridge, Cambridge, United Kingdom
| | | | - S. J. Wigmore
- Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - K. Stevenson
- Queen Elizabeth University Hospital, Glasgow, United Kingdom
| | - D. Kingsmore
- Queen Elizabeth University Hospital, Glasgow, United Kingdom
| | - N. S. Sheerin
- Newcastle Biomedical Research Centre and the NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, Newcastle University, Newcastle, United Kingdom
| | - O. Bestard
- L’Hospitalet de Llobregat, Bellvitge University Hospital, Kidney Transplant Unit, Barcelona, Spain
| | | | - L. Abberley
- GlaxoSmithKline, Philadelphia, Pennsylvania, United States of America
| | - M. Busz
- GlaxoSmithKline, Philadelphia, Pennsylvania, United States of America
| | - S. DeWall
- GlaxoSmithKline, Philadelphia, Pennsylvania, United States of America
| | - M. Birchler
- GlaxoSmithKline, Philadelphia, Pennsylvania, United States of America
| | - D. Krull
- GlaxoSmithKline, Philadelphia, Pennsylvania, United States of America
| | - K. S. Thorneloe
- GlaxoSmithKline, Philadelphia, Pennsylvania, United States of America
- * E-mail:
| | - A. Weber
- GlaxoSmithKline, Philadelphia, Pennsylvania, United States of America
| | - L. Devey
- GlaxoSmithKline, Philadelphia, Pennsylvania, United States of America
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4
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Suchanek O, Wijeyesinghe S, Ferdinand J, Tuong ZK, Chandra A, Clare S, Bashford-Rogers R, Lawley T, Okkenhaug K, Masopust D, Clatworthy M. MO064TISSUE-RESIDENT B CELLS DETERMINE SUSCEPTIBILITY TO URINARY TRACT INFECTION BY ORCHESTRATING MACROPHAGE POLARISATION. Nephrol Dial Transplant 2020. [DOI: 10.1093/ndt/gfaa140.mo064] [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: 11/13/2022] Open
Abstract
Abstract
Background
Urinary tract infection (UTI) is an important clinical problem. More than half of women and 1 in 10 men will be affected during their lifetime. Many of these affect the lower urinary tract but recurrent pyelonephritis can lead to scarring and chronic kidney disease. There is an increasing appreciation that tissue-resident immune cells, such as macrophages, play an important role in defence against infection, but only little is known about B lymphocytes in this context. Here we sought to address the question of whether B cells reside in the kidney and bladder in homeostasis and to determine their phenotype and contribution to local organ immunity.
Methods and Results
Using intravenous labelling and parabiosis, we identified a population of bona-fide self-renewing, tissue-resident B cells that included non-naïve and innate-like CD5+ B-1 cells, in murine kidneys and urinary bladder (but also in liver and lung). The size and phenotype of this B cell subset was influenced by genetic background, age, and microbiome, with an expanded population evident after co-housing with pet-store mice. Although kidney B cells had less diverse Igh repertoire compared to blood, their seeding was largely independent of their B-cell receptor specificity. In human kidneys we found a similar enrichment for non-naïve B cells compared to blood and spleen.
Using two strains of genetically modified mice with higher (PI3KδE1020K-B) or lower (μMT-) numbers of tissue-resident B cells, we tested the function of these cells during UTI. Surprisingly, the number of tissue-resident B cells inversely correlated with bacterial clearance. We found that these B cells were spatially co-localised with kidney macrophages and skewed their polarization towards an anti-inflammatory M2 phenotype, leading to reduced anti-microbial responses. This effect was, at least in part, driven via IL-10.
Conclusion
In conclusion, our data identify a critical role for tissue-resident B cells in modulating local immunity in the urinary tract, determining the inflammatory ‘set-point’ of resident and recruited myeloid cells, with important clinical implications for the use of B-cell depleting therapies and conditions such as infection, transplant rejection, fibrosis or autoimmunity.
Graphical Abstract
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Affiliation(s)
- Ondrej Suchanek
- MRC Laboratory of Molecular Biology, Molecular Immunity Unit, Cambridge, United Kingdom
- University of Cambridge, Department of Medicine, Cambridge, United Kingdom
- Addenbrooke's Hospital, Department of Nephrology, Cambridge, United Kingdom
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Sathi Wijeyesinghe
- University of Minnesota, Department of Microbiology and Immunology, Centre for Immunology, Minneapolis, United States of America
| | - John Ferdinand
- MRC Laboratory of Molecular Biology, Molecular Immunity Unit, Cambridge, United Kingdom
- University of Cambridge, Department of Medicine, Cambridge, United Kingdom
| | - Zewen K Tuong
- MRC Laboratory of Molecular Biology, Molecular Immunity Unit, Cambridge, United Kingdom
- University of Cambridge, Department of Medicine, Cambridge, United Kingdom
| | - Anita Chandra
- University of Cambridge, Department Of Pathology, Cambridge, United Kingdom
| | - Simon Clare
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | | | | | - Klaus Okkenhaug
- University of Cambridge, Department Of Pathology, Cambridge, United Kingdom
| | - David Masopust
- University of Minnesota, Department of Microbiology and Immunology, Centre for Immunology, Minneapolis, United States of America
| | - Menna Clatworthy
- MRC Laboratory of Molecular Biology, Molecular Immunity Unit, Cambridge, United Kingdom
- University of Cambridge, Department of Medicine, Cambridge, United Kingdom
- Addenbrooke's Hospital, Department of Nephrology, Cambridge, United Kingdom
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5
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Farkas AM, Baranyi U, Böhmig GA, Unger L, Hopf S, Wahrmann M, Regele H, Mahr B, Schwarz C, Hock K, Pilat N, Kristo I, Mraz J, Lupinek C, Thalhamer J, Bond G, Kuessel L, Wlodek E, Martin J, Clatworthy M, Pettigrew G, Valenta R, Wekerle T. Allograft rejection is associated with development of functional IgE specific for donor MHC antigens. J Allergy Clin Immunol 2019; 143:335-345.e12. [PMID: 30009843 DOI: 10.1016/j.jaci.2018.06.034] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 07/26/2017] [Revised: 06/07/2018] [Accepted: 06/14/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND Donor-specific antibodies of the IgG isotype are measured routinely for diagnostic purposes in renal transplant recipients and are associated with antibody-mediated rejection and long-term graft loss. OBJECTIVE This study aimed to investigate whether MHC-specific antibodies of the IgE isotype are induced during allograft rejection. METHODS Anti-MHC/HLA IgE levels were measured in sera of mice grafted with skin or heart transplants from various donor strains and in sera of kidney transplant patients with high levels of HLA IgG. Mediator release was triggered in vitro by stimulating basophils that were coated with murine or human IgE-positive serum, respectively, with specific recombinant MHC/HLA antigens. Kidney tissue samples obtained from organ donors were analyzed by using flow cytometry for cells expressing the high-affinity receptor for IgE (FcεRI). RESULTS Donor MHC class I- and MHC class II-specific IgE was found on acute rejection of skin and heart grafts in several murine strain combinations, as well as during chronic antibody-mediated heart graft rejection. Anti-HLA IgE, including donor HLA class I and II specificities, was identified in a group of sensitized transplant recipients. Murine and human anti-MHC/HLA IgE triggered mediator release in coated basophils on stimulation with specific MHC/HLA antigens. HLA-specific IgE was not linked to atopy, and allergen-specific IgE present in allergic patients did not cross-react with HLA antigens. FcεRI+ cells were found in the human renal cortex and medulla and provide targets for HLA-specific IgE. CONCLUSION These results demonstrate that MHC/HLA-specific IgE develops during an alloresponse and is functional in mediating effector mechanisms.
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Affiliation(s)
- Andreas M Farkas
- Section of Transplantation Immunology, Department of Surgery, Medical University of Vienna, Vienna, Austria
| | - Ulrike Baranyi
- Section of Transplantation Immunology, Department of Surgery, Medical University of Vienna, Vienna, Austria; Cardiac Surgery Laboratory, Medical University of Vienna, Vienna, Austria
| | - Georg A Böhmig
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Lukas Unger
- Section of Transplantation Immunology, Department of Surgery, Medical University of Vienna, Vienna, Austria
| | - Stefan Hopf
- Section of Transplantation Immunology, Department of Surgery, Medical University of Vienna, Vienna, Austria
| | - Markus Wahrmann
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Heinz Regele
- Institute of Clinical Pathology, Medical University of Vienna, Vienna, Austria
| | - Benedikt Mahr
- Section of Transplantation Immunology, Department of Surgery, Medical University of Vienna, Vienna, Austria
| | - Christoph Schwarz
- Section of Transplantation Immunology, Department of Surgery, Medical University of Vienna, Vienna, Austria
| | - Karin Hock
- Section of Transplantation Immunology, Department of Surgery, Medical University of Vienna, Vienna, Austria
| | - Nina Pilat
- Section of Transplantation Immunology, Department of Surgery, Medical University of Vienna, Vienna, Austria
| | - Ivan Kristo
- Section of Transplantation Immunology, Department of Surgery, Medical University of Vienna, Vienna, Austria
| | - Jasmin Mraz
- Section of Transplantation Immunology, Department of Surgery, Medical University of Vienna, Vienna, Austria
| | - Christian Lupinek
- Division of Immunopathology, Department of Pathophysiology and Allergy Research, Center of Physiology and Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Josef Thalhamer
- Department of Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Gregor Bond
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Lorenz Kuessel
- Department for Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
| | - Elizabeth Wlodek
- Department of Surgery, University of Cambridge, Cambridge, United Kingdom
| | - Jack Martin
- Department of Surgery, University of Cambridge, Cambridge, United Kingdom
| | - Menna Clatworthy
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Gavin Pettigrew
- Department of Surgery, University of Cambridge, Cambridge, United Kingdom
| | - Rudolf Valenta
- Division of Immunopathology, Department of Pathophysiology and Allergy Research, Center of Physiology and Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Thomas Wekerle
- Section of Transplantation Immunology, Department of Surgery, Medical University of Vienna, Vienna, Austria.
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6
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Young MD, Mitchell TJ, Vieira Braga FA, Tran MGB, Stewart BJ, Ferdinand JR, Collord G, Botting RA, Popescu DM, Loudon KW, Vento-Tormo R, Stephenson E, Cagan A, Farndon SJ, Del Castillo Velasco-Herrera M, Guzzo C, Richoz N, Mamanova L, Aho T, Armitage JN, Riddick ACP, Mushtaq I, Farrell S, Rampling D, Nicholson J, Filby A, Burge J, Lisgo S, Maxwell PH, Lindsay S, Warren AY, Stewart GD, Sebire N, Coleman N, Haniffa M, Teichmann SA, Clatworthy M, Behjati S. Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors. Science 2018; 361:594-599. [PMID: 30093597 PMCID: PMC6104812 DOI: 10.1126/science.aat1699] [Citation(s) in RCA: 426] [Impact Index Per Article: 71.0] [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: 02/01/2018] [Accepted: 07/02/2018] [Indexed: 12/20/2022]
Abstract
Messenger RNA encodes cellular function and phenotype. In the context of human cancer, it defines the identities of malignant cells and the diversity of tumor tissue. We studied 72,501 single-cell transcriptomes of human renal tumors and normal tissue from fetal, pediatric, and adult kidneys. We matched childhood Wilms tumor with specific fetal cell types, thus providing evidence for the hypothesis that Wilms tumor cells are aberrant fetal cells. In adult renal cell carcinoma, we identified a canonical cancer transcriptome that matched a little-known subtype of proximal convoluted tubular cell. Analyses of the tumor composition defined cancer-associated normal cells and delineated a complex vascular endothelial growth factor (VEGF) signaling circuit. Our findings reveal the precise cellular identities and compositions of human kidney tumors.
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Affiliation(s)
| | - Thomas J Mitchell
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | | | - Maxine G B Tran
- UCL Division of Surgery and Interventional Science, Royal Free Hospital, London NW3 2PS, UK
- Specialist Centre for Kidney Cancer, Royal Free Hospital, London NW3 2PS, UK
| | - Benjamin J Stewart
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QQ, UK
| | - John R Ferdinand
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QQ, UK
| | - Grace Collord
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Rachel A Botting
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Dorin-Mirel Popescu
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Kevin W Loudon
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QQ, UK
| | | | - Emily Stephenson
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Alex Cagan
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Sarah J Farndon
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
- UCL Great Ormond Street Hospital Institute of Child Health, London WC1N 1E, UK
| | | | | | - Nathan Richoz
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QQ, UK
| | | | - Tevita Aho
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - James N Armitage
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | | | - Imran Mushtaq
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Stephen Farrell
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Dyanne Rampling
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - James Nicholson
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Andrew Filby
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Johanna Burge
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Steven Lisgo
- Human Developmental Biology Resource, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Patrick H Maxwell
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Susan Lindsay
- Human Developmental Biology Resource, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Anne Y Warren
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Grant D Stewart
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Neil Sebire
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
- UCL Great Ormond Street Hospital Institute of Child Health, London WC1N 1E, UK
| | - Nicholas Coleman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Muzlifah Haniffa
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
- Department of Dermatology, Royal Victoria Infirmary, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 4LP, UK
| | | | - Menna Clatworthy
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK.
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QQ, UK
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
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7
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Hernandez‐Fuentes MP, Franklin C, Rebollo‐Mesa I, Mollon J, Delaney F, Perucha E, Stapleton C, Borrows R, Byrne C, Cavalleri G, Clarke B, Clatworthy M, Feehally J, Fuggle S, Gagliano SA, Griffin S, Hammad A, Higgins R, Jardine A, Keogan M, Leach T, MacPhee I, Mark PB, Marsh J, Maxwell P, McKane W, McLean A, Newstead C, Augustine T, Phelan P, Powis S, Rowe P, Sheerin N, Solomon E, Stephens H, Thuraisingham R, Trembath R, Topham P, Vaughan R, Sacks SH, Conlon P, Opelz G, Soranzo N, Weale ME, Lord GM. Long- and short-term outcomes in renal allografts with deceased donors: A large recipient and donor genome-wide association study. Am J Transplant 2018; 18:1370-1379. [PMID: 29392897 PMCID: PMC6001640 DOI: 10.1111/ajt.14594] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [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: 05/30/2017] [Revised: 10/28/2017] [Accepted: 11/13/2017] [Indexed: 01/25/2023]
Abstract
Improvements in immunosuppression have modified short-term survival of deceased-donor allografts, but not their rate of long-term failure. Mismatches between donor and recipient HLA play an important role in the acute and chronic allogeneic immune response against the graft. Perfect matching at clinically relevant HLA loci does not obviate the need for immunosuppression, suggesting that additional genetic variation plays a critical role in both short- and long-term graft outcomes. By combining patient data and samples from supranational cohorts across the United Kingdom and European Union, we performed the first large-scale genome-wide association study analyzing both donor and recipient DNA in 2094 complete renal transplant-pairs with replication in 5866 complete pairs. We studied deceased-donor grafts allocated on the basis of preferential HLA matching, which provided some control for HLA genetic effects. No strong donor or recipient genetic effects contributing to long- or short-term allograft survival were found outside the HLA region. We discuss the implications for future research and clinical application.
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Affiliation(s)
| | | | | | - Jennifer Mollon
- King's College LondonMRC Centre for TransplantationLondonUK,Department of HaematologyUniversity of Cambridge, Cambridge, UK
| | - Florence Delaney
- King's College LondonMRC Centre for TransplantationLondonUK,NIHR Biomedical Research Centre at Guy's and St Thomas’NHS Foundation Trust and King's College LondonLondonUK
| | | | | | - Richard Borrows
- Renal Institute of BirminghamDepartment of Nephrology and TransplantationBirminghamUK
| | - Catherine Byrne
- Nottingham Renal and Transplant UnitNottingham University Hospitals NHS TrustNottinghamUK
| | | | - Brendan Clarke
- Transplant and Cellular ImmunologyLeeds Teaching Hospitals NHS TrustLeedsUK
| | | | | | - Susan Fuggle
- Transplant Immunology & ImmunogeneticsChurchill HospitalOxfordUK
| | - Sarah A. Gagliano
- Center for Statistical GeneticsDepartment of BiostatisticsUniversity of MichiganAnn ArborMIUSA
| | - Sian Griffin
- Cardiff & Vale University Health BoardCardiff UniversityCardiffUK
| | - Abdul Hammad
- The Royal Liverpool and Broadgreen University HospitalsLiverpoolUK
| | - Robert Higgins
- University Hospitals Coventry and Warwickshire NHS TrustCoventryUK
| | - Alan Jardine
- School of MedicineDentistry and NursingUniversity of GlasgowGlasgowUK
| | | | | | | | - Patrick B. Mark
- School of MedicineDentistry and NursingUniversity of GlasgowGlasgowUK
| | - James Marsh
- Epsom and St Helier University Hospitals TrustCarshaltonUK
| | - Peter Maxwell
- School of MedicineDentistry and Biomedical SciencesQueens University BelfastBelfastUK
| | - William McKane
- Sheffield Kidney InstituteSheffield Teaching Hospitals NHS Foundation TrustSheffieldUK
| | - Adam McLean
- Kidney and TransplantImperial College Healthcare NHS TrustLondonUK
| | | | - Titus Augustine
- Central Manchester University Hospitals NHS TrustManchesterUK
| | | | - Steve Powis
- Division of MedicineUniversity College LondonLondonUK
| | | | - Neil Sheerin
- The Medical SchoolNewcastle University NewcastleNewcastle upon TyneUK
| | - Ellen Solomon
- Division of Genetics& Molecular MedicineKing's College LondonLondonUK
| | | | | | - Richard Trembath
- Division of Genetics& Molecular MedicineKing's College LondonLondonUK
| | | | - Robert Vaughan
- Clinical Transplantation Laboratory at Guy's HospitalGuy's and St Thomas’ NHS TrustLondonUK
| | - Steven H. Sacks
- King's College LondonMRC Centre for TransplantationLondonUK,NIHR Biomedical Research Centre at Guy's and St Thomas’NHS Foundation Trust and King's College LondonLondonUK
| | - Peter Conlon
- Royal College of Surgeons in IrelandDublinIreland,Beaumont HospitalDublinIreland
| | - Gerhard Opelz
- University of HeidelbergTransplantation ImmunologyHeidelbergGermany
| | - Nicole Soranzo
- Welcome Trust Sanger InstituteHuman GeneticsCambridgeUK,Department of HaematologyUniversity of Cambridge, Cambridge, UK
| | - Michael E. Weale
- Division of Genetics& Molecular MedicineKing's College LondonLondonUK,Present address:
Genomics plcOxfordUK
| | - Graham M. Lord
- King's College LondonMRC Centre for TransplantationLondonUK,NIHR Biomedical Research Centre at Guy's and St Thomas’NHS Foundation Trust and King's College LondonLondonUK
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8
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Morrison M, Ferdinand J, Chhatwal A, Borthwick L, Scott III W, Clatworthy M, Fisher A. Identifying Potential Predictive Biomarkers of Successful Ex-vivo Lung Perfusion. J Heart Lung Transplant 2018. [DOI: 10.1016/j.healun.2018.01.606] [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: 10/17/2022] Open
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9
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Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N. The Human Cell Atlas. eLife 2017; 6:e27041. [PMID: 29206104 DOI: 10.1101/121202] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 11/30/2017] [Indexed: 05/28/2023] Open
Abstract
The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body. The Human Cell Atlas Project is an international collaborative effort that aims to define all human cell types in terms of distinctive molecular profiles (such as gene expression profiles) and to connect this information with classical cellular descriptions (such as location and morphology). An open comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease. Here we describe the idea, its potential utility, early proofs-of-concept, and some design considerations for the Human Cell Atlas, including a commitment to open data, code, and community.
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Affiliation(s)
- Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
- Howard Hughes Medical Institute, Chevy Chase, United States
| | - Sarah A Teichmann
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, United Kingdom
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
- Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Christophe Benoist
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States
| | - Ewan Birney
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Bernd Bodenmiller
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Institute of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
| | - Peter Campbell
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Piero Carninci
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, United Kingdom
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Menna Clatworthy
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular Biology, University of Cambridge, Cambridge, United Kingdom
| | - Hans Clevers
- Hubrecht Institute, Princess Maxima Center for Pediatric Oncology and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bart Deplancke
- Institute of Bioengineering, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Ian Dunham
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - James Eberwine
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Roland Eils
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany
| | - Wolfgang Enard
- Department of Biology II, Ludwig Maximilian University Munich, Martinsried, Germany
| | - Andrew Farmer
- Takara Bio United States, Inc., Mountain View, United States
| | - Lars Fugger
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, and MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Berthold Göttgens
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, United States
- Massachusetts General Hospital Cancer Center, Boston, United States
| | - Muzlifah Haniffa
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Martin Hemberg
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Seung Kim
- Departments of Developmental Biology and of Medicine, Stanford University School of Medicine, Stanford, United States
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research and the Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Arnold Kriegstein
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, United States
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, United States
| | - Sten Linnarsson
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Emma Lundberg
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Genetics, Stanford University, Stanford, United States
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - John C Marioni
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Miriam Merad
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Musa Mhlanga
- Division of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine (IDM), Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Martijn Nawijn
- Department of Pathology and Medical Biology, GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Mihai Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Garry Nolan
- Department of Microbiology and Immunology, Stanford University, Stanford, United States
| | - Dana Pe'er
- Computational and Systems Biology Program, Sloan Kettering Institute, New York, United States
| | | | - Chris P Ponting
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephen Quake
- Department of Applied Physics and Department of Bioengineering, Stanford University, Stanford, United States
- Chan Zuckerberg Biohub, San Francisco, United States
| | - Wolf Reik
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
- Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom
| | | | - Joshua Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Rahul Satija
- Department of Biology, New York University, New York, United States
- New York Genome Center, New York University, New York, United States
| | - Ton N Schumacher
- Division of Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Alex Shalek
- Broad Institute of MIT and Harvard, Cambridge, United States
- Institute for Medical Engineering & Science (IMES) and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
- Ragon Institute of MGH, MIT and Harvard, Cambridge, United States
| | - Ehud Shapiro
- Department of Computer Science and Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Padmanee Sharma
- Department of Genitourinary Medical Oncology, Department of Immunology, MD Anderson Cancer Center, University of Texas, Houston, United States
| | - Jay W Shin
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Oliver Stegle
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Michael Stratton
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | | | - Fabian J Theis
- Institute of Computational Biology, German Research Center for Environmental Health, Helmholtz Center Munich, Neuherberg, Germany
- Department of Mathematics, Technical University of Munich, Garching, Germany
| | - Matthias Uhlen
- Science for Life Laboratory and Department of Proteomics, KTH Royal Institute of Technology, Stockholm, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Danish Technical University, Lyngby, Denmark
| | | | - Allon Wagner
- Department of Electrical Engineering and Computer Science and the Center for Computational Biology, University of California, Berkeley, Berkeley, United States
| | - Fiona Watt
- Centre for Stem Cells and Regenerative Medicine, King's College London, London, United Kingdom
| | - Jonathan Weissman
- Howard Hughes Medical Institute, Chevy Chase, United States
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States
- Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
| | - Barbara Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Ramnik Xavier
- Broad Institute of MIT and Harvard, Cambridge, United States
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, United States
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, United States
| | - Nir Yosef
- Ragon Institute of MGH, MIT and Harvard, Cambridge, United States
- Department of Electrical Engineering and Computer Science and the Center for Computational Biology, University of California, Berkeley, Berkeley, United States
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10
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Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N. The Human Cell Atlas. eLife 2017; 6:e27041. [PMID: 29206104 PMCID: PMC5762154 DOI: 10.7554/elife.27041] [Citation(s) in RCA: 1156] [Impact Index Per Article: 165.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 11/30/2017] [Indexed: 12/12/2022] Open
Abstract
The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body. The Human Cell Atlas Project is an international collaborative effort that aims to define all human cell types in terms of distinctive molecular profiles (such as gene expression profiles) and to connect this information with classical cellular descriptions (such as location and morphology). An open comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease. Here we describe the idea, its potential utility, early proofs-of-concept, and some design considerations for the Human Cell Atlas, including a commitment to open data, code, and community.
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Affiliation(s)
- Aviv Regev
- Broad Institute of MIT and HarvardCambridgeUnited States
- Department of BiologyMassachusetts Institute of TechnologyCambridgeUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
| | - Sarah A Teichmann
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
- Cavendish Laboratory, Department of PhysicsUniversity of CambridgeCambridgeUnited Kingdom
| | - Eric S Lander
- Broad Institute of MIT and HarvardCambridgeUnited States
- Department of BiologyMassachusetts Institute of TechnologyCambridgeUnited States
- Department of Systems BiologyHarvard Medical SchoolBostonUnited States
| | - Ido Amit
- Department of ImmunologyWeizmann Institute of ScienceRehovotIsrael
| | - Christophe Benoist
- Division of Immunology, Department of Microbiology and ImmunobiologyHarvard Medical SchoolBostonUnited States
| | - Ewan Birney
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
| | - Bernd Bodenmiller
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
- Institute of Molecular Life SciencesUniversity of ZürichZürichSwitzerland
| | - Peter Campbell
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- Department of HaematologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Piero Carninci
- Cavendish Laboratory, Department of PhysicsUniversity of CambridgeCambridgeUnited Kingdom
- Division of Genomic TechnologiesRIKEN Center for Life Science TechnologiesYokohamaJapan
| | - Menna Clatworthy
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular BiologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Hans Clevers
- Hubrecht Institute, Princess Maxima Center for Pediatric Oncology and University Medical Center UtrechtUtrechtThe Netherlands
| | - Bart Deplancke
- Institute of Bioengineering, School of Life SciencesSwiss Federal Institute of Technology (EPFL)LausanneSwitzerland
| | - Ian Dunham
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
| | - James Eberwine
- Department of Systems Pharmacology and Translational TherapeuticsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Roland Eils
- Division of Theoretical Bioinformatics (B080)German Cancer Research Center (DKFZ)HeidelbergGermany
- Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuantHeidelberg UniversityHeidelbergGermany
| | - Wolfgang Enard
- Department of Biology IILudwig Maximilian University MunichMartinsriedGermany
| | - Andrew Farmer
- Takara Bio United States, Inc.Mountain ViewUnited States
| | - Lars Fugger
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, and MRC Human Immunology Unit, Weatherall Institute of Molecular MedicineJohn Radcliffe Hospital, University of OxfordOxfordUnited Kingdom
| | - Berthold Göttgens
- Department of HaematologyUniversity of CambridgeCambridgeUnited Kingdom
- Wellcome Trust-MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Nir Hacohen
- Broad Institute of MIT and HarvardCambridgeUnited States
- Massachusetts General Hospital Cancer CenterBostonUnited States
| | - Muzlifah Haniffa
- Institute of Cellular MedicineNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | - Martin Hemberg
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Seung Kim
- Departments of Developmental Biology and of MedicineStanford University School of MedicineStanfordUnited States
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research and the Translational Gastroenterology Unit, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
- Oxford NIHR Biomedical Research CentreJohn Radcliffe HospitalOxfordUnited Kingdom
| | - Arnold Kriegstein
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell ResearchUniversity of California, San FranciscoSan FranciscoUnited States
| | - Ed Lein
- Allen Institute for Brain ScienceSeattleUnited States
| | - Sten Linnarsson
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
| | - Emma Lundberg
- Science for Life Laboratory, School of BiotechnologyKTH Royal Institute of TechnologyStockholmSweden
- Department of GeneticsStanford UniversityStanfordUnited States
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene TechnologyKTH Royal Institute of TechnologyStockholmSweden
| | | | - John C Marioni
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Miriam Merad
- Precision Immunology InstituteIcahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Musa Mhlanga
- Division of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine (IDM), Department of Integrative Biomedical Sciences, Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
| | - Martijn Nawijn
- Department of Pathology and Medical Biology, GRIAC Research InstituteUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Mihai Netea
- Department of Internal Medicine and Radboud Center for Infectious DiseasesRadboud University Medical CenterNijmegenThe Netherlands
| | - Garry Nolan
- Department of Microbiology and ImmunologyStanford UniversityStanfordUnited States
| | - Dana Pe'er
- Computational and Systems Biology ProgramSloan Kettering InstituteNew YorkUnited States
| | | | - Chris P Ponting
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Stephen Quake
- Department of Applied Physics and Department of BioengineeringStanford UniversityStanfordUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Wolf Reik
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- Epigenetics ProgrammeThe Babraham InstituteCambridgeUnited Kingdom
- Centre for Trophoblast ResearchUniversity of CambridgeCambridgeUnited Kingdom
| | | | - Joshua Sanes
- Center for Brain Science and Department of Molecular and Cellular BiologyHarvard UniversityCambridgeUnited States
| | - Rahul Satija
- Department of BiologyNew York UniversityNew YorkUnited States
- New York Genome CenterNew York UniversityNew YorkUnited States
| | - Ton N Schumacher
- Division of ImmunologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Alex Shalek
- Broad Institute of MIT and HarvardCambridgeUnited States
- Institute for Medical Engineering & Science (IMES) and Department of ChemistryMassachusetts Institute of TechnologyCambridgeUnited States
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
| | - Ehud Shapiro
- Department of Computer Science and Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Padmanee Sharma
- Department of Genitourinary Medical Oncology, Department of Immunology, MD Anderson Cancer CenterUniversity of TexasHoustonUnited States
| | - Jay W Shin
- Division of Genomic TechnologiesRIKEN Center for Life Science TechnologiesYokohamaJapan
| | - Oliver Stegle
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
| | - Michael Stratton
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | | | - Fabian J Theis
- Institute of Computational BiologyGerman Research Center for Environmental Health, Helmholtz Center MunichNeuherbergGermany
- Department of MathematicsTechnical University of MunichGarchingGermany
| | - Matthias Uhlen
- Science for Life Laboratory and Department of ProteomicsKTH Royal Institute of TechnologyStockholmSweden
- Novo Nordisk Foundation Center for BiosustainabilityDanish Technical UniversityLyngbyDenmark
| | | | - Allon Wagner
- Department of Electrical Engineering and Computer Science and the Center for Computational BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Fiona Watt
- Centre for Stem Cells and Regenerative MedicineKing's College LondonLondonUnited Kingdom
| | - Jonathan Weissman
- Howard Hughes Medical InstituteChevy ChaseUnited States
- Department of Cellular & Molecular PharmacologyUniversity of California, San FranciscoSan FranciscoUnited States
- California Institute for Quantitative Biomedical ResearchUniversity of California, San FranciscoSan FranciscoUnited States
- Center for RNA Systems BiologyUniversity of California, San FranciscoSan FranciscoUnited States
| | - Barbara Wold
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaUnited States
| | - Ramnik Xavier
- Broad Institute of MIT and HarvardCambridgeUnited States
- Center for Computational and Integrative BiologyMassachusetts General HospitalBostonUnited States
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel DiseaseMassachusetts General HospitalBostonUnited States
- Center for Microbiome Informatics and TherapeuticsMassachusetts Institute of TechnologyCambridgeUnited States
| | - Nir Yosef
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
- Department of Electrical Engineering and Computer Science and the Center for Computational BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Human Cell Atlas Meeting Participants
- Broad Institute of MIT and HarvardCambridgeUnited States
- Department of BiologyMassachusetts Institute of TechnologyCambridgeUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
- Cavendish Laboratory, Department of PhysicsUniversity of CambridgeCambridgeUnited Kingdom
- Department of Systems BiologyHarvard Medical SchoolBostonUnited States
- Department of ImmunologyWeizmann Institute of ScienceRehovotIsrael
- Division of Immunology, Department of Microbiology and ImmunobiologyHarvard Medical SchoolBostonUnited States
- Institute of Molecular Life SciencesUniversity of ZürichZürichSwitzerland
- Department of HaematologyUniversity of CambridgeCambridgeUnited Kingdom
- Division of Genomic TechnologiesRIKEN Center for Life Science TechnologiesYokohamaJapan
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular BiologyUniversity of CambridgeCambridgeUnited Kingdom
- Hubrecht Institute, Princess Maxima Center for Pediatric Oncology and University Medical Center UtrechtUtrechtThe Netherlands
- Institute of Bioengineering, School of Life SciencesSwiss Federal Institute of Technology (EPFL)LausanneSwitzerland
- Department of Systems Pharmacology and Translational TherapeuticsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
- Division of Theoretical Bioinformatics (B080)German Cancer Research Center (DKFZ)HeidelbergGermany
- Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuantHeidelberg UniversityHeidelbergGermany
- Department of Biology IILudwig Maximilian University MunichMartinsriedGermany
- Takara Bio United States, Inc.Mountain ViewUnited States
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, and MRC Human Immunology Unit, Weatherall Institute of Molecular MedicineJohn Radcliffe Hospital, University of OxfordOxfordUnited Kingdom
- Wellcome Trust-MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUnited Kingdom
- Massachusetts General Hospital Cancer CenterBostonUnited States
- Institute of Cellular MedicineNewcastle UniversityNewcastle upon TyneUnited Kingdom
- Departments of Developmental Biology and of MedicineStanford University School of MedicineStanfordUnited States
- Peter Medawar Building for Pathogen Research and the Translational Gastroenterology Unit, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
- Oxford NIHR Biomedical Research CentreJohn Radcliffe HospitalOxfordUnited Kingdom
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell ResearchUniversity of California, San FranciscoSan FranciscoUnited States
- Allen Institute for Brain ScienceSeattleUnited States
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
- Science for Life Laboratory, School of BiotechnologyKTH Royal Institute of TechnologyStockholmSweden
- Department of GeneticsStanford UniversityStanfordUnited States
- Science for Life Laboratory, Department of Gene TechnologyKTH Royal Institute of TechnologyStockholmSweden
- National Institute of Biomedical GenomicsKalyaniIndia
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
- Precision Immunology InstituteIcahn School of Medicine at Mount SinaiNew YorkUnited States
- Division of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine (IDM), Department of Integrative Biomedical Sciences, Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
- Department of Pathology and Medical Biology, GRIAC Research InstituteUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
- Department of Internal Medicine and Radboud Center for Infectious DiseasesRadboud University Medical CenterNijmegenThe Netherlands
- Department of Microbiology and ImmunologyStanford UniversityStanfordUnited States
- Computational and Systems Biology ProgramSloan Kettering InstituteNew YorkUnited States
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
- Department of Applied Physics and Department of BioengineeringStanford UniversityStanfordUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
- Epigenetics ProgrammeThe Babraham InstituteCambridgeUnited Kingdom
- Centre for Trophoblast ResearchUniversity of CambridgeCambridgeUnited Kingdom
- Center for Brain Science and Department of Molecular and Cellular BiologyHarvard UniversityCambridgeUnited States
- Department of BiologyNew York UniversityNew YorkUnited States
- New York Genome CenterNew York UniversityNew YorkUnited States
- Division of ImmunologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Institute for Medical Engineering & Science (IMES) and Department of ChemistryMassachusetts Institute of TechnologyCambridgeUnited States
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
- Department of Computer Science and Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
- Department of Genitourinary Medical Oncology, Department of Immunology, MD Anderson Cancer CenterUniversity of TexasHoustonUnited States
- Institute of Computational BiologyGerman Research Center for Environmental Health, Helmholtz Center MunichNeuherbergGermany
- Department of MathematicsTechnical University of MunichGarchingGermany
- Science for Life Laboratory and Department of ProteomicsKTH Royal Institute of TechnologyStockholmSweden
- Novo Nordisk Foundation Center for BiosustainabilityDanish Technical UniversityLyngbyDenmark
- Hubrecht Institute and University Medical Center UtrechtUtrechtThe Netherlands
- Department of Electrical Engineering and Computer Science and the Center for Computational BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Centre for Stem Cells and Regenerative MedicineKing's College LondonLondonUnited Kingdom
- Department of Cellular & Molecular PharmacologyUniversity of California, San FranciscoSan FranciscoUnited States
- California Institute for Quantitative Biomedical ResearchUniversity of California, San FranciscoSan FranciscoUnited States
- Center for RNA Systems BiologyUniversity of California, San FranciscoSan FranciscoUnited States
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaUnited States
- Center for Computational and Integrative BiologyMassachusetts General HospitalBostonUnited States
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel DiseaseMassachusetts General HospitalBostonUnited States
- Center for Microbiome Informatics and TherapeuticsMassachusetts Institute of TechnologyCambridgeUnited States
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11
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Trotter PB, Robb M, Summers D, Watson CJE, Clatworthy M, Bradley JA, Hill QA, Neuberger J. Donors With Immune Thrombocytopenia: Do They Pose a Risk to Transplant Recipients? Am J Transplant 2017; 17:796-802. [PMID: 27935215 DOI: 10.1111/ajt.14105] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [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: 07/31/2016] [Revised: 09/26/2016] [Accepted: 10/21/2016] [Indexed: 01/25/2023]
Abstract
Transplant-mediated alloimmune thrombocytopenia (TMAT) from donors with immune thrombocytopenia (ITP) can result in significant bleeding complications in the recipient. The risk to a recipient of TMAT if they receive an organ from a donor with ITP is unknown. The outcomes of recipients of organs from deceased donors with ITP recorded in the UK Transplant Registry between 2000 and 2015 were reviewed. Twenty-one deceased organ donors had a predonation diagnosis of ITP. These donors were significantly more likely to have died from intracranial hemorrhage than were all other deceased organ donors (85% vs. 57%, p < 0.001). Organs from donors with ITP resulted in 49 organ transplants (31 kidney, 14 liver, four heart), with only one case of TMAT, which occurred in a liver transplant recipient and resulted in death from bleeding complications 18 days posttransplantation. The recipient of a kidney from the same organ donor was not affected. Unadjusted 5-year patient and graft survival was significantly worse for liver transplant recipients from donors with ITP compared with liver transplant recipients from donors without ITP (64% vs. 85%, p = 0.012). Organs from donors with ITP may be considered for transplantation, but livers should be used with caution.
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Affiliation(s)
- P B Trotter
- 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.,Organ Donation and Transplantation Directorate, NHS Blood and Transplant, Bristol, UK
| | - M Robb
- Organ Donation and Transplantation Directorate, NHS Blood and Transplant, Bristol, UK
| | - D Summers
- 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.,Organ Donation and Transplantation Directorate, NHS Blood and Transplant, Bristol, UK
| | - C J E Watson
- 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
| | - M Clatworthy
- 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
| | - J A Bradley
- 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
| | - Q A Hill
- Department of Haematology, St James's University Hospital, Leeds, UK
| | - J Neuberger
- Organ Donation and Transplantation Directorate, NHS Blood and Transplant, Bristol, UK
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12
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Coles TM, Dwyer KA, Mordin M, Williams V, Clatworthy M, Yates P, Hamilton W. Psychometric Evaluation Of The Patient's Knee Implant Performance (PKIP) Questionnaire For The Assessment Of Primary Total Knee Arthroplasty. Value Health 2014; 17:A568. [PMID: 27201888 DOI: 10.1016/j.jval.2014.08.1895] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Affiliation(s)
- T M Coles
- RTI Health Solutions, Research Triangle Park, NC, USA
| | - K A Dwyer
- DePuy Orthopaedics, Inc, Warsaw, IN, USA
| | - M Mordin
- RTI Health Solutions, Ann Arbor, MI, USA
| | - V Williams
- RTI Health Solutions, Research Triangle Park, NC, USA
| | | | - P Yates
- Murdoch Orthopaedic Clinic, Murdoch, New Zealand
| | - W Hamilton
- Anderson Orthopaedic Research Institute, Alexandria, VA, USA
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13
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Affiliation(s)
| | - Kannan Natarajan
- Laboratory of Immunology, Molecular Biology Section NIAID, NIHBETHESDAMDUnited States
| | - Menna Clatworthy
- Laboratory of Systems BiologyLymphocyte Biology Section Cambridge Inst. for Med. Res., U.K.BETHESDAMDUnited States
- NIAID, NIHCambridgeUnited Kingdom
| | - Ze Wang
- Laboratory of Systems Biology, Lymphocyte Biology Section NIAID, NIHBETHESDAMDUnited States
| | - Ronald Germain
- Laboratory of Systems Biology, Lymphocyte Biology Section NIAID, NIHBETHESDAMDUnited States
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14
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Angulo I, Vadas O, Garçon F, Banham-Hall E, Plagnol V, Leahy TR, Baxendale H, Coulter T, Curtis J, Wu C, Blake-Palmer K, Perisic O, Smyth D, Maes M, Fiddler C, Juss J, Cilliers D, Markelj G, Chandra A, Farmer G, Kielkowska A, Clark J, Kracker S, Debré M, Picard C, Pellier I, Jabado N, Morris JA, Barcenas-Morales G, Fischer A, Stephens L, Hawkins P, Barrett JC, Abinun M, Clatworthy M, Durandy A, Doffinger R, Chilvers ER, Cant AJ, Kumararatne D, Okkenhaug K, Williams RL, Condliffe A, Nejentsev S. Phosphoinositide 3-kinase δ gene mutation predisposes to respiratory infection and airway damage. Science 2013; 342:866-71. [PMID: 24136356 DOI: 10.1126/science.1243292] [Citation(s) in RCA: 431] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Genetic mutations cause primary immunodeficiencies (PIDs) that predispose to infections. Here, we describe activated PI3K-δ syndrome (APDS), a PID associated with a dominant gain-of-function mutation in which lysine replaced glutamic acid at residue 1021 (E1021K) in the p110δ protein, the catalytic subunit of phosphoinositide 3-kinase δ (PI3Kδ), encoded by the PIK3CD gene. We found E1021K in 17 patients from seven unrelated families, but not among 3346 healthy subjects. APDS was characterized by recurrent respiratory infections, progressive airway damage, lymphopenia, increased circulating transitional B cells, increased immunoglobulin M, and reduced immunoglobulin G2 levels in serum and impaired vaccine responses. The E1021K mutation enhanced membrane association and kinase activity of p110δ. Patient-derived lymphocytes had increased levels of phosphatidylinositol 3,4,5-trisphosphate and phosphorylated AKT protein and were prone to activation-induced cell death. Selective p110δ inhibitors IC87114 and GS-1101 reduced the activity of the mutant enzyme in vitro, which suggested a therapeutic approach for patients with APDS.
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Affiliation(s)
- Ivan Angulo
- Department of Medicine, University of Cambridge, Cambridge, UK
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15
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Maddison R, Prapavessis H, Clatworthy M, Hall C, Foley L, Harper T, Cupal D, Brewer B. Guided imagery to improve functional outcomes post-anterior cruciate ligament repair: randomized-controlled pilot trial. Scand J Med Sci Sports 2011; 22:816-21. [PMID: 21564307 DOI: 10.1111/j.1600-0838.2011.01325.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Imagery can improve functional outcomes post-anterior cruciate ligament repair (ACLR). Research is needed to investigate potential mechanisms for this effect. The aim of this study was to (a) evaluate the effectiveness of an imagery intervention to improve functional outcomes post-ACLR, and (b) explore potential mechanisms. A randomized-controlled pilot trial was conducted. Participants were randomized to guided imagery and standard rehabilitation or standard rehabilitation alone (control). The primary outcome was knee strength 6-month post-operatively. Secondary outcomes were knee laxity at 6-months, and change in psychological (self-efficacy) and neurohormonal (adrenaline, noradrenaline, dopamine) variables. Participants (n=21; 62% male) were 34.86 (SD 8.84) years. Following the intervention, no statistical differences between groups for knee strength extension at 180°/s (t=-0.43, P=0.67), or at 60°/s (t=-0.72, P=0.48) were found. A statistically significant effect was found for knee laxity, F=4.67, P<0.05, mean difference of -3.02 (95% CI -4.44 to -1.60), favoring the intervention. No differences were found for self-efficacy; however, an overall effect was found for noradrenaline, F(1, 19) 19.65, P<0.001, η(2) =0.52, and dopamine, F(1, 19) 6.23, P=0.02, η(2) =0.29, favoring the intervention. This imagery intervention improved knee laxity and healing-related neurobiological factors.
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Affiliation(s)
- R Maddison
- Clinical Trials Research Unit, School of Population Health, Faculty of Medicine and Health Sciences, University of Auckland, Auckland, New Zealand
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16
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Abstract
Daycase ACL reconstruction is commonly performed under general anaesthesia with a patella tendon graft. We report our experience with hamstring reconstruction under regional anaesthesia. Over a 14-month period, 104 daycase arthroscopic ACL reconstructions were performed by one surgeon and one anaesthetist. All operations were performed under spinal anaesthesia with a femoral nerve block. Patients were discharged with oral analgesia, brace and a cryocuff. One hundred and two patients were prospectively evaluated with a visual analogue pain score (0-10) and a patient satisfaction questionnaire. Of these 102 patients, 101 (99%) were happy to be discharged on the same day. One patient was admitted from the daycase unit, and one patient was re-admitted. Patients were very satisfied with the pain relief provided. The mean visual analogue pain score was 1.0 at discharge, 1.8 in the middle of the first night, and 2.1 on the first post-op day. Patients experienced significantly more pain the day after surgery than the evening of surgery (p=0.04). We conclude that hamstring ACL reconstruction under regional anaesthesia is well tolerated by patients as a daycase procedure.
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Affiliation(s)
- A D Shaw
- Department of Orthopaedic Surgery, Victoria Infirmary, Langside Road, Glasgow G42, United Kingdom.
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Affiliation(s)
- A Amendola
- Department of Orthopedics, University of Iowa Sports Medicine Center, Iowa City, Iowa 52242, USA
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Amendola A, Menon M, Clatworthy M, Fowler PJ. The effect of fixation technique on graft position in anterior cruciate ligament reconstruction. Iowa Orthop J 2003; 23:29-35. [PMID: 14575246 PMCID: PMC1888394] [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] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
The purpose of this paper was to determine the extent to which the technique used in ACL reconstruction and fixation influences graft placement. This is a Comparative Radiographic cohort study. Precise graft placement is one of the most crucial components of a successful anterior cruciate ligament (ACL) reconstruction. Two commonly used techniques of ACL reconstruction are arthroscopic bone-patellar tendon-bone (B-PT-B) autograft with interference screw fixation and semi-tendinosus and gracilis (ST + G) tendon autograft with endobutton femoral and multiple staple belt buckle tibial fixation. Using radiographic measurements of bone tunnel position following ACL reconstruction this study quantified the extent to which these techniques influenced graft placement. Femoral and tibial tunnel position in ACL reconstruction was determined using the post-operative radiographs of 40 male patients who had undergone ACL reconstruction (20 B-PT-B and 20 ST + G). The primary outcome measure was location of bone tunnel position following ACL reconstruction. Measurements were based on the guidelines of Amis et al. Femoral tunnel position of B-PT-B grafts was an average of 9.36% more anterior in the sagittal plane than with ST + G grafts. The mean position of B-PT-B grafts was at 31.11% (SD = 5.45%). The mean position of the ST + G grafts was 21.76% (SD = 6.62%). This difference between the two was found to be significant (p < .001). As demonstrated by this study, placement and orientation may vary to accommodate technique and fixation. Clinical outcomes measured were similar in both groups.
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Affiliation(s)
- A Amendola
- University of Iowa, Sports Medicine Center, Department of Orthopaedic Surgery, Iowa City, 52242, USA.
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19
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Abstract
Posterior cruciate ligament (PCL) injuries have a reported incidence of between 3 and 37%, depending on the clinical setting. The most common mechanism of injury in motor vehicle accidents is a dashboard injury or direct force to the proximal anterior tibia. Sports related injuries result from hyperflexion of the knee with the foot typically plantarflexed. The latter mechanism is the most common cause of isolated PCL injuries, while in the trauma population as many as 95% of patients with knee injuries have combined ligamentous damage. Improved knowledge at an anatomical, biomechanical and clinical level has provided the orthopaedist with a more defined treatment algorithm. Isolated, partial PCL injuries (grades I and II) can best be treated nonoperatively while complete injuries (grade III) may require operative treatment based on clinical symptoms. All combined ligamentous injuries usually respond best with surgical management.
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Affiliation(s)
- A T Janousek
- Center for Sports Medicine and Rehabilitation, University of Pittsburgh Medical Center, Pennsylvania, USA
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Abstract
In this article, the authors assess the natural history of osteoarthritis in the anterior cruciate ligament deficient knee, and examine the factors which may influence its progression: meniscal resection, osteochondral lesions, malalignment, concomitant ligamentous pathology, biological factors, and surgery. The role of anterior cruciate reconstruction, high tibial osteotomy in the coronal and sagittal plane, meniscal allografts, and combined procedures will be reviewed. Finally, the authors' approach to this increasingly common problem is presented.
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Affiliation(s)
- M Clatworthy
- Fowler Kennedy Sport Medicine Clinic, University of Western Ontario, London, Canada
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Lyall HA, Cohen B, Clatworthy M, Constant CR. Results of the Souter-Strathclyde total elbow arthroplasty in patients with rheumatoid arthritis. A preliminary report. J Arthroplasty 1994; 9:279-84. [PMID: 8077976 DOI: 10.1016/0883-5403(94)90082-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The results of 19 consecutive Souter-Strathclyde total elbow arthroplasties (Zimmer, London) in 17 patients with a mean follow-up time of 41 months are reported. Pain relief was achieved in all cases, with 13 elbows becoming entirely pain-free. The mean range of flexion increased 24 degrees and extension improved 8 degrees, with upper limb function greatly improved. The complication rate was 32%, including three nerve palsies, of which two resolved completely, and three early postoperative dislocations. There were two cases of prosthetic loosening, one following revision surgery for a traumatic humeral fracture in the early postoperative period. The authors consider the overall functional results with the Souter-Strathclyde prosthesis to be satisfactory in this group of patients.
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Affiliation(s)
- H A Lyall
- Department of Orthopaedic and Trauma Surgery, Addenbrooke's Hospital, Cambridge, United Kingdom
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