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Chan M, Linn MMN, O'Hagan T, Guerra-Assunção JA, Lackenby A, Workman S, Dacre A, Burns SO, Breuer J, Hart J, Tadros S, Lowe DM. Persistent SARS-CoV-2 PCR Positivity Despite Anti-viral Treatment in Immunodeficient Patients. J Clin Immunol 2023:10.1007/s10875-023-01504-9. [PMID: 37148422 PMCID: PMC10163859 DOI: 10.1007/s10875-023-01504-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 04/27/2023] [Indexed: 05/08/2023]
Abstract
PURPOSE COVID-19 infection in immunodeficient individuals can result in chronically poor health, persistent or relapsing SARS-CoV-2 PCR positivity, and long-term infectious potential. While clinical trials have demonstrated promising outcomes using anti-SARS-CoV-2 medicines in immunocompetent hosts, their ability to achieve sustained viral clearance in immunodeficient patients remains unknown. We therefore aimed to study long-term virological outcomes in patients treated at our centre. METHODS We followed up immunocompromised inpatients treated with casirivimab-imdevimab (Ronapreve) between September and December 2021, and immunocompromised patients who received sotrovimab, molnupiravir, nirmatrelvir/ritonavir (Paxlovid), or no treatment from December 2021 to March 2022. Nasopharyngeal swab and sputum samples were obtained either in hospital or in the community until sustained viral clearance, defined as 3 consecutive negative PCR samples, was achieved. Positive samples were sequenced and analysed for mutations of interest. RESULTS We observed sustained viral clearance in 71 of 103 patients, none of whom died. Of the 32/103 patients where sustained clearance was not confirmed, 6 died (between 2 and 34 days from treatment). Notably, we observed 25 cases of sputum positivity despite negative nasopharyngeal swab samples, as well as recurrence of SARS-CoV-2 positivity following a negative sample in 12 cases. Patients were then divided into those who cleared within 28 days and those with PCR positivity beyond 28 days. We noted lower B cell counts in the group with persistent PCR positivity (mean (SD) 0.06 (0.10) ×109/L vs 0.22 (0.28) ×109/L, p = 0.015) as well as lower IgA (median (IQR) 0.00 (0.00-0.15) g/L vs 0.40 (0.00-0.95) g/L, p = 0.001) and IgM (median (IQR) 0.05 (0.00-0.28) g/L vs 0.35 (0.10-1.10) g/L, p = 0.005). No differences were seen in CD4+ or CD8+ T cell counts. Antiviral treatment did not impact risk of persistent PCR positivity. CONCLUSION Persistent SARS-CoV-2 PCR positivity is common among immunodeficient individuals, especially those with antibody deficiencies, regardless of anti-viral treatment. Peripheral B cell count and serum IgA and IgM levels are predictors of viral persistence.
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Affiliation(s)
- Michele Chan
- Department of Clinical Immunology, Royal Free London NHS Foundation Trust, London, UK
- University College London Medical School, London, UK
| | - Me Me Nay Linn
- Department of Clinical Immunology, Royal Free London NHS Foundation Trust, London, UK
| | - Thomas O'Hagan
- Department of Clinical Immunology, Royal Free London NHS Foundation Trust, London, UK
| | | | | | - Sarita Workman
- Department of Clinical Immunology, Royal Free London NHS Foundation Trust, London, UK
| | - Anna Dacre
- Department of Clinical Immunology, Royal Free London NHS Foundation Trust, London, UK
| | - Siobhan O Burns
- Department of Clinical Immunology, Royal Free London NHS Foundation Trust, London, UK
- Institute of Immunity and Transplantation, University College London, Pears Building, Rowland Hill Street, London, NW3 2PP, UK
| | - Judith Breuer
- Institute of Child Health, University College London, London, UK
| | - Jennifer Hart
- Department of Virology, Royal Free London NHS Foundation Trust, London, UK
| | - Susan Tadros
- Department of Clinical Immunology, Royal Free London NHS Foundation Trust, London, UK
- Institute of Immunity and Transplantation, University College London, Pears Building, Rowland Hill Street, London, NW3 2PP, UK
| | - David M Lowe
- Department of Clinical Immunology, Royal Free London NHS Foundation Trust, London, UK.
- Institute of Immunity and Transplantation, University College London, Pears Building, Rowland Hill Street, London, NW3 2PP, UK.
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2
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Morfopoulou S, Buddle S, Torres Montaguth OE, Atkinson L, Guerra-Assunção JA, Moradi Marjaneh M, Zennezini Chiozzi R, Storey N, Campos L, Hutchinson JC, Counsell JR, Pollara G, Roy S, Venturini C, Antinao Diaz JF, Siam A, Tappouni LJ, Asgarian Z, Ng J, Hanlon KS, Lennon A, McArdle A, Czap A, Rosenheim J, Andrade C, Anderson G, Lee JCD, Williams R, Williams CA, Tutill H, Bayzid N, Martin Bernal LM, Macpherson H, Montgomery KA, Moore C, Templeton K, Neill C, Holden M, Gunson R, Shepherd SJ, Shah P, Cooray S, Voice M, Steele M, Fink C, Whittaker TE, Santilli G, Gissen P, Kaufer BB, Reich J, Andreani J, Simmonds P, Alrabiah DK, Castellano S, Chikowore P, Odam M, Rampling T, Houlihan C, Hoschler K, Talts T, Celma C, Gonzalez S, Gallagher E, Simmons R, Watson C, Mandal S, Zambon M, Chand M, Hatcher J, De S, Baillie K, Semple MG, Martin J, Ushiro-Lumb I, Noursadeghi M, Deheragoda M, Hadzic N, Grammatikopoulos T, Brown R, Kelgeri C, Thalassinos K, Waddington SN, Jacques TS, Thomson E, Levin M, Brown JR, Breuer J. Genomic investigations of unexplained acute hepatitis in children. Nature 2023; 617:564-573. [PMID: 36996872 PMCID: PMC10170458 DOI: 10.1038/s41586-023-06003-w] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [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: 07/25/2022] [Accepted: 03/23/2023] [Indexed: 04/01/2023]
Abstract
Since its first identification in Scotland, over 1,000 cases of unexplained paediatric hepatitis in children have been reported worldwide, including 278 cases in the UK1. Here we report an investigation of 38 cases, 66 age-matched immunocompetent controls and 21 immunocompromised comparator participants, using a combination of genomic, transcriptomic, proteomic and immunohistochemical methods. We detected high levels of adeno-associated virus 2 (AAV2) DNA in the liver, blood, plasma or stool from 27 of 28 cases. We found low levels of adenovirus (HAdV) and human herpesvirus 6B (HHV-6B) in 23 of 31 and 16 of 23, respectively, of the cases tested. By contrast, AAV2 was infrequently detected and at low titre in the blood or the liver from control children with HAdV, even when profoundly immunosuppressed. AAV2, HAdV and HHV-6 phylogeny excluded the emergence of novel strains in cases. Histological analyses of explanted livers showed enrichment for T cells and B lineage cells. Proteomic comparison of liver tissue from cases and healthy controls identified increased expression of HLA class 2, immunoglobulin variable regions and complement proteins. HAdV and AAV2 proteins were not detected in the livers. Instead, we identified AAV2 DNA complexes reflecting both HAdV-mediated and HHV-6B-mediated replication. We hypothesize that high levels of abnormal AAV2 replication products aided by HAdV and, in severe cases, HHV-6B may have triggered immune-mediated hepatic disease in genetically and immunologically predisposed children.
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Affiliation(s)
- Sofia Morfopoulou
- Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK
- Section for Paediatrics, Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Sarah Buddle
- Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Oscar Enrique Torres Montaguth
- Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Laura Atkinson
- Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - José Afonso Guerra-Assunção
- Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Mahdi Moradi Marjaneh
- Section for Paediatrics, Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
- Section of Virology, Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Riccardo Zennezini Chiozzi
- University College London Mass Spectrometry Science Technology Platform, Division of Biosciences, University College London, London, UK
| | - Nathaniel Storey
- Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Luis Campos
- Histopathology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - J Ciaran Hutchinson
- Histopathology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - John R Counsell
- Research Department of Targeted Intervention, Division of Surgery and Interventional Science, University College London, London, UK
| | - Gabriele Pollara
- Division of Infection and Immunity, University College London, London, UK
| | - Sunando Roy
- Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Cristina Venturini
- Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Juan F Antinao Diaz
- Research Department of Targeted Intervention, Division of Surgery and Interventional Science, University College London, London, UK
| | - Ala'a Siam
- Research Department of Targeted Intervention, Division of Surgery and Interventional Science, University College London, London, UK
- Gene Transfer Technology Group, EGA-Institute for Women's Health, University College London, London, UK
| | - Luke J Tappouni
- Research Department of Targeted Intervention, Division of Surgery and Interventional Science, University College London, London, UK
| | - Zeinab Asgarian
- Research Department of Targeted Intervention, Division of Surgery and Interventional Science, University College London, London, UK
| | - Joanne Ng
- Gene Transfer Technology Group, EGA-Institute for Women's Health, University College London, London, UK
| | - Killian S Hanlon
- Research Department of Targeted Intervention, Division of Surgery and Interventional Science, University College London, London, UK
| | - Alexander Lennon
- Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Andrew McArdle
- Section for Paediatrics, Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Agata Czap
- Division of Infection and Immunity, University College London, London, UK
| | - Joshua Rosenheim
- Division of Infection and Immunity, University College London, London, UK
| | - Catarina Andrade
- Histopathology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Glenn Anderson
- Histopathology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Jack C D Lee
- Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Rachel Williams
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Charlotte A Williams
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Helena Tutill
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Nadua Bayzid
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Luz Marina Martin Bernal
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Hannah Macpherson
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London, UK
| | - Kylie-Ann Montgomery
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London, UK
| | - Catherine Moore
- Wales Specialist Virology Centre, Public Health Wales Microbiology Cardiff, University Hospital of Wales, Cardiff, UK
| | - Kate Templeton
- Department of Medical Microbiology, Edinburgh Royal Infirmary, Edinburgh, UK
| | - Claire Neill
- Public Health Agency Northern Ireland, Belfast, UK
| | - Matt Holden
- School of Medicine, University of St. Andrews, St. Andrews, UK
- Public Health Scotland, Edinburgh, UK
| | - Rory Gunson
- West of Scotland Specialist Virology Centre, Glasgow, UK
| | | | - Priyen Shah
- Section for Paediatrics, Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Samantha Cooray
- Section for Paediatrics, Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Marie Voice
- Micropathology Ltd, University of Warwick Science Park, Coventry, UK
| | - Michael Steele
- Micropathology Ltd, University of Warwick Science Park, Coventry, UK
| | - Colin Fink
- Micropathology Ltd, University of Warwick Science Park, Coventry, UK
| | - Thomas E Whittaker
- Molecular and Cellular Immunology, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Giorgia Santilli
- Molecular and Cellular Immunology, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Paul Gissen
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | | | - Jana Reich
- Institute of Virology, Freie Universität Berlin, Berlin, Germany
| | - Julien Andreani
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Centre Hospitalier Universitaire (CHU) Grenoble-Alpes, Grenoble, France
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Dimah K Alrabiah
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
- National Centre for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Sergi Castellano
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
- University College London Genomics, University College London, London, UK
| | | | - Miranda Odam
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Tommy Rampling
- Division of Infection and Immunity, University College London, London, UK
- UK Health Security Agency, London, UK
- Hospital for Tropical Diseases, University College London Hospitals NHS Foundation Trust, London, UK
| | - Catherine Houlihan
- Division of Infection and Immunity, University College London, London, UK
- UK Health Security Agency, London, UK
- Department of Clinical Virology, University College London Hospitals, London, UK
| | | | | | | | | | | | | | | | | | | | | | - James Hatcher
- Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Surjo De
- Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | | | - Malcolm Gracie Semple
- Pandemic Institute, University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children's Hospital NHS Foundation Trust, Liverpool, UK
| | - Joanne Martin
- Centre for Genomics and Child Health, The Blizard Institute, Queen Mary University of London, London, UK
| | | | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London, UK
| | | | | | | | - Rachel Brown
- Department of Cellular Pathology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Chayarani Kelgeri
- Liver Unit, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Konstantinos Thalassinos
- University College London Mass Spectrometry Science Technology Platform, Division of Biosciences, University College London, London, UK
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
| | - Simon N Waddington
- Gene Transfer Technology Group, EGA-Institute for Women's Health, University College London, London, UK
- Medical Research Council Antiviral Gene Therapy Research Unit, Faculty of Health Sciences, University of the Witswatersrand, Johannesburg, South Africa
| | - Thomas S Jacques
- Histopathology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
- Developmental Biology and Cancer Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Emma Thomson
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Michael Levin
- Section for Paediatrics, Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Julianne R Brown
- Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Judith Breuer
- Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK.
- Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.
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3
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Reuschl AK, Mesner D, Shivkumar M, Whelan MVX, Pallett LJ, Guerra-Assunção JA, Madansein R, Dullabh KJ, Sigal A, Thornhill JP, Herrera C, Fidler S, Noursadeghi M, Maini MK, Jolly C. HIV-1 Vpr drives a tissue residency-like phenotype during selective infection of resting memory T cells. Cell Rep 2022; 39:110650. [PMID: 35417711 PMCID: PMC9350556 DOI: 10.1016/j.celrep.2022.110650] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 02/23/2022] [Accepted: 03/17/2022] [Indexed: 12/03/2022] Open
Abstract
HIV-1 replicates in CD4+ T cells, leading to AIDS. Determining how HIV-1 shapes its niche to create a permissive environment is central to informing efforts to limit pathogenesis, disturb reservoirs, and achieve a cure. A key roadblock in understanding HIV-T cell interactions is the requirement to activate T cells in vitro to make them permissive to infection. This dramatically alters T cell biology and virus-host interactions. Here we show that HIV-1 cell-to-cell spread permits efficient, productive infection of resting memory T cells without prior activation. Strikingly, we find that HIV-1 infection primes resting T cells to gain characteristics of tissue-resident memory T cells (TRM), including upregulating key surface markers and the transcription factor Blimp-1 and inducing a transcriptional program overlapping the core TRM transcriptional signature. This reprogramming is driven by Vpr and requires Vpr packaging into virions and manipulation of STAT5. Thus, HIV-1 reprograms resting T cells, with implications for viral replication and persistence.
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Affiliation(s)
- Ann-Kathrin Reuschl
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK.
| | - Dejan Mesner
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Maitreyi Shivkumar
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Matthew V X Whelan
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Laura J Pallett
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | | | - Rajhmun Madansein
- Department of Cardiothoracic Surgery, University of KwaZulu-Natal, Durban 4091, South Africa; Centre for the AIDS Programme of Research in South Africa, Durban 4091, South Africa
| | - Kaylesh J Dullabh
- Department of Cardiothoracic Surgery, University of KwaZulu-Natal, Durban 4091, South Africa
| | - Alex Sigal
- Africa Health Research Institute, Durban 4001, South Africa; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4091, South Africa; Max Planck Institute for Infection Biology, 10117 Berlin, Germany
| | - John P Thornhill
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford OX1 3XY, UK; Department of Infectious Disease, Faculty of Medicine, Imperial College, London W2 1NY, UK
| | - Carolina Herrera
- Department of Infectious Disease, Faculty of Medicine, Imperial College, London W2 1NY, UK
| | - Sarah Fidler
- Department of Infectious Disease, Faculty of Medicine, Imperial College, London W2 1NY, UK; Imperial College NIHR Biomedical Research Centre, London W2 1NY, UK
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Mala K Maini
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Clare Jolly
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK.
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4
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Chandran A, Rosenheim J, Nageswaran G, Swadling L, Pollara G, Gupta RK, Burton AR, Guerra-Assunção JA, Woolston A, Ronel T, Pade C, Gibbons JM, Sanz-Magallon Duque De Estrada B, Robert de Massy M, Whelan M, Semper A, Brooks T, Altmann DM, Boyton RJ, McKnight Á, Captur G, Manisty C, Treibel TA, Moon JC, Tomlinson GS, Maini MK, Chain BM, Noursadeghi M. Rapid synchronous type 1 IFN and virus-specific T cell responses characterize first wave non-severe SARS-CoV-2 infections. Cell Rep Med 2022; 3:100557. [PMID: 35474751 PMCID: PMC8895494 DOI: 10.1016/j.xcrm.2022.100557] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 11/22/2021] [Accepted: 02/09/2022] [Indexed: 12/15/2022]
Abstract
Effective control of SARS-CoV-2 infection on primary exposure may reveal correlates of protective immunity to future variants, but we lack insights into immune responses before or at the time virus is first detected. We use blood transcriptomics, multiparameter flow cytometry, and T cell receptor (TCR) sequencing spanning the time of incident non-severe infection in unvaccinated virus-naive individuals to identify rapid type 1 interferon (IFN) responses common to other acute respiratory viruses and cell proliferation responses that discriminate SARS-CoV-2 from other viruses. These peak by the time the virus is first detected and sometimes precede virus detection. Cell proliferation is most evident in CD8 T cells and associated with specific expansion of SARS-CoV-2-reactive TCRs, in contrast to virus-specific antibodies, which lag by 1-2 weeks. Our data support a protective role for early type 1 IFN and CD8 T cell responses, with implications for development of universal T cell vaccines.
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Affiliation(s)
- Aneesh Chandran
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Joshua Rosenheim
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Gayathri Nageswaran
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Leo Swadling
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Gabriele Pollara
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Rishi K. Gupta
- Institute for Global Health, University College London, London WC1E 6BT, UK
| | - Alice R. Burton
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | | | - Annemarie Woolston
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Tahel Ronel
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Corinna Pade
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, UK
| | - Joseph M. Gibbons
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, UK
| | | | - Marc Robert de Massy
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Matthew Whelan
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Amanda Semper
- National Infection Service, Public Health England, Porton Down, Salisbury SP4 0JQ, UK
| | - Tim Brooks
- National Infection Service, Public Health England, Porton Down, Salisbury SP4 0JQ, UK
| | - Daniel M. Altmann
- Department of Immunology and Inflammation, Imperial College London, London SW7 2BX, UK
| | - Rosemary J. Boyton
- Department of Infectious Disease, Imperial College London, London SW7 2BX, UK
- Lung Division, Royal Brompton and Harefield Hospitals, Guy’s and St Thomas' NHS Foundation Trust, London, UK
| | - Áine McKnight
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, UK
| | - Gabriella Captur
- Institute of Cardiovascular Sciences, University College London, London WC1E 6BT, UK
- MRC Unit for Lifelong Health and Ageing, University College London, London WC1E 6BT, UK
| | - Charlotte Manisty
- Institute of Cardiovascular Sciences, University College London, London WC1E 6BT, UK
| | | | - James C. Moon
- Institute of Cardiovascular Sciences, University College London, London WC1E 6BT, UK
| | - Gillian S. Tomlinson
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Mala K. Maini
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Benjamin M. Chain
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - COVIDsortium Investigators
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
- Institute for Global Health, University College London, London WC1E 6BT, UK
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, UK
- National Infection Service, Public Health England, Porton Down, Salisbury SP4 0JQ, UK
- Department of Immunology and Inflammation, Imperial College London, London SW7 2BX, UK
- Department of Infectious Disease, Imperial College London, London SW7 2BX, UK
- Lung Division, Royal Brompton and Harefield Hospitals, Guy’s and St Thomas' NHS Foundation Trust, London, UK
- Institute of Cardiovascular Sciences, University College London, London WC1E 6BT, UK
- MRC Unit for Lifelong Health and Ageing, University College London, London WC1E 6BT, UK
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5
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Boshier FAT, Venturini C, Stirrup O, Guerra-Assunção JA, Alcolea-Medina A, Becket AH, Byott M, Charalampous T, Filipe ADS, Frampton D, Glaysher S, Khan T, Kulasegara-Shylini R, Kele B, Monahan IM, Mollett G, Parker M, Pelosi E, Randell P, Roy S, Taylor JF, Weller SJ, Wilson-Davies E, Wade P, Williams R, Copas AJ, Cutino-Moguel T, Freemantle N, Hayward AC, Holmes A, Hughes J, Mahungu TW, Nebbia G, Nastouli E, Partridge DG, Pope CF, Price JR, Robson SC, Saeed K, Shin GY, de Silva TI, Snell LB, Thomson EC, Witney AA, Breuer J. The Alpha variant was not associated with excess nosocomial SARS-CoV-2 infection in a multi-centre UK hospital study. J Infect 2021; 83:693-700. [PMID: 34610391 PMCID: PMC8487101 DOI: 10.1016/j.jinf.2021.09.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 09/12/2021] [Indexed: 12/15/2022]
Abstract
OBJECTIVES Recently emerging SARS-CoV-2 variants have been associated with an increased rate of transmission within the community. We sought to determine whether this also resulted in increased transmission within hospitals. METHODS We collected viral sequences and epidemiological data of patients with community and healthcare associated SARS-CoV-2 infections, sampled from 16th November 2020 to 10th January 2021, from nine hospitals participating in the COG-UK HOCI study. Outbreaks were identified using ward information, lineage and pairwise genetic differences between viral sequences. RESULTS Mixed effects logistic regression analysis of 4184 sequences showed healthcare-acquired infections were no more likely to be identified as the Alpha variant than community acquired infections. Nosocomial outbreaks were investigated based on overlapping ward stay and SARS-CoV-2 genome sequence similarity. There was no significant difference in the number of patients involved in outbreaks caused by the Alpha variant compared to outbreaks caused by other lineages. CONCLUSIONS We find no evidence to support it causing more nosocomial transmission than previous lineages. This suggests that the stringent infection prevention measures already in place in UK hospitals contained the spread of the Alpha variant as effectively as other less transmissible lineages, providing reassurance of their efficacy against emerging variants of concern.
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Affiliation(s)
- Florencia A T Boshier
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Cristina Venturini
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Oliver Stirrup
- Institute for Global Health, University College London, London, United Kingdom
| | - José Afonso Guerra-Assunção
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom; Department of Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Adela Alcolea-Medina
- Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom; Infection Sciences, Viapath, London, United Kingdom
| | - Angela H Becket
- Centre for Enzyme Innovation, University of Portsmouth, Portsmouth PO1 2DT, United Kingdom; School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
| | - Matthew Byott
- Advanced Pathogen Diagnostics Unit, University College London Hospitals NHS Foundation Trust, London, United Kingdom; The Francis Crick Institute, London, United Kingdom
| | - Themoula Charalampous
- Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Dan Frampton
- Advanced Pathogen Diagnostics Unit, University College London Hospitals NHS Foundation Trust, London, United Kingdom; Division of Infection and Immunity, University College London, London, United Kingdom
| | - Sharon Glaysher
- Portsmouth Hospitals University NHS Trust, Queen Alexandra Hospital, Portsmouth PO6 3LY, United Kingdom
| | - Tabassum Khan
- Division of Infection, The Royal London Hospital, Barts Health, United Kingdom
| | | | - Beatrix Kele
- Division of Infection, The Royal London Hospital, Barts Health, United Kingdom
| | - Irene M Monahan
- Institute for Infection and Immunity, St George's University of London, Cranmer Terrace, London SW17 0RE, United Kingdom
| | - Guy Mollett
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Matthew Parker
- Sheffield Bioinformatics Core, The University of Sheffield, Sheffield, United Kingdom; Sheffield Institute for Translational Neuroscience, The University of Sheffield, Sheffield, United Kingdom; Sheffield Biomedical Research Centre, The University of Sheffield, Sheffield, United Kingdom
| | - Emanuela Pelosi
- Southampton Specialist Virology Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Paul Randell
- Department of Infection and Immunity, North West London Pathology, London, United Kingdom
| | - Sunando Roy
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Joshua F Taylor
- Department of Microbiology, South West London Pathology, Jenner Wing, St. George's Hospital, Blackshaw Road, London SW17 0QT, United Kingdom
| | - Sophie J Weller
- Department of Virology, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Eleri Wilson-Davies
- Southampton Specialist Virology Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Phillip Wade
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom; The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Rachel Williams
- Department of Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Andrew J Copas
- Institute for Global Health, University College London, London, United Kingdom
| | | | - Nick Freemantle
- Institute for Clinical Trials and Methodology, University College London, London, United Kingdom
| | - Andrew C Hayward
- Institute of Epidemiology and Health Care, University College London, London, United Kingdom
| | - Alison Holmes
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, United Kingdom; Imperial College Healthcare NHS Trust, Hammersmith Hospital, London, United Kingdom
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Tabitha W Mahungu
- Department of Virology, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Gaia Nebbia
- Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom; Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, United Kingdom
| | - Eleni Nastouli
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom; Advanced Pathogen Diagnostics Unit, University College London Hospitals NHS Foundation Trust, London, United Kingdom; Department of Clinical Virology, University College London Hospitals NHS Foundation Trust, London, United Kingdom; The Francis Crick Institute, London, United Kingdom
| | - David G Partridge
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom; The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Cassie F Pope
- Institute for Infection and Immunity, St George's University of London, Cranmer Terrace, London SW17 0RE, United Kingdom; Infection Care Group, St George's University Hospitals NHS Foundation Trust, Blackshaw Road, London SW17 0QT, United Kingdom
| | - James R Price
- Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Samuel C Robson
- Centre for Enzyme Innovation, University of Portsmouth, Portsmouth PO1 2DT, United Kingdom; School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom; School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DT, United Kingdom
| | - Kordo Saeed
- Department of Infection, University Hospital Southampton NHS Foundation Trust, Tremona Road, Southampton, United Kingdom; Faculty of Medicine, Clinical and Experimental Sciences, University of Southampton, Tremona Road, Southampton, United Kingdom
| | - Gee Yen Shin
- Department of Clinical Virology, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Thushan I de Silva
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom; The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Luke B Snell
- Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom; Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, United Kingdom
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Adam A Witney
- Institute for Infection and Immunity, St George's University of London, Cranmer Terrace, London SW17 0RE, United Kingdom
| | - Judith Breuer
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom; Department of Microbiology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom.
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Guerra-Assunção JA, van Kampen JJ, Roy S, Remeijer L, Breuer J, Verjans GMM. Cluster of Symptomatic Graft-to-Host Transmission of Herpes Simplex Virus Type 1 in an Endothelial Keratoplasty Setting. Ophthalmology Science 2021; 1:100051. [PMID: 36247820 PMCID: PMC9562293 DOI: 10.1016/j.xops.2021.100051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/29/2021] [Accepted: 08/03/2021] [Indexed: 11/26/2022]
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Stirrup O, Boshier F, Venturini C, Guerra-Assunção JA, Alcolea-Medina A, Beckett A, Charalampous T, da Silva Filipe A, Glaysher S, Khan T, Kulasegaran Shylini R, Kele B, Monahan I, Mollett G, Parker M, Pelosi E, Randell P, Roy S, Taylor J, Weller S, Wilson-Davies E, Wade P, Williams R, Copas A, Cutino-Moguel MT, Freemantle N, Hayward AC, Holmes A, Hughes J, Mahungu T, Nebbia G, Partridge D, Pope C, Price J, Robson S, Saeed K, de Silva T, Snell L, Thomson E, Witney AA, Breuer J. SARS-CoV-2 lineage B.1.1.7 is associated with greater disease severity among hospitalised women but not men: multicentre cohort study. BMJ Open Respir Res 2021; 8:e001029. [PMID: 34544733 PMCID: PMC8453594 DOI: 10.1136/bmjresp-2021-001029] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/08/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND SARS-CoV-2 lineage B.1.1.7 has been associated with an increased rate of transmission and disease severity among subjects testing positive in the community. Its impact on hospitalised patients is less well documented. METHODS We collected viral sequences and clinical data of patients admitted with SARS-CoV-2 and hospital-onset COVID-19 infections (HOCIs), sampled 16 November 2020 to 10 January 2021, from eight hospitals participating in the COG-UK-HOCI study. Associations between the variant and the outcomes of all-cause mortality and intensive therapy unit (ITU) admission were evaluated using mixed effects Cox models adjusted by age, sex, comorbidities, care home residence, pregnancy and ethnicity. FINDINGS Sequences were obtained from 2341 inpatients (HOCI cases=786) and analysis of clinical outcomes was carried out in 2147 inpatients with all data available. The HR for mortality of B.1.1.7 compared with other lineages was 1.01 (95% CI 0.79 to 1.28, p=0.94) and for ITU admission was 1.01 (95% CI 0.75 to 1.37, p=0.96). Analysis of sex-specific effects of B.1.1.7 identified increased risk of mortality (HR 1.30, 95% CI 0.95 to 1.78, p=0.096) and ITU admission (HR 1.82, 95% CI 1.15 to 2.90, p=0.011) in females infected with the variant but not males (mortality HR 0.82, 95% CI 0.61 to 1.10, p=0.177; ITU HR 0.74, 95% CI 0.52 to 1.04, p=0.086). INTERPRETATION In common with smaller studies of patients hospitalised with SARS-CoV-2, we did not find an overall increase in mortality or ITU admission associated with B.1.1.7 compared with other lineages. However, women with B.1.1.7 may be at an increased risk of admission to intensive care and at modestly increased risk of mortality.
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Affiliation(s)
- Oliver Stirrup
- Institute for Global Health, University College London, London, UK
| | - Florencia Boshier
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Cristina Venturini
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - José Afonso Guerra-Assunção
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
- Department of Genetics & Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Adela Alcolea-Medina
- Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, UK
- Infection Sciences, Viapath, London, UK
| | - Angela Beckett
- Centre for Enzyme Innovation, University of Portsmouth, Portsmouth, UK
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | - Themoula Charalampous
- Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, UK
| | | | - Sharon Glaysher
- Portsmouth Hospitals University NHS Trust, Queen Alexandra Hospital, Portsmouth, UK
| | - Tabassum Khan
- Division of Infection, The Royal London Hospital, Barts Health NHS Trust, London, UK
| | | | - Beatrix Kele
- Division of Infection, The Royal London Hospital, Barts Health NHS Trust, London, UK
| | - Irene Monahan
- Institute for Infection and Immunity, St George's University of London, London, UK
| | - Guy Mollett
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Matthew Parker
- Sheffield Bioinformatics Core, The University of Sheffield, Sheffield, UK
- Sheffield Institute for Translational Neuroscience, The University of Sheffield, Sheffield, UK
- Sheffield Biomedical Research Centre, The University of Sheffield, Sheffield, UK
| | - Emanuela Pelosi
- Southampton Specialist Virology Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Paul Randell
- Department of Infection and Immunity, North West London Pathology, London, UK
| | - Sunando Roy
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Joshua Taylor
- Department of Microbiology, South West London Pathology, St. George's Hospital, London, UK
| | - Sophie Weller
- Department of Virology, Royal Free London NHS Foundation Trust, London, UK
| | - Eleri Wilson-Davies
- Southampton Specialist Virology Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Phillip Wade
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Rachel Williams
- Department of Genetics & Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Andrew Copas
- Institute for Global Health, University College London, London, UK
| | | | - Nick Freemantle
- Institute of Clinical Trials and Methodology, University College London, London, UK
| | - Andrew C Hayward
- Institute of Epidemiology and Health Care, University College London, London, UK
| | - Alison Holmes
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Tabitha Mahungu
- Department of Virology, Royal Free London NHS Foundation Trust, London, UK
| | - Gaia Nebbia
- Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, UK
- Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | - David Partridge
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Cassie Pope
- Institute for Infection and Immunity, St George's University of London, London, UK
- Infection Care Group, St George's University Hospitals NHS Foundation Trust, London, UK
| | - James Price
- Imperial College Healthcare NHS Trust, London, UK
| | - Samuel Robson
- Centre for Enzyme Innovation, University of Portsmouth, Portsmouth, UK
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK
| | - Kordo Saeed
- Microbiology Innovation and Research Unit (MIRU), Department of Microbiology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
- Faculty of Medicine, Clinical and Experimental Sciences, University of Southampton, Southampton, UK
| | - Thushan de Silva
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Luke Snell
- Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, UK
- Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | - Emma Thomson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Adam A Witney
- Institute for Infection and Immunity, St George's University of London, London, UK
| | - Judith Breuer
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
- Department of Microbiology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
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Baltas I, Boshier FAT, Williams CA, Bayzid N, Cotic M, Guerra-Assunção JA, Irish-Tavares D, Haque T, Hart J, Roy S, Williams R, Breuer J, Mahungu TW. Post-vaccination COVID-19: A case-control study and genomic analysis of 119 breakthrough infections in partially vaccinated individuals. Clin Infect Dis 2021; 75:305-313. [PMID: 34410361 PMCID: PMC8513403 DOI: 10.1093/cid/ciab714] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Indexed: 11/29/2022] Open
Abstract
Background Post-vaccination infections challenge the control of the coronavirus disease 2019 (COVID-19) pandemic. Methods We matched 119 cases of post-vaccination severe acute respiratory syndrome coronavirus 2 infection with BNT162b2 mRNA or ChAdOx1 nCOV-19 to 476 unvaccinated patients with COVID-19 (September 2020–March 2021) according to age and sex. Differences in 60-day all-cause mortality, hospital admission, and hospital length of stay were evaluated. Phylogenetic, single-nucleotide polymorphism (SNP), and minority variant allele (MVA) full-genome sequencing analysis was performed. Results Overall, 116 of 119 cases developed COVID-19 post–first vaccination dose (median, 14 days). Thirteen of 119 (10.9%) cases and 158 of 476 (33.2%) controls died (P < .001), corresponding to the 4.5 number needed to treat (NNT). Multivariably, vaccination was associated with a 69.3% (95% confidence interval [CI]: 45.8 to 82.6) relative risk (RR) reduction in mortality. Similar results were seen in subgroup analysis for patients with infection onset ≥14 days after first vaccination and across vaccine subgroups. Hospital admissions (odds ratio, 0.80; 95% CI: .51 to 1.28) and length of stay (–1.89 days; 95% CI: –4.57 to 0.78) were lower for cases, while cycle threshold values were higher (30.8 vs 28.8, P = .053). B.1.1.7 was the predominant lineage in cases (100 of 108, 92.6%) and controls (341 of 446, 76.5%). Genomic analysis identified 1 post-vaccination case that harbored the E484K vaccine-escape mutation (B.1.525 lineage). Conclusions Previous vaccination reduces mortality when B.1.1.7 is the predominant lineage. No significant lineage-specific genomic changes during phylogenetic, SNP, and MVA analysis were detected.
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Affiliation(s)
- Ioannis Baltas
- Department of Virology, Royal Free London NHS Foundation Trust, London, United Kingdom.,Institute of Education, University College London, London, United Kingdom
| | - Florencia A T Boshier
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Charlotte A Williams
- Department of Genetics & Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Nadua Bayzid
- Department of Genetics & Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Marius Cotic
- Department of Genetics & Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - José Afonso Guerra-Assunção
- Department of Genetics & Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Dianne Irish-Tavares
- Department of Microbiology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Tanzina Haque
- Department of Microbiology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Jennifer Hart
- Department of Microbiology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Sunando Roy
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Rachel Williams
- Department of Genetics & Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Judith Breuer
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom.,Department of Microbiology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Tabitha W Mahungu
- Department of Virology, Royal Free London NHS Foundation Trust, London, United Kingdom
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Turati VA, Guerra-Assunção JA, Potter NE, Gupta R, Ecker S, Daneviciute A, Tarabichi M, Webster AP, Ding C, May G, James C, Brown J, Conde L, Russell LJ, Ancliff P, Inglott S, Cazzaniga G, Biondi A, Hall GW, Lynch M, Hubank M, Macaulay I, Beck S, Van Loo P, Jacobsen SE, Greaves M, Herrero J, Enver T. Chemotherapy induces canalization of cell state in childhood B-cell precursor acute lymphoblastic leukemia. Nat Cancer 2021; 2:835-852. [PMID: 34734190 PMCID: PMC7611923 DOI: 10.1038/s43018-021-00219-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 05/11/2021] [Indexed: 05/01/2023]
Abstract
Comparison of intratumor genetic heterogeneity in cancer at diagnosis and relapse suggests that chemotherapy induces bottleneck selection of subclonal genotypes. However, evolutionary events subsequent to chemotherapy could also explain changes in clonal dominance seen at relapse. We, therefore, investigated the mechanisms of selection in childhood B-cell precursor acute lymphoblastic leukemia (BCP-ALL) during induction chemotherapy where maximal cytoreduction occurs. To distinguish stochastic versus deterministic events, individual leukemias were transplanted into multiple xenografts and chemotherapy administered. Analyses of the immediate post-treatment leukemic residuum at single-cell resolution revealed that chemotherapy has little impact on genetic heterogeneity. Rather, it acts on extensive, previously unappreciated, transcriptional and epigenetic heterogeneity in BCP-ALL, dramatically reducing the spectrum of cell states represented, leaving a genetically polyclonal but phenotypically uniform population with hallmark signatures relating to developmental stage, cell cycle and metabolism. Hence, canalization of cell state accounts for a significant component of bottleneck selection during induction chemotherapy.
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Affiliation(s)
| | | | | | - Rajeev Gupta
- UCL Cancer Institute, University College London, United Kingdom
| | - Simone Ecker
- UCL Cancer Institute, University College London, United Kingdom
| | | | | | - Amy P. Webster
- UCL Cancer Institute, University College London, United Kingdom
| | - Chuling Ding
- UCL Cancer Institute, University College London, United Kingdom
| | - Gillian May
- UCL Cancer Institute, University College London, United Kingdom
| | - Chela James
- UCL Cancer Institute, University College London, United Kingdom
| | - John Brown
- UCL Cancer Institute, University College London, United Kingdom
| | - Lucia Conde
- UCL Cancer Institute, University College London, United Kingdom
| | - Lisa J. Russell
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, UK
| | - Phil Ancliff
- Great Ormond Street Hospital, London, United Kingdom
| | - Sarah Inglott
- Great Ormond Street Hospital, London, United Kingdom
| | - Giovanni Cazzaniga
- Centro Ricerca M. Tettamanti, University of Milano Bicocca, Monza, Italy
| | - Andrea Biondi
- University of Milano-Bicocca, Department of Pediatrics, Fondazione MBBM/Ospedale San Gerardo, Monza, Italy
| | | | - Mark Lynch
- Fluidigm Corporation, San Francisco, CA, USA
| | - Mike Hubank
- Institute of Cancer Research, Sutton, United Kingdom
- Royal Marsden Hospital, Sutton, United Kingdom
| | | | - Stephan Beck
- UCL Cancer Institute, University College London, United Kingdom
| | | | - Sten E. Jacobsen
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
- Center for Hematology and Regenerative Medicine, Department of Medicine and Department of Cell and Molecular Biology, Karolinska Institutet and Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Mel Greaves
- Institute of Cancer Research, Sutton, United Kingdom
| | - Javier Herrero
- UCL Cancer Institute, University College London, United Kingdom
| | - Tariq Enver
- UCL Cancer Institute, University College London, United Kingdom
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Ramos-Sevillano E, Ercoli G, Guerra-Assunção JA, Felgner P, Ramiro de Assis R, Nakajima R, Goldblatt D, Tetteh KKA, Heyderman RS, Gordon SB, Ferreria DM, Brown JS. Protective Effect of Nasal Colonisation with ∆cps/piaA and ∆cps/proABCStreptococcus pneumoniae Strains against Recolonisation and Invasive Infection. Vaccines (Basel) 2021; 9:vaccines9030261. [PMID: 33804077 PMCID: PMC8000150 DOI: 10.3390/vaccines9030261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Nasopharyngeal administration of live virulence-attenuated Streptococcus pneumoniae strains is a potential novel preventative strategy. One target for creating reduced virulence S. pneumoniae strains is the capsule, but loss of the capsule reduces the duration of S. pneumoniae colonisation in mice which could impair protective efficacy against subsequent infection. OBJECTIVES To assess protective efficacy of nasopharyngeal administration of unencapsulated S. pneumoniae strains in murine infection models. METHODS Strains containing cps locus deletions combined with the S. pneumoniae virulence factors psaA (reduces colonisation) or proABC (no effect on colonisation) were constructed and their virulence phenotypes and ability to prevent recolonisation or invasive infection assessed using mouse infection models. Serological responses to colonisation were compared between strains using ELISAs, immunoblots and 254 S. pneumoniae protein antigen array. MEASUREMENTS AND MAIN RESULTS The ∆cps/piaA and ∆cps/proABC strains were strongly attenuated in virulence in both invasive infection models and had a reduced ability to colonise the nasopharynx. ELISAs, immunoblots and protein arrays showed colonisation with either strain stimulated weaker serological responses than the wild type strain. Mice previously colonised with these strains were protected against septicaemic pneumonia but, unlike mice colonised with the wild type strain, not against S. pneumoniae recolonisation. CONCLUSIONS Colonisation with the ∆cps/piaA and ∆cps/proABC strains prevented subsequent septicaemia, but in contrast, to published data for encapsulated double mutant strains they did not prevent recolonisation with S. pneumoniae. These data suggest targeting the cps locus is a less effective option for creating live attenuated strains that prevent S. pneumoniae infections.
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Affiliation(s)
- Elisa Ramos-Sevillano
- Centre for Inflammation and Tissue Repair, UCL Respiratory, Division of Medicine, University College London, Rayne Institute, London WC1E 6JF, UK;
- Correspondence: (E.R.-S.); (J.S.B.); Tel.: +44-20-7679-6008 (J.S.B.); Fax: +44-20-7679-6973 (J.S.B.)
| | - Giuseppe Ercoli
- Centre for Inflammation and Tissue Repair, UCL Respiratory, Division of Medicine, University College London, Rayne Institute, London WC1E 6JF, UK;
| | | | - Philip Felgner
- Vaccine Research and Development Center, Department of Physiology and Biophysics, University of California Irvine, Irvine, CA 92697-4560, USA; (P.F.); (R.R.d.A.); (R.N.)
| | - Rafael Ramiro de Assis
- Vaccine Research and Development Center, Department of Physiology and Biophysics, University of California Irvine, Irvine, CA 92697-4560, USA; (P.F.); (R.R.d.A.); (R.N.)
| | - Rie Nakajima
- Vaccine Research and Development Center, Department of Physiology and Biophysics, University of California Irvine, Irvine, CA 92697-4560, USA; (P.F.); (R.R.d.A.); (R.N.)
| | - David Goldblatt
- Immunobiology Section, UCL Great Ormond Street Institute of Child Health, NIHR Biomedical Research Centre, London WC1N 1EH, UK;
| | - Kevin Kweku Adjei Tetteh
- Faculty of Infectious and Tropical Diseases, London School of Tropical Medicine and Hygiene, London WC1E 7HT, UK;
| | - Robert Simon Heyderman
- Research Department of Infection, Division of Infection and Immunity, University College London, Rayne Institute, London WC1E 6JF, UK;
| | - Stephen Brian Gordon
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre 30096, Malawi;
| | - Daniela Mulari Ferreria
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK;
| | - Jeremy Stuart Brown
- Centre for Inflammation and Tissue Repair, UCL Respiratory, Division of Medicine, University College London, Rayne Institute, London WC1E 6JF, UK;
- Correspondence: (E.R.-S.); (J.S.B.); Tel.: +44-20-7679-6008 (J.S.B.); Fax: +44-20-7679-6973 (J.S.B.)
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11
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Litchfield K, Reading JL, Puttick C, Thakkar K, Abbosh C, Bentham R, Watkins TBK, Rosenthal R, Biswas D, Rowan A, Lim E, Al Bakir M, Turati V, Guerra-Assunção JA, Conde L, Furness AJS, Saini SK, Hadrup SR, Herrero J, Lee SH, Van Loo P, Enver T, Larkin J, Hellmann MD, Turajlic S, Quezada SA, McGranahan N, Swanton C. Meta-analysis of tumor- and T cell-intrinsic mechanisms of sensitization to checkpoint inhibition. Cell 2021; 184:596-614.e14. [PMID: 33508232 PMCID: PMC7933824 DOI: 10.1016/j.cell.2021.01.002] [Citation(s) in RCA: 423] [Impact Index Per Article: 141.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 06/26/2020] [Accepted: 01/04/2021] [Indexed: 12/22/2022]
Abstract
Checkpoint inhibitors (CPIs) augment adaptive immunity. Systematic pan-tumor analyses may reveal the relative importance of tumor-cell-intrinsic and microenvironmental features underpinning CPI sensitization. Here, we collated whole-exome and transcriptomic data for >1,000 CPI-treated patients across seven tumor types, utilizing standardized bioinformatics workflows and clinical outcome criteria to validate multivariable predictors of CPI sensitization. Clonal tumor mutation burden (TMB) was the strongest predictor of CPI response, followed by total TMB and CXCL9 expression. Subclonal TMB, somatic copy alteration burden, and histocompatibility leukocyte antigen (HLA) evolutionary divergence failed to attain pan-cancer significance. Dinucleotide variants were identified as a source of immunogenic epitopes associated with radical amino acid substitutions and enhanced peptide hydrophobicity/immunogenicity. Copy-number analysis revealed two additional determinants of CPI outcome supported by prior functional evidence: 9q34 (TRAF2) loss associated with response and CCND1 amplification associated with resistance. Finally, single-cell RNA sequencing (RNA-seq) of clonal neoantigen-reactive CD8 tumor-infiltrating lymphocytes (TILs), combined with bulk RNA-seq analysis of CPI-responding tumors, identified CCR5 and CXCL13 as T-cell-intrinsic markers of CPI sensitivity.
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Affiliation(s)
- Kevin Litchfield
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - James L Reading
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - Clare Puttick
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Krupa Thakkar
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - Chris Abbosh
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - Robert Bentham
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Rachel Rosenthal
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Dhruva Biswas
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Andrew Rowan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Emilia Lim
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Maise Al Bakir
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Virginia Turati
- Stem Cell Group, Cancer Institute, University College London, London WC1E 6DD, UK
| | - José Afonso Guerra-Assunção
- Bill Lyons Informatics Centre, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - Lucia Conde
- Bill Lyons Informatics Centre, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - Andrew J S Furness
- Renal and Skin Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Sunil Kumar Saini
- Department of Health Technology, Technical University of Denmark, Copenhagen, Denmark
| | - Sine R Hadrup
- Department of Health Technology, Technical University of Denmark, Copenhagen, Denmark
| | - Javier Herrero
- Bill Lyons Informatics Centre, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - Se-Hoon Lee
- Department of Health Sciences and Technology, Samsung Advanced Institute of Health Sciences and Technology, Sungkyunkwan University, Seoul, South Korea; Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Tariq Enver
- Stem Cell Group, Cancer Institute, University College London, London WC1E 6DD, UK
| | - James Larkin
- Renal and Skin Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Matthew D Hellmann
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, and Parker Center for Cancer Immunotherapy, 885 2nd Avenue, New York, NY 10017, USA
| | - Samra Turajlic
- Renal and Skin Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; Cancer Dynamics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Sergio A Quezada
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK.
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK.
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK.
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12
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Larrea E, Fernandez-Mercado M, Guerra-Assunção JA, Wang J, Goicoechea I, Gaafar A, Ceberio I, Lobo C, Okosun J, Enright AJ, Fitzgibbon J, Lawrie CH. Identification of Recurrent Mutations in the microRNA-Binding Sites of B-Cell Lymphoma-Associated Genes in Follicular Lymphoma. Int J Mol Sci 2020; 21:ijms21228795. [PMID: 33233721 PMCID: PMC7699894 DOI: 10.3390/ijms21228795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/11/2020] [Accepted: 11/18/2020] [Indexed: 11/16/2022] Open
Abstract
Follicular lymphoma (FL) is a common indolent B-cell lymphoma that can transform into the more aggressive transformed FL (tFL). However, the molecular process driving this transformation is uncertain. In this work, we aimed to identify microRNA (miRNA)-binding sites recurrently mutated in follicular lymphoma patients, as well as in transformed FL patients. Using whole-genome sequencing data from FL tumors, we discovered 544 mutations located in bioinformatically predicted microRNA-binding sites. We then studied these specific regions using targeted sequencing in a cohort of 55 FL patients, found 16 recurrent mutations, and identified a further 69 variants. After filtering for QC, we identified 21 genes with mutated miRNA-binding sites that were also enriched for B-cell-associated genes by Gene Ontology. Over 40% of mutations identified in these genes were present exclusively in tFL patients. We validated the predicted miRNA-binding sites of five of the genes by luciferase assay and demonstrated that the identified mutations in BCL2 and EZH2 genes impaired the binding efficiency of miR-5008 and miR-144 and regulated the endogenous levels of messenger RNA (mRNA).
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Affiliation(s)
- Erika Larrea
- Molecular Oncology Group, Biodonostia Research Institute, 20014 San Sebastián, Spain; (E.L.); (M.F.-M.); (I.G.)
- Chinese Institute for Brain Research (CIBR), Beijing 102206, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Marta Fernandez-Mercado
- Molecular Oncology Group, Biodonostia Research Institute, 20014 San Sebastián, Spain; (E.L.); (M.F.-M.); (I.G.)
- Biomedical Engineering, School of Engineering, University of Navarra, 20014 San Sebastian, Spain
| | | | - Jun Wang
- Barts Cancer Institute, Queen Mary University of London, London EC1M 6BE, UK; (J.W.); (J.O.); (J.F.)
| | - Ibai Goicoechea
- Molecular Oncology Group, Biodonostia Research Institute, 20014 San Sebastián, Spain; (E.L.); (M.F.-M.); (I.G.)
- Multiple Myeloma Group, Centro de Investigación Médica Aplicada (CIMA), Pamplona, 31008 Navarra, Spain
| | - Ayman Gaafar
- Department of Pathology, Cruces Hospital, 48903 Bilbao, Spain;
| | - Izaskun Ceberio
- Hematology Department, Hospital Universitario Donostia, 20014 San Sebastián, Spain;
| | - Carmen Lobo
- Department of Pathology, Hospital Universitario Donostia, 20014 San Sebastián, Spain;
| | - Jessica Okosun
- Barts Cancer Institute, Queen Mary University of London, London EC1M 6BE, UK; (J.W.); (J.O.); (J.F.)
| | - Anton J. Enright
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK;
| | - Jude Fitzgibbon
- Barts Cancer Institute, Queen Mary University of London, London EC1M 6BE, UK; (J.W.); (J.O.); (J.F.)
| | - Charles H. Lawrie
- Molecular Oncology Group, Biodonostia Research Institute, 20014 San Sebastián, Spain; (E.L.); (M.F.-M.); (I.G.)
- IKERBASQUE, Basque Foundation for Science, 48009 Bilbao, Spain
- Radcliffe Department of Medicine, University of Oxford, Oxford OX4 3DU, UK
- Correspondence: ; Tel.: +34-943-006138
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13
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Guerra-Assunção JA, Conde L, Moghul I, Webster AP, Ecker S, Chervova O, Chatzipantsiou C, Prieto PP, Beck S, Herrero J. GenomeChronicler: The Personal Genome Project UK Genomic Report Generator Pipeline. Front Genet 2020; 11:518644. [PMID: 33193602 PMCID: PMC7541957 DOI: 10.3389/fgene.2020.518644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 09/02/2020] [Indexed: 11/13/2022] Open
Abstract
In recent years, there has been a significant increase in whole genome sequencing data of individual genomes produced by research projects as well as direct to consumer service providers. While many of these sources provide their users with an interpretation of the data, there is a lack of free, open tools for generating reports exploring the data in an easy to understand manner. GenomeChronicler was developed as part of the Personal Genome Project UK (PGP-UK) to address this need. PGP-UK provides genomic, transcriptomic, epigenomic and self-reported phenotypic data under an open-access model with full ethical approval. As a result, the reports generated by GenomeChronicler are intended for research purposes only and include information relating to potentially beneficial and potentially harmful variants, but without clinical curation. GenomeChronicler can be used with data from whole genome or whole exome sequencing, producing a genome report containing information on variant statistics, ancestry and known associated phenotypic traits. Example reports are available from the PGP-UK data page (personalgenomes.org.uk/data). The objective of this method is to leverage existing resources to find known phenotypes associated with the genotypes detected in each sample. The provided trait data is based primarily upon information available in SNPedia, but also collates data from ClinVar, GETevidence, and gnomAD to provide additional details on potential health implications, presence of genotype in other PGP participants and population frequency of each genotype. The analysis can be run in a self-contained environment without requiring internet access, making it a good choice for cases where privacy is essential or desired: any third party project can embed GenomeChronicler within their off-line safe-haven environments. GenomeChronicler can be run for one sample at a time, or in parallel making use of the Nextflow workflow manager. The source code is available from GitHub (https://github.com/PGP-UK/GenomeChronicler), container recipes are available for Docker and Singularity, as well as a pre-built container from SingularityHub (https://singularity-hub.org/collections/3664) enabling easy deployment in a variety of settings. Users without access to computational resources to run GenomeChronicler can access the software from the Lifebit CloudOS platform (https://lifebit.ai/cloudos) enabling the production of reports and variant calls from raw sequencing data in a scalable fashion.
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Affiliation(s)
- José Afonso Guerra-Assunção
- Infection and Immunity, University College London, London, United Kingdom.,Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London, United Kingdom
| | - Lucia Conde
- Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London, United Kingdom
| | - Ismail Moghul
- Medical Genomics, UCL Cancer Institute, University College London, London, United Kingdom
| | - Amy P Webster
- Medical Genomics, UCL Cancer Institute, University College London, London, United Kingdom
| | - Simone Ecker
- Medical Genomics, UCL Cancer Institute, University College London, London, United Kingdom
| | - Olga Chervova
- Medical Genomics, UCL Cancer Institute, University College London, London, United Kingdom
| | | | | | - Stephan Beck
- Medical Genomics, UCL Cancer Institute, University College London, London, United Kingdom
| | - Javier Herrero
- Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London, United Kingdom
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14
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León TE, Rapoz-D'Silva T, Bertoli C, Rahman S, Magnussen M, Philip B, Farah N, Richardson SE, Ahrabi S, Guerra-Assunção JA, Gupta R, Nacheva EP, Henderson S, Herrero J, Linch DC, de Bruin RAM, Mansour MR. EZH2-Deficient T-cell Acute Lymphoblastic Leukemia Is Sensitized to CHK1 Inhibition through Enhanced Replication Stress. Cancer Discov 2020; 10:998-1017. [PMID: 32349972 PMCID: PMC7611258 DOI: 10.1158/2159-8290.cd-19-0789] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 03/13/2020] [Accepted: 04/24/2020] [Indexed: 11/16/2022]
Abstract
Loss-of-function mutations of EZH2, the enzymatic component of PRC2, have been associated with poor outcome and chemotherapy resistance in T-cell acute lymphoblastic leukemia (T-ALL). Using isogenic T-ALL cells, with and without CRISPR/Cas9-induced EZH2-inactivating mutations, we performed a cell-based synthetic lethal drug screen. EZH2-deficient cells exhibited increased sensitivity to structurally diverse inhibitors of CHK1, an interaction that could be validated genetically. Furthermore, small-molecule inhibition of CHK1 had efficacy in delaying tumor progression in isogenic EZH2-deficient, but not EZH2 wild-type, T-ALL cells in vivo, as well as in a primary cell model of PRC2-mutant ALL. Mechanistically, EZH2 deficiency resulted in a gene-expression signature of immature T-ALL cells, marked transcriptional upregulation of MYCN, increased replication stress, and enhanced dependency on CHK1 for cell survival. Finally, we demonstrate this phenotype is mediated through derepression of a distal PRC2-regulated MYCN enhancer. In conclusion, we highlight a novel and clinically exploitable pathway in high-risk EZH2-mutated T-ALL. SIGNIFICANCE: Loss-of-function mutations of PRC2 genes are associated with chemotherapy resistance in T-ALL, yet no specific therapy for this aggressive subtype is currently clinically available. Our work demonstrates that loss of EZH2 activity leads to MYCN-driven replication stress, resulting in increased sensitivity to CHK1 inhibition, a finding with immediate clinical relevance.This article is highlighted in the In This Issue feature, p. 890.
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Affiliation(s)
- Theresa E León
- Department of Haematology, UCL Cancer Institute, University College London, London, United Kingdom
| | - Tanya Rapoz-D'Silva
- Department of Haematology, UCL Cancer Institute, University College London, London, United Kingdom
| | - Cosetta Bertoli
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Sunniyat Rahman
- Department of Haematology, UCL Cancer Institute, University College London, London, United Kingdom
| | - Michael Magnussen
- Department of Haematology, UCL Cancer Institute, University College London, London, United Kingdom
| | - Brian Philip
- Department of Haematology, UCL Cancer Institute, University College London, London, United Kingdom
| | - Nadine Farah
- Department of Haematology, UCL Cancer Institute, University College London, London, United Kingdom
| | - Simon E Richardson
- Department of Haematology, UCL Cancer Institute, University College London, London, United Kingdom
| | - Sara Ahrabi
- Department of Haematology, UCL Cancer Institute, University College London, London, United Kingdom
| | | | - Rajeev Gupta
- Stem Cell Laboratory, UCL Cancer Institute, University College London, London, United Kingdom
| | - Elisabeth P Nacheva
- Health Service Laboratories LLP, UCL Cancer Institute, London, United Kingdom
| | - Stephen Henderson
- Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London, United Kingdom
| | - Javier Herrero
- Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London, United Kingdom
| | - David C Linch
- Department of Haematology, UCL Cancer Institute, University College London, London, United Kingdom
| | - Robertus A M de Bruin
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Marc R Mansour
- Department of Haematology, UCL Cancer Institute, University College London, London, United Kingdom.
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15
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Joshi K, de Massy MR, Ismail M, Reading JL, Uddin I, Woolston A, Hatipoglu E, Oakes T, Rosenthal R, Peacock T, Ronel T, Noursadeghi M, Turati V, Furness AJS, Georgiou A, Wong YNS, Ben Aissa A, Sunderland MW, Jamal-Hanjani M, Veeriah S, Birkbak NJ, Wilson GA, Hiley CT, Ghorani E, Guerra-Assunção JA, Herrero J, Enver T, Hadrup SR, Hackshaw A, Peggs KS, McGranahan N, Swanton C, Quezada SA, Chain B. Publisher Correction: Spatial heterogeneity of the T cell receptor repertoire reflects the mutational landscape in lung cancer. Nat Med 2020; 26:1148. [PMID: 32494063 DOI: 10.1038/s41591-020-0866-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Kroopa Joshi
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Marc Robert de Massy
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Mazlina Ismail
- Division of Infection and Immunity, University College London, London, UK
| | - James L Reading
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Imran Uddin
- Division of Infection and Immunity, University College London, London, UK
| | - Annemarie Woolston
- Division of Infection and Immunity, University College London, London, UK
| | - Emine Hatipoglu
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Theres Oakes
- Division of Infection and Immunity, University College London, London, UK
| | - Rachel Rosenthal
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Thomas Peacock
- Division of Infection and Immunity, University College London, London, UK
- Computation, Mathematics and Physics in the Life Sciences and Experimental Biology, Department of Computer Science, University College London, London, UK
| | - Tahel Ronel
- Division of Infection and Immunity, University College London, London, UK
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London, UK
| | - Virginia Turati
- Department of Cancer Biology, University College London Cancer Institute, London, UK
| | - Andrew J S Furness
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Andrew Georgiou
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Yien Ning Sophia Wong
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Assma Ben Aissa
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Mariana Werner Sunderland
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Nicolai J Birkbak
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Gareth A Wilson
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Crispin T Hiley
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Ehsan Ghorani
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | | | - Javier Herrero
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Tariq Enver
- University College London Cancer Institute, London, UK
| | - Sine R Hadrup
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Allan Hackshaw
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Karl S Peggs
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
| | - Sergio A Quezada
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
| | - Benny Chain
- Division of Infection and Immunity, University College London, London, UK.
- Department of Computer Sciences, University College London, London, UK.
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16
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Ghorani E, Reading JL, Henry JY, Massy MRD, Rosenthal R, Turati V, Joshi K, Furness AJS, Ben Aissa A, Saini SK, Ramskov S, Georgiou A, Sunderland MW, Wong YNS, Mucha MVD, Day W, Galvez-Cancino F, Becker PD, Uddin I, Oakes T, Ismail M, Ronel T, Woolston A, Jamal-Hanjani M, Veeriah S, Birkbak NJ, Wilson GA, Litchfield K, Conde L, Guerra-Assunção JA, Blighe K, Biswas D, Salgado R, Lund T, Bakir MA, Moore DA, Hiley CT, Loi S, Sun Y, Yuan Y, AbdulJabbar K, Turajilic S, Herrero J, Enver T, Hadrup SR, Hackshaw A, Peggs KS, McGranahan N, Chain B, Swanton C, Quezada SA. The T cell differentiation landscape is shaped by tumour mutations in lung cancer. Nat Cancer 2020; 1:546-561. [PMID: 32803172 PMCID: PMC7115931 DOI: 10.1038/s43018-020-0066-y] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/20/2020] [Indexed: 01/06/2023]
Abstract
Tumour mutational burden (TMB) predicts immunotherapy outcome in non-small cell lung cancer (NSCLC), consistent with immune recognition of tumour neoantigens. However, persistent antigen exposure is detrimental for T cell function. How TMB affects CD4 and CD8 T cell differentiation in untreated tumours, and whether this affects patient outcomes is unknown. Here we paired high-dimensional flow cytometry, exome, single-cell and bulk RNA sequencing from patients with resected, untreated NSCLC to examine these relationships. TMB was associated with compartment-wide T cell differentiation skewing, characterized by loss of TCF7-expressing progenitor-like CD4 T cells, and an increased abundance of dysfunctional CD8 and CD4 T cell subsets, with significant phenotypic and transcriptional similarity to neoantigen-reactive CD8 T cells. A gene signature of redistribution from progenitor-like to dysfunctional states associated with poor survival in lung and other cancer cohorts. Single-cell characterization of these populations informs potential strategies for therapeutic manipulation in NSCLC.
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Affiliation(s)
- Ehsan Ghorani
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - James L Reading
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
| | - Jake Y Henry
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Marc Robert de Massy
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Rachel Rosenthal
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Virginia Turati
- Department of Cancer Biology, University College London Cancer Institute, London, UK
| | - Kroopa Joshi
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Andrew J S Furness
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Assma Ben Aissa
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Sunil Kumar Saini
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Sofie Ramskov
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Andrew Georgiou
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Mariana Werner Sunderland
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Yien Ning Sophia Wong
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Maria Vila De Mucha
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - William Day
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Felipe Galvez-Cancino
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Pablo D Becker
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Imran Uddin
- Division of Infection and Immunity, University College London, London, UK
| | - Theres Oakes
- Division of Infection and Immunity, University College London, London, UK
| | - Mazlina Ismail
- Division of Infection and Immunity, University College London, London, UK
| | - Tahel Ronel
- Division of Infection and Immunity, University College London, London, UK
| | - Annemarie Woolston
- Division of Infection and Immunity, University College London, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Nicolai J Birkbak
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Gareth A Wilson
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Kevin Litchfield
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Lucia Conde
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | | | - Kevin Blighe
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Dhruva Biswas
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | | | - Tom Lund
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Maise Al Bakir
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - David A Moore
- Department of Pathology, University College London Cancer Institute, London, UK
| | - Crispin T Hiley
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Sherene Loi
- Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
| | - Yuxin Sun
- Division of Infection and Immunity, University College London, London, UK
| | - Yinyin Yuan
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Khalid AbdulJabbar
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Samra Turajilic
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Javier Herrero
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Tariq Enver
- Department of Cancer Biology, University College London Cancer Institute, London, UK
| | - Sine R Hadrup
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Allan Hackshaw
- Cancer Research UK and University College London Cancer Trials Centre, London, UK
| | - Karl S Peggs
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Benny Chain
- Division of Infection and Immunity, University College London, London, UK
- Department of Computer Sciences, University College London, London, UK
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- University College London Hospitals, London, UK.
| | - Sergio A Quezada
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
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17
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Chervova O, Conde L, Guerra-Assunção JA, Moghul I, Webster AP, Berner A, Larose Cadieux E, Tian Y, Voloshin V, Jesus TF, Hamoudi R, Herrero J, Beck S. The Personal Genome Project-UK, an open access resource of human multi-omics data. Sci Data 2019; 6:257. [PMID: 31672996 PMCID: PMC6823446 DOI: 10.1038/s41597-019-0205-4] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/12/2019] [Indexed: 12/20/2022] Open
Abstract
Integrative analysis of multi-omics data is a powerful approach for gaining functional insights into biological and medical processes. Conducting these multifaceted analyses on human samples is often complicated by the fact that the raw sequencing output is rarely available under open access. The Personal Genome Project UK (PGP-UK) is one of few resources that recruits its participants under open consent and makes the resulting multi-omics data freely and openly available. As part of this resource, we describe the PGP-UK multi-omics reference panel consisting of ten genomic, methylomic and transcriptomic data. Specifically, we outline the data processing, quality control and validation procedures which were implemented to ensure data integrity and exclude sample mix-ups. In addition, we provide a REST API to facilitate the download of the entire PGP-UK dataset. The data are also available from two cloud-based environments, providing platforms for free integrated analysis. In conclusion, the genotype-validated PGP-UK multi-omics human reference panel described here provides a valuable new open access resource for integrated analyses in support of personal and medical genomics.
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Affiliation(s)
- Olga Chervova
- UCL Cancer Institute, University College London, London, UK.
| | - Lucia Conde
- UCL Cancer Institute, University College London, London, UK
| | | | - Ismail Moghul
- UCL Cancer Institute, University College London, London, UK
| | - Amy P Webster
- UCL Cancer Institute, University College London, London, UK
| | - Alison Berner
- UCL Cancer Institute, University College London, London, UK.,Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Elizabeth Larose Cadieux
- UCL Cancer Institute, University College London, London, UK.,The Francis Crick Institute, London, UK
| | - Yuan Tian
- UCL Cancer Institute, University College London, London, UK
| | | | - Tiago F Jesus
- Lifebit Biotech Ltd., 219 Kensington High Street, London, W86BD, UK
| | - Rifat Hamoudi
- College of Medicine, University of Sharjah, Sharjah, UAE.,Division of Surgery and Interventional Science, University College London, London, UK
| | - Javier Herrero
- UCL Cancer Institute, University College London, London, UK
| | - Stephan Beck
- UCL Cancer Institute, University College London, London, UK.
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18
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Joshi K, de Massy MR, Ismail M, Reading JL, Uddin I, Woolston A, Hatipoglu E, Oakes T, Rosenthal R, Peacock T, Ronel T, Noursadeghi M, Turati V, Furness AJS, Georgiou A, Wong YNS, Ben Aissa A, Sunderland MW, Jamal-Hanjani M, Veeriah S, Birkbak NJ, Wilson GA, Hiley CT, Ghorani E, Guerra-Assunção JA, Herrero J, Enver T, Hadrup SR, Hackshaw A, Peggs KS, McGranahan N, Swanton C, Quezada SA, Chain B. Spatial heterogeneity of the T cell receptor repertoire reflects the mutational landscape in lung cancer. Nat Med 2019; 25:1549-1559. [PMID: 31591606 PMCID: PMC6890490 DOI: 10.1038/s41591-019-0592-2] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [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: 05/02/2019] [Accepted: 08/20/2019] [Indexed: 12/22/2022]
Abstract
Somatic mutations together with immunoediting drive extensive heterogeneity within non-small-cell lung cancer (NSCLC). Herein we examine heterogeneity of the T cell antigen receptor (TCR) repertoire. The number of TCR sequences selectively expanded in tumors varies within and between tumors and correlates with the number of nonsynonymous mutations. Expanded TCRs can be subdivided into TCRs found in all tumor regions (ubiquitous) and those present in a subset of regions (regional). The number of ubiquitous and regional TCRs correlates with the number of ubiquitous and regional nonsynonymous mutations, respectively. Expanded TCRs form part of clusters of TCRs of similar sequence, suggestive of a spatially constrained antigen-driven process. CD8+ tumor-infiltrating lymphocytes harboring ubiquitous TCRs display a dysfunctional tissue-resident phenotype. Ubiquitous TCRs are preferentially detected in the blood at the time of tumor resection as compared to routine follow-up. These findings highlight a noninvasive method to identify and track relevant tumor-reactive TCRs for use in adoptive T cell immunotherapy.
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MESH Headings
- Aged
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/pathology
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/immunology
- Carcinoma, Non-Small-Cell Lung/pathology
- Carcinoma, Non-Small-Cell Lung/therapy
- Female
- Genetic Heterogeneity
- Humans
- Immunotherapy, Adoptive
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/pathology
- Male
- Middle Aged
- Mutation
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
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Affiliation(s)
- Kroopa Joshi
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Marc Robert de Massy
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Mazlina Ismail
- Division of Infection and Immunity, University College London, London, UK
| | - James L Reading
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Imran Uddin
- Division of Infection and Immunity, University College London, London, UK
| | - Annemarie Woolston
- Division of Infection and Immunity, University College London, London, UK
| | - Emine Hatipoglu
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Theres Oakes
- Division of Infection and Immunity, University College London, London, UK
| | - Rachel Rosenthal
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Thomas Peacock
- Division of Infection and Immunity, University College London, London, UK
- Computation, Mathematics and Physics in the Life Sciences and Experimental Biology, Department of Computer Science, University College London, London, UK
| | - Tahel Ronel
- Division of Infection and Immunity, University College London, London, UK
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London, UK
| | - Virginia Turati
- Department of Cancer Biology, University College London Cancer Institute, London, UK
| | - Andrew J S Furness
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Andrew Georgiou
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Yien Ning Sophia Wong
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Assma Ben Aissa
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Mariana Werner Sunderland
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Nicolai J Birkbak
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Gareth A Wilson
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Crispin T Hiley
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Ehsan Ghorani
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | | | - Javier Herrero
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Tariq Enver
- University College London Cancer Institute, London, UK
| | - Sine R Hadrup
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Allan Hackshaw
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Karl S Peggs
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
| | - Sergio A Quezada
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
| | - Benny Chain
- Division of Infection and Immunity, University College London, London, UK.
- Department of Computer Sciences, University College London, London, UK.
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19
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Beck S, Berner AM, Bignell G, Bond M, Callanan MJ, Chervova O, Conde L, Corpas M, Ecker S, Elliott HR, Fioramonti SA, Flanagan AM, Gaentzsch R, Graham D, Gribbin D, Guerra-Assunção JA, Hamoudi R, Harding V, Harrison PL, Herrero J, Hofmann J, Jones E, Khan S, Kaye J, Kerr P, Libertini E, Marks L, McCormack L, Moghul I, Pontikos N, Rajanayagam S, Rana K, Semega-Janneh M, Smith CP, Strom L, Umur S, Webster AP, Williams EH, Wint K, Wood JN. Personal Genome Project UK (PGP-UK): a research and citizen science hybrid project in support of personalized medicine. BMC Med Genomics 2018; 11:108. [PMID: 30482208 PMCID: PMC6257975 DOI: 10.1186/s12920-018-0423-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 10/17/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Molecular analyses such as whole-genome sequencing have become routine and are expected to be transformational for future healthcare and lifestyle decisions. Population-wide implementation of such analyses is, however, not without challenges, and multiple studies are ongoing to identify what these are and explore how they can be addressed. METHODS Defined as a research project, the Personal Genome Project UK (PGP-UK) is part of the global PGP network and focuses on open data sharing and citizen science to advance and accelerate personalized genomics and medicine. RESULTS Here we report our findings on using an open consent recruitment protocol, active participant involvement, open access release of personal genome, methylome and transcriptome data and associated analyses, including 47 new variants predicted to affect gene function and innovative reports based on the analysis of genetic and epigenetic variants. For this pilot study, we recruited 10 participants willing to actively engage as citizen scientists with the project. In addition, we introduce Genome Donation as a novel mechanism for openly sharing previously restricted data and discuss the first three donations received. Lastly, we present GenoME, a free, open-source educational app suitable for the lay public to allow exploration of personal genomes. CONCLUSIONS Our findings demonstrate that citizen science-based approaches like PGP-UK have an important role to play in the public awareness, acceptance and implementation of genomics and personalized medicine.
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20
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Chhetri JB, Drousioti E, Guerra-Assunção JA, Herrero J, Ooi SKT. Generation of a cancer testis antigen mCherry reporter HCT116 colorectal carcinoma cell line. Heliyon 2018; 4:e00858. [PMID: 30364636 PMCID: PMC6197641 DOI: 10.1016/j.heliyon.2018.e00858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 09/26/2018] [Accepted: 10/10/2018] [Indexed: 11/03/2022] Open
Abstract
In the context of cancer immunotherapy, agents that target the immune system to cancer cells need to fulfil two criteria: 1) that they are only expressed on the desired target cell and 2) that they can elicit a potent immunological response. Cancer Testis Antigens are a large disparate family of factors ordinarily expressed in the germ-line but aberrantly expressed across multiple types of cancer. The ability to enforce their expression on tumour cells is an attractive strategy that could render such cells potent targets of the immune system, but very little is known about their regulation. We describe the generation of an mCherry reporter cell line using HCT116 colorectal carcinoma cells that we anticipate will be useful for screen-based approaches to identify novel regulators of CTA expression. Discoveries arising from their use could in future be exploited to enhance tumour cell immunogenicity and improve cancer immuno-therapy.
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Affiliation(s)
- Jyoti B Chhetri
- Department of Cancer Biology, UCL Cancer Institute, London, WC1E 6BT, UK
| | - Elena Drousioti
- Department of Cancer Biology, UCL Cancer Institute, London, WC1E 6BT, UK
| | | | - Javier Herrero
- Bill Lyons Informatics Centre, UCL Cancer Institute, London, WC1E 6BT, UK
| | - Steen K T Ooi
- Department of Cancer Biology, UCL Cancer Institute, London, WC1E 6BT, UK
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21
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Sobkowiak B, Glynn JR, Houben RMGJ, Mallard K, Phelan JE, Guerra-Assunção JA, Banda L, Mzembe T, Viveiros M, McNerney R, Parkhill J, Crampin AC, Clark TG. Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data. BMC Genomics 2018; 19:613. [PMID: 30107785 PMCID: PMC6092779 DOI: 10.1186/s12864-018-4988-z] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 07/31/2018] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Mixed, polyclonal Mycobacterium tuberculosis infection occurs in natural populations. Developing an effective method for detecting such cases is important in measuring the success of treatment and reconstruction of transmission between patients. Using whole genome sequence (WGS) data, we assess two methods for detecting mixed infection: (i) a combination of the number of heterozygous sites and the proportion of heterozygous sites to total SNPs, and (ii) Bayesian model-based clustering of allele frequencies from sequencing reads at heterozygous sites. RESULTS In silico and in vitro artificially mixed and known pure M. tuberculosis samples were analysed to determine the specificity and sensitivity of each method. We found that both approaches were effective in distinguishing between pure strains and mixed infection where there was relatively high (> 10%) proportion of a minor strain in the mixture. A large dataset of clinical isolates (n = 1963) from the Karonga Prevention Study in Northern Malawi was tested to examine correlations with patient characteristics and outcomes with mixed infection. The frequency of mixed infection in the population was found to be around 10%, with an association with year of diagnosis, but no association with age, sex, HIV status or previous tuberculosis. CONCLUSIONS Mixed Mycobacterium tuberculosis infection was identified in silico using whole genome sequence data. The methods presented here can be applied to population-wide analyses of tuberculosis to estimate the frequency of mixed infection, and to identify individual cases of mixed infections. These cases are important when considering the evolution and transmission of the disease, and in patient treatment.
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Affiliation(s)
- Benjamin Sobkowiak
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Judith R. Glynn
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Rein M. G. J. Houben
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
- TB Modelling Group, TB Centre, London School of Hygiene and Tropical Medicine, London, UK
| | - Kim Mallard
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Jody E. Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - José Afonso Guerra-Assunção
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Bill Lyons Informatics Centre, University College London, London, UK
| | | | | | - Miguel Viveiros
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Amelia C. Crampin
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
- Karonga Prevention Study, Chilumba, Malawi
| | - Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
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22
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Zhang R, Witkowska K, Afonso Guerra-Assunção J, Ren M, Ng FL, Mauro C, Tucker AT, Caulfield MJ, Ye S. A blood pressure-associated variant of the SLC39A8 gene influences cellular cadmium accumulation and toxicity. Hum Mol Genet 2016; 25:4117-4126. [PMID: 27466201 PMCID: PMC5291231 DOI: 10.1093/hmg/ddw236] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [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: 04/15/2016] [Revised: 06/13/2016] [Accepted: 07/11/2016] [Indexed: 02/05/2023] Open
Abstract
Genome-wide association studies have revealed a relationship between inter-individual variation in blood pressure and the single nucleotide polymorphism rs13107325 in the SLC39A8 gene. This gene encodes the ZIP8 protein which co-transports divalent metal cations, including heavy metal cadmium, the accumulation of which has been associated with increased blood pressure. The polymorphism results in two variants of ZIP8 with either an alanine (Ala) or a threonine (Thr) at residue 391. We investigated the functional impact of this variant on protein conformation, cadmium transport, activation of signalling pathways and cell viability in relation to blood pressure regulation. Following incubation with cadmium, higher intracellular cadmium was detected in cultured human embryonic kidney cells (HEK293) expressing heterologous ZIP8-Ala391, compared with HEK293 cells expressing heterologous ZIP8-Thr391. This Ala391-associated cadmium accumulation also increased the phosphorylation of the signal transduction molecule ERK2, activation of the transcription factor NFκB, and reduced cell viability. Similarly, vascular endothelial cells with the Ala/Ala genotype had higher intracellular cadmium concentration and lower cell viability than their Ala/Thr counterpart following cadmium exposure. These results indicate that the ZIP8 Ala391-to-Thr391 substitution has an effect on intracellular cadmium accumulation and cell toxicity, providing a potential mechanistic explanation for the association of this genetic variant with blood pressure.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Shu Ye
- William Harvey Research Institute
- Department of Cardiovascular Sciences, University of Leicester, Leicester LE3 9QP, UK
- NIHR Biomedical Research Centre in Cardiovascular Disease, Leicester LE3 9QP, UK
- Shantou University Medical College, Shantou 515041, People's Republic of China
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23
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Metherell LA, Guerra-Assunção JA, Sternberg MJ, David A. Three-Dimensional Model of Human Nicotinamide Nucleotide Transhydrogenase (NNT) and Sequence-Structure Analysis of its Disease-Causing Variations. Hum Mutat 2016; 37:1074-84. [PMID: 27459240 PMCID: PMC5026163 DOI: 10.1002/humu.23046] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 06/23/2016] [Accepted: 06/28/2016] [Indexed: 12/22/2022]
Abstract
Defective mitochondrial proteins are emerging as major contributors to human disease. Nicotinamide nucleotide transhydrogenase (NNT), a widely expressed mitochondrial protein, has a crucial role in the defence against oxidative stress. NNT variations have recently been reported in patients with familial glucocorticoid deficiency (FGD) and in patients with heart failure. Moreover, knockout animal models suggest that NNT has a major role in diabetes mellitus and obesity. In this study, we used experimental structures of bacterial transhydrogenases to generate a structural model of human NNT (H‐NNT). Structure‐based analysis allowed the identification of H‐NNT residues forming the NAD binding site, the proton canal and the large interaction site on the H‐NNT dimer. In addition, we were able to identify key motifs that allow conformational changes adopted by domain III in relation to its functional status, such as the flexible linker between domains II and III and the salt bridge formed by H‐NNT Arg882 and Asp830. Moreover, integration of sequence and structure data allowed us to study the structural and functional effect of deleterious amino acid substitutions causing FGD and left ventricular non‐compaction cardiomyopathy. In conclusion, interpretation of the function–structure relationship of H‐NNT contributes to our understanding of mitochondrial disorders.
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Affiliation(s)
- Louise A Metherell
- Centre for Endocrinology, William Harvey Research Institute, Queen Mary University of London, Charterhouse Square, London, UK
| | - José Afonso Guerra-Assunção
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK
| | - Michael J Sternberg
- Centre for Integrative System Biology and Bioinformatics, Imperial College London, London, UK
| | - Alessia David
- Centre for Integrative System Biology and Bioinformatics, Imperial College London, London, UK.
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24
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Okosun J, Wolfson RL, Wang J, Araf S, Wilkins L, Castellano BM, Escudero-Ibarz L, Al Seraihi AF, Richter J, Bernhart SH, Efeyan A, Iqbal S, Matthews J, Clear A, Guerra-Assunção JA, Bödör C, Quentmeier H, Mansbridge C, Johnson P, Davies A, Strefford JC, Packham G, Barrans S, Jack A, Du MQ, Calaminici M, Lister TA, Auer R, Montoto S, Gribben JG, Siebert R, Chelala C, Zoncu R, Sabatini DM, Fitzgibbon J. Recurrent mTORC1-activating RRAGC mutations in follicular lymphoma. Nat Genet 2016; 48:183-8. [PMID: 26691987 PMCID: PMC4731318 DOI: 10.1038/ng.3473] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [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: 10/12/2015] [Accepted: 11/23/2015] [Indexed: 12/13/2022]
Abstract
Follicular lymphoma is an incurable B cell malignancy characterized by the t(14;18) translocation and mutations affecting the epigenome. Although frequent gene mutations in key signaling pathways, including JAK-STAT, NOTCH and NF-κB, have also been defined, the spectrum of these mutations typically overlaps with that in the closely related diffuse large B cell lymphoma (DLBCL). Using a combination of discovery exome and extended targeted sequencing, we identified recurrent somatic mutations in RRAGC uniquely enriched in patients with follicular lymphoma (17%). More than half of the mutations preferentially co-occurred with mutations in ATP6V1B2 and ATP6AP1, which encode components of the vacuolar H(+)-ATP ATPase (V-ATPase) known to be necessary for amino acid-induced activation of mTORC1. The RagC variants increased raptor binding while rendering mTORC1 signaling resistant to amino acid deprivation. The activating nature of the RRAGC mutations, their existence in the dominant clone and their stability during disease progression support their potential as an excellent candidate for therapeutic targeting.
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Affiliation(s)
- Jessica Okosun
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Rachel L Wolfson
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jun Wang
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Shamzah Araf
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Lucy Wilkins
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Brian M Castellano
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | - Leire Escudero-Ibarz
- Division of Molecular Histopathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Ahad Fahad Al Seraihi
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Julia Richter
- Institute of Human Genetics, University Hospital Schleswig-Holstein Campus Kiel and Christian Albrechts University Kiel, Kiel, Germany
| | - Stephan H Bernhart
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
| | - Alejo Efeyan
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Sameena Iqbal
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Janet Matthews
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Andrew Clear
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | | | - Csaba Bödör
- MTA-SE Lendulet Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Hilmar Quentmeier
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | - Peter Johnson
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Andrew Davies
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Jonathan C Strefford
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Graham Packham
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Sharon Barrans
- Haematological Malignancy Diagnostic Service, St. James's Institute of Oncology, Leeds, UK
| | - Andrew Jack
- Haematological Malignancy Diagnostic Service, St. James's Institute of Oncology, Leeds, UK
| | - Ming-Qing Du
- Division of Molecular Histopathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Maria Calaminici
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - T Andrew Lister
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Rebecca Auer
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Silvia Montoto
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - John G Gribben
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Reiner Siebert
- Institute of Human Genetics, University Hospital Schleswig-Holstein Campus Kiel and Christian Albrechts University Kiel, Kiel, Germany
| | - Claude Chelala
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Roberto Zoncu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | - David M Sabatini
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Jude Fitzgibbon
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
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25
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Glynn JR, Guerra-Assunção JA, Houben RMGJ, Sichali L, Mzembe T, Mwaungulu LK, Mwaungulu JN, McNerney R, Khan P, Parkhill J, Crampin AC, Clark TG. Whole Genome Sequencing Shows a Low Proportion of Tuberculosis Disease Is Attributable to Known Close Contacts in Rural Malawi. PLoS One 2015; 10:e0132840. [PMID: 26181760 PMCID: PMC4504505 DOI: 10.1371/journal.pone.0132840] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 06/18/2015] [Indexed: 12/12/2022] Open
Abstract
Background The proportion of tuberculosis attributable to transmission from close contacts is not well known. Comparison of the genome of strains from index patients and prior contacts allows transmission to be confirmed or excluded. Methods In Karonga District, Malawi, all tuberculosis patients are asked about prior contact with others with tuberculosis. All available strains from culture-positive patients were sequenced. Up to 10 single nucleotide polymorphisms between index patients and their prior contacts were allowed for confirmation, and ≥ 100 for exclusion. The population attributable fraction was estimated from the proportion of confirmed transmissions and the proportion of patients with contacts. Results From 1997–2010 there were 1907 new culture-confirmed tuberculosis patients, of whom 32% reported at least one family contact and an additional 11% had at least one other contact; 60% of contacts had smear-positive disease. Among case-contact pairs with sequences available, transmission was confirmed from 38% (62/163) smear-positive prior contacts and 0/17 smear-negative prior contacts. Confirmed transmission was more common in those related to the prior contact (42.4%, 56/132) than in non-relatives (19.4%, 6/31, p = 0.02), and in those with more intense contact, to younger index cases, and in more recent years. The proportion of tuberculosis attributable to known contacts was estimated to be 9.4% overall. Conclusions In this population known contacts only explained a small proportion of tuberculosis cases. Even those with a prior family contact with smear positive tuberculosis were more likely to have acquired their infection elsewhere.
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Affiliation(s)
- Judith R. Glynn
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
- * E-mail:
| | - José Afonso Guerra-Assunção
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Rein M. G. J. Houben
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | | | | | | | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Palwasha Khan
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | - Amelia C. Crampin
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Karonga Prevention Study, Chilumba, Malawi
| | - Taane G. Clark
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
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26
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Coll F, McNerney R, Preston MD, Guerra-Assunção JA, Warry A, Hill-Cawthorne G, Mallard K, Nair M, Miranda A, Alves A, Perdigão J, Viveiros M, Portugal I, Hasan Z, Hasan R, Glynn JR, Martin N, Pain A, Clark TG. Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences. Genome Med 2015; 7:51. [PMID: 26019726 PMCID: PMC4446134 DOI: 10.1186/s13073-015-0164-0] [Citation(s) in RCA: 264] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 04/16/2015] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium tuberculosis drug resistance (DR) challenges effective tuberculosis disease control. Current molecular tests examine limited numbers of mutations, and although whole genome sequencing approaches could fully characterise DR, data complexity has restricted their clinical application. A library (1,325 mutations) predictive of DR for 15 anti-tuberculosis drugs was compiled and validated for 11 of them using genomic-phenotypic data from 792 strains. A rapid online ‘TB-Profiler’ tool was developed to report DR and strain-type profiles directly from raw sequences. Using our DR mutation library, in silico diagnostic accuracy was superior to some commercial diagnostics and alternative databases. The library will facilitate sequence-based drug-susceptibility testing.
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Affiliation(s)
- Francesc Coll
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Mark D Preston
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - José Afonso Guerra-Assunção
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Andrew Warry
- Advanced Data Analysis Centre, University of Nottingham, Wollaton Road, Nottingham, NG8 1BB UK
| | - Grant Hill-Cawthorne
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia ; Sydney Emerging Infections and Biosecurity Institute and School of Public Health, University of Sydney, Sydney, Australia
| | - Kim Mallard
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Mridul Nair
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Anabela Miranda
- Tuberculosis Laboratory, Instituto Nacional de Saude Dr. Ricardo Jorge, Porto, Portugal
| | - Adriana Alves
- Tuberculosis Laboratory, Instituto Nacional de Saude Dr. Ricardo Jorge, Porto, Portugal
| | - João Perdigão
- Centro de Patogénese Molecular, Faculdade de Farmácia da Universidade de Lisboa, Lisbon, Portugal
| | - Miguel Viveiros
- Grupo de Micobactérias, Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Isabel Portugal
- Centro de Patogénese Molecular, Faculdade de Farmácia da Universidade de Lisboa, Lisbon, Portugal
| | - Zahra Hasan
- Department of Pathology & Microbiology, Aga Khan University Hospital, Karachi, Pakistan
| | - Rumina Hasan
- Department of Pathology & Microbiology, Aga Khan University Hospital, Karachi, Pakistan
| | - Judith R Glynn
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK ; Karonga Prevention Study, Chilumba, Malawi
| | - Nigel Martin
- Department of Computer Science, Birkbeck College, University of London, Malet Street, London, WC1E 7HX UK
| | - Arnab Pain
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
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27
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Smedley D, Haider S, Durinck S, Pandini L, Provero P, Allen J, Arnaiz O, Awedh MH, Baldock R, Barbiera G, Bardou P, Beck T, Blake A, Bonierbale M, Brookes AJ, Bucci G, Buetti I, Burge S, Cabau C, Carlson JW, Chelala C, Chrysostomou C, Cittaro D, Collin O, Cordova R, Cutts RJ, Dassi E, Di Genova A, Djari A, Esposito A, Estrella H, Eyras E, Fernandez-Banet J, Forbes S, Free RC, Fujisawa T, Gadaleta E, Garcia-Manteiga JM, Goodstein D, Gray K, Guerra-Assunção JA, Haggarty B, Han DJ, Han BW, Harris T, Harshbarger J, Hastings RK, Hayes RD, Hoede C, Hu S, Hu ZL, Hutchins L, Kan Z, Kawaji H, Keliet A, Kerhornou A, Kim S, Kinsella R, Klopp C, Kong L, Lawson D, Lazarevic D, Lee JH, Letellier T, Li CY, Lio P, Liu CJ, Luo J, Maass A, Mariette J, Maurel T, Merella S, Mohamed AM, Moreews F, Nabihoudine I, Ndegwa N, Noirot C, Perez-Llamas C, Primig M, Quattrone A, Quesneville H, Rambaldi D, Reecy J, Riba M, Rosanoff S, Saddiq AA, Salas E, Sallou O, Shepherd R, Simon R, Sperling L, Spooner W, Staines DM, Steinbach D, Stone K, Stupka E, Teague JW, Dayem Ullah AZ, Wang J, Ware D, Wong-Erasmus M, Youens-Clark K, Zadissa A, Zhang SJ, Kasprzyk A. The BioMart community portal: an innovative alternative to large, centralized data repositories. Nucleic Acids Res 2015; 43:W589-98. [PMID: 25897122 PMCID: PMC4489294 DOI: 10.1093/nar/gkv350] [Citation(s) in RCA: 491] [Impact Index Per Article: 54.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 04/02/2015] [Indexed: 01/17/2023] Open
Abstract
The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations.
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Affiliation(s)
- Damian Smedley
- Wellcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Syed Haider
- The Weatherall Institute Of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Steffen Durinck
- Genentech, Inc. 1 DNA Way South San Francisco, CA 94080, USA
| | - Luca Pandini
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Paolo Provero
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy Dept of Molecular Biotechnology and Health Sciences University of Turin, Italy
| | - James Allen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Olivier Arnaiz
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris Sud, 1 avenue de la terrasse, 91198 Gif sur Yvette, France
| | - Mohammad Hamza Awedh
- Department of Electrical and Computer Engineering, Faculty of Engineering, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Richard Baldock
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Giulia Barbiera
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | | | - Tim Beck
- Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Andrew Blake
- MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK
| | | | - Anthony J Brookes
- Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Gabriele Bucci
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Iwan Buetti
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Sarah Burge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | | | | | - Claude Chelala
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | | | - Davide Cittaro
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | | | - Raul Cordova
- International Potato Center (CIP), Lima, 1558, Peru
| | - Rosalind J Cutts
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Erik Dassi
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Alex Di Genova
- Center for Mathematical Modeling and Center for Genome Regulation, University of Chile, Beauchef 851, 7th floor, Chile
| | - Anis Djari
- Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet-Tolosan, France
| | | | | | - Eduardo Eyras
- Catalan Institute for Research and Advanced Studies (ICREA), Passeig Lluis Companys 23, E-08010 Barcelona, Spain Universitat Pompeu Fabra, Dr Aiguader 88 E-08003 Barcelona, Spain
| | | | - Simon Forbes
- Wellcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Robert C Free
- Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | | | - Emanuela Gadaleta
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Jose M Garcia-Manteiga
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - David Goodstein
- Department of Energy, Joint Genome Institute, Walnut Creek, USA
| | - Kristian Gray
- HUGO Gene Nomenclature Committee (HGNC), European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - José Afonso Guerra-Assunção
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Bernard Haggarty
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Dong-Jin Han
- Medicinal Bioconvergence Research Center, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea Information Center for Bio-pharmacological Network, Seoul National University, Suwon 443-270, Republic of Korea
| | - Todd Harris
- Ontario Institute for Cancer Research, Toronto, M5G 0A3, Canada
| | - Jayson Harshbarger
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230-0045, Japan
| | - Robert K Hastings
- Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Richard D Hayes
- Department of Energy, Joint Genome Institute, Walnut Creek, USA
| | - Claire Hoede
- Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet-Tolosan, France
| | - Shen Hu
- School of Dentistry and Dental Research Institute, University of California Los Angeles (UCLA), Los Angeles, CA 90095-1668, USA
| | | | - Lucie Hutchins
- Mouse Genomic Informatics Group, The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Zhengyan Kan
- Oncology Computational Biology, Pfizer, La Jolla, USA
| | - Hideya Kawaji
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230-0045, Japan RIKEN Preventive Medicine and Diagnosis Innovation Program, Saitama 351-0198, Japan
| | - Aminah Keliet
- INRA URGI Centre de Versailles, bâtiment 18 Route de Saint Cyr 78026 Versailles, France
| | - Arnaud Kerhornou
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Sunghoon Kim
- Medicinal Bioconvergence Research Center, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Rhoda Kinsella
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Christophe Klopp
- Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet-Tolosan, France
| | - Lei Kong
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, P.R. China
| | - Daniel Lawson
- VectorBase, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Dejan Lazarevic
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Ji-Hyun Lee
- Medicinal Bioconvergence Research Center, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea Information Center for Bio-pharmacological Network, Seoul National University, Suwon 443-270, Republic of Korea
| | - Thomas Letellier
- INRA URGI Centre de Versailles, bâtiment 18 Route de Saint Cyr 78026 Versailles, France
| | - Chuan-Yun Li
- Institute of Molecular Medicine, Peking University, Beijing, China
| | - Pietro Lio
- Computer Laboratory, University of Cambridge, Cambridge, CB3 0FD, UK
| | - Chu-Jun Liu
- Institute of Molecular Medicine, Peking University, Beijing, China
| | - Jie Luo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Alejandro Maass
- Center for Mathematical Modeling and Center for Genome Regulation, University of Chile, Beauchef 851, 7th floor, Chile Department of Mathematical Engineering, University of Chile, Av. Beauchef 851, 5th floor, Santiago, Chile
| | - Jerome Mariette
- Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet-Tolosan, France
| | - Thomas Maurel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stefania Merella
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Azza Mostafa Mohamed
- Departament of Biochemistry, Faculty of Science for Girls, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Ibounyamine Nabihoudine
- Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet-Tolosan, France
| | - Nelson Ndegwa
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, PO Box 281, 17177 Stockholm, Sweden
| | - Céline Noirot
- Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet-Tolosan, France
| | | | - Michael Primig
- Inserm U1085 IRSET, University of Rennes 1, 35042 Rennes, France
| | - Alessandro Quattrone
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Hadi Quesneville
- INRA URGI Centre de Versailles, bâtiment 18 Route de Saint Cyr 78026 Versailles, France
| | - Davide Rambaldi
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | | | - Michela Riba
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Steven Rosanoff
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Amna Ali Saddiq
- Department of Biological Sciences, Faculty of Science for Girls, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Elisa Salas
- International Potato Center (CIP), Lima, 1558, Peru
| | | | - Rebecca Shepherd
- Wellcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | | | - Linda Sperling
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris Sud, 1 avenue de la terrasse, 91198 Gif sur Yvette, France
| | - William Spooner
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA Eagle Genomics Ltd., Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Daniel M Staines
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Delphine Steinbach
- INRA URGI Centre de Versailles, bâtiment 18 Route de Saint Cyr 78026 Versailles, France
| | - Kevin Stone
- Mouse Genomic Informatics Group, The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Elia Stupka
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Jon W Teague
- Wellcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Abu Z Dayem Ullah
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Jun Wang
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, P.R. China
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Marie Wong-Erasmus
- Human Longevity, Inc. 10835 Road to the Cure 140 San Diego, CA 92121, USA
| | - Ken Youens-Clark
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Amonida Zadissa
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Shi-Jian Zhang
- Institute of Molecular Medicine, Peking University, Beijing, China
| | - Arek Kasprzyk
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
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Guerra-Assunção JA, Crampin AC, Houben RMGJ, Mzembe T, Mallard K, Coll F, Khan P, Banda L, Chiwaya A, Pereira RPA, McNerney R, Fine PEM, Parkhill J, Clark TG, Glynn JR. Large-scale whole genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area. eLife 2015; 4. [PMID: 25732036 PMCID: PMC4384740 DOI: 10.7554/elife.05166] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 01/22/2015] [Indexed: 11/13/2022] Open
Abstract
To improve understanding of the factors influencing tuberculosis transmission and the
role of pathogen variation, we sequenced all available specimens from patients
diagnosed over 15 years in a whole district in Malawi. Mycobacterium
tuberculosis lineages were assigned and transmission networks
constructed, allowing ≤10 single nucleotide polymorphisms (SNPs) difference.
We defined disease as due to recent infection if the network-determined source was
within 5 years, and assessed transmissibility from forward transmissions resulting in
disease. High-quality sequences were available for 1687 disease episodes (72% of all
culture-positive episodes): 66% of patients linked to at least one other patient. The
between-patient mutation rate was 0.26 SNPs/year (95% CI 0.21–0.31). We showed
striking differences by lineage in the proportion of disease due to recent
transmission and in transmissibility (highest for lineage-2 and lowest for lineage-1)
that were not confounded by immigration, HIV status or drug resistance. Transmissions
resulting in disease decreased markedly over time. DOI:http://dx.doi.org/10.7554/eLife.05166.001 Tuberculosis is an important public health threat around the globe and is
particularly common in developing countries. It is difficult to control the spread of
the disease because the bacteria that cause it can spread when an infected individual
coughs or sneezes. It may take years for an infected individual to develop symptoms
of tuberculosis so it can be hard to trace the source of an outbreak, and people
infected with HIV are particularly susceptible to the disease. The bacterium that causes the majority of cases of tuberculosis is called
Mycobacterium tuberculosis. There are several different varieties
or ‘lineages’ of M. tuberculosis, and it is thought
that they may vary in their ability to spread and cause disease. However, the results
of previous studies have been inconsistent and there also seems to be a lot of
variation between strains within the same lineage. In this study, Guerra-Assunção et al. used an approach called whole
genome sequencing alongside more traditional methods to study the spread of
tuberculosis in Malawi. They sequenced the genomes of every available sample of
M. tuberculosis collected from patients in the Karonga district
of Malawi over a 15-year period. This produced high-quality DNA sequence data about
the bacteria responsible for almost 1700 cases of disease. Using this massive amount of data, Guerra-Assunção et al. constructed
networks that showed how the bacteria had spread in the community. This revealed that
there were differences between the ability of the various M.
tuberculosis lineages to cause disease and to spread in communities. For
example, lineage 1 was less likely than the other lineages to cause disease soon
after infecting an individual and was less able to spread. The data also show that the proportion of cases of disease due to recent infection
declined substantially during the 15-year period. This indicates that the
tuberculosis and HIV control programmes in the area have been successful. Guerra-Assunção et al.'s findings show that it is possible to
understand how tuberculosis is transmitted on a large scale. The next challenge is to
understand why the lineages differ in their ability to cause disease and spread
between individuals. DOI:http://dx.doi.org/10.7554/eLife.05166.002
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Affiliation(s)
- J A Guerra-Assunção
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - A C Crampin
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - R M G J Houben
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - T Mzembe
- Karonga Prevention Study, Malawi, Malawi
| | - K Mallard
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - F Coll
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - P Khan
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - L Banda
- Karonga Prevention Study, Malawi, Malawi
| | - A Chiwaya
- Karonga Prevention Study, Malawi, Malawi
| | - R P A Pereira
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - R McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - P E M Fine
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - J Parkhill
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - T G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - J R Glynn
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
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Guerra-Assunção JA, Houben RMGJ, Crampin AC, Mzembe T, Mallard K, Coll F, Khan P, Banda L, Chiwaya A, Pereira RPA, McNerney R, Harris D, Parkhill J, Clark TG, Glynn JR. Recurrence due to relapse or reinfection with Mycobacterium tuberculosis: a whole-genome sequencing approach in a large, population-based cohort with a high HIV infection prevalence and active follow-up. J Infect Dis 2014; 211:1154-63. [PMID: 25336729 PMCID: PMC4354982 DOI: 10.1093/infdis/jiu574] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [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] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Recurrent tuberculosis is a major health burden and may be due to relapse with the original strain or reinfection with a new strain. METHODS In a population-based study in northern Malawi, patients with tuberculosis diagnosed from 1996 to 2010 were actively followed after the end of treatment. Whole-genome sequencing with approximately 100-fold coverage was performed on all available cultures. Results of IS6110 restriction fragment-length polymorphism analyses were available for cultures performed up to 2008. RESULTS Based on our data, a difference of ≤10 single-nucleotide polymorphisms (SNPs) was used to define relapse, and a difference of >100 SNPs was used to define reinfection. There was no evidence of mixed infections among those classified as reinfections. Of 1471 patients, 139 had laboratory-confirmed recurrences: 55 had relapse, and 20 had reinfection; for 64 type of recurrence was unclassified. Almost all relapses occurred in the first 2 years. Human immunodeficiency virus infection was associated with reinfection but not relapse. Relapses were associated with isoniazid resistance, treatment before 2007, and lineage-3 strains. We identified several gene variants associated with relapse. Lineage-2 (Beijing) was overrepresented and lineage-1 underrepresented among the reinfecting strains (P = .004). CONCLUSIONS While some of the factors determining recurrence depend on the patient and their treatment, differences in the Mycobacterium tuberculosis genome appear to have a role in both relapse and reinfection.
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Affiliation(s)
| | - Rein M G J Houben
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine
| | - Amelia C Crampin
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine Karonga Prevention Study, Malawi
| | | | - Kim Mallard
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine
| | - Francesc Coll
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine
| | - Palwasha Khan
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine
| | | | | | - Rui P A Pereira
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine
| | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine
| | - David Harris
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Taane G Clark
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine
| | - Judith R Glynn
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine
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Cutts RJ, Guerra-Assunção JA, Gadaleta E, Dayem Ullah AZ, Chelala C. BCCTBbp: the Breast Cancer Campaign Tissue Bank bioinformatics portal. Nucleic Acids Res 2014; 43:D831-6. [PMID: 25332396 PMCID: PMC4384036 DOI: 10.1093/nar/gku984] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
BCCTBbp (http://bioinformatics.breastcancertissuebank.org) was initially developed as the data-mining portal of the Breast Cancer Campaign Tissue Bank (BCCTB), a vital resource of breast cancer tissue for researchers to support and promote cutting-edge research. BCCTBbp is dedicated to maximising research on patient tissues by initially storing genomics, methylomics, transcriptomics, proteomics and microRNA data that has been mined from the literature and linking to pathways and mechanisms involved in breast cancer. Currently, the portal holds 146 datasets comprising over 227 795 expression/genomic measurements from various breast tissues (e.g. normal, malignant or benign lesions), cell lines and body fluids. BCCTBbp can be used to build on breast cancer knowledge and maximise the value of existing research. By recording a large number of annotations on samples and studies, and linking to other databases, such as NCBI, Ensembl and Reactome, a wide variety of different investigations can be carried out. Additionally, BCCTBbp has a dedicated analytical layer allowing researchers to further analyse stored datasets. A future important role for BCCTBbp is to make available all data generated on BCCTB tissues thus building a valuable resource of information on the tissues in BCCTB that will save repetition of experiments and expand scientific knowledge.
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Affiliation(s)
- Rosalind J Cutts
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - José Afonso Guerra-Assunção
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Emanuela Gadaleta
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Abu Z Dayem Ullah
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Claude Chelala
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
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Alsford S, Currier RB, Guerra-Assunção JA, Clark TG, Horn D. Cathepsin-L can resist lysis by human serum in Trypanosoma brucei brucei. PLoS Pathog 2014; 10:e1004130. [PMID: 24830321 PMCID: PMC4022737 DOI: 10.1371/journal.ppat.1004130] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [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: 10/16/2013] [Accepted: 04/02/2014] [Indexed: 11/18/2022] Open
Abstract
Closely related African trypanosomes cause lethal diseases but display distinct host ranges. Specifically, Trypanosoma brucei brucei causes nagana in livestock but fails to infect humans, while Trypanosoma brucei gambiense and Trypanosoma brucei rhodesiense cause sleeping sickness in humans. T. b. brucei fails to infect humans because it is sensitive to innate immune complexes found in normal human serum known as trypanolytic factor (TLF) 1 and 2; the lytic component is apolipoprotein-L1 in both TLFs. TLF resistance mechanisms of T. b. gambiense and T. b. rhodesiense are now known to arise through either gain or loss-of-function, but our understanding of factors that render T. b. brucei susceptible to lysis by human serum remains incomplete. We conducted a genome-scale RNA interference (RNAi) library screen for reduced sensitivity to human serum. Among only four high-confidence ‘hits’ were all three genes previously shown to sensitize T. b. brucei to human serum, the haptoglobin-haemoglobin receptor (HpHbR), inhibitor of cysteine peptidase (ICP) and the lysosomal protein, p67, thereby demonstrating the pivotal roles these factors play. The fourth gene identified encodes a predicted protein with eleven trans-membrane domains. Using chemical and genetic approaches, we show that ICP sensitizes T. b. brucei to human serum by modulating the essential cathepsin, CATL, a lysosomal cysteine peptidase. A second cathepsin, CATB, likely to be dispensable for growth in in vitro culture, has little or no impact on human-serum sensitivity. Our findings reveal major and novel determinants of human-serum sensitivity in T. b. brucei. They also shed light on the lysosomal protein-protein interactions that render T. b. brucei exquisitely sensitive to lytic factors in human serum, and indicate that CATL, an important potential drug target, has the capacity to resist these factors. The interplay among host innate immunity and resistance mechanisms in African trypanosomes has a major impact on the host range of these tsetse-fly transmitted parasites, defining their ability to cause disease in humans. A genome-scale RNAi screen identified a highly restricted set of four genes that sensitise trypanosomes to human serum: those encoding the haptoglobin-haemoglobin receptor, a predicted trans-membrane channel, a lysosomal membrane-protein and the cysteine peptidase inhibitor. An analysis of the cysteine peptidases revealed cathepsin-L as the protease regulated by the inhibitor – and with the capacity to render the parasite resistant to lysis by human serum. These findings emphasise the importance of parasite factors for the delivery and stability of host toxins. They also shed light on the control of proteolysis by parasites and potential unanticipated consequences of therapies that target the parasite proteases.
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Affiliation(s)
- Sam Alsford
- London School of Hygiene & Tropical Medicine, London, United Kingdom
- * E-mail:
| | - Rachel B. Currier
- London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | - Taane G. Clark
- London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - David Horn
- Division of Biological Chemistry & Drug Discovery, College of Life Sciences, University of Dundee, Dundee, United Kingdom
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Coll F, Preston M, Guerra-Assunção JA, Hill-Cawthorn G, Harris D, Perdigão J, Viveiros M, Portugal I, Drobniewski F, Gagneux S, Glynn JR, Pain A, Parkhill J, McNerney R, Martin N, Clark TG. PolyTB: a genomic variation map for Mycobacterium tuberculosis. Tuberculosis (Edinb) 2014; 94:346-54. [PMID: 24637013 PMCID: PMC4066953 DOI: 10.1016/j.tube.2014.02.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Accepted: 02/08/2014] [Indexed: 12/21/2022]
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis (Mtb) is the second major cause of death from an infectious disease worldwide. Recent advances in DNA sequencing are leading to the ability to generate whole genome information in clinical isolates of M. tuberculosis complex (MTBC). The identification of informative genetic variants such as phylogenetic markers and those associated with drug resistance or virulence will help barcode Mtb in the context of epidemiological, diagnostic and clinical studies. Mtb genomic datasets are increasingly available as raw sequences, which are potentially difficult and computer intensive to process, and compare across studies. Here we have processed the raw sequence data (>1500 isolates, eight studies) to compile a catalogue of SNPs (n = 74,039, 63% non-synonymous, 51.1% in more than one isolate, i.e. non-private), small indels (n = 4810) and larger structural variants (n = 800). We have developed the PolyTB web-based tool (http://pathogenseq.lshtm.ac.uk/polytb) to visualise the resulting variation and important meta-data (e.g. in silico inferred strain-types, location) within geographical map and phylogenetic views. This resource will allow researchers to identify polymorphisms within candidate genes of interest, as well as examine the genomic diversity and distribution of strains. PolyTB source code is freely available to researchers wishing to develop similar tools for their pathogen of interest.
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Affiliation(s)
- Francesc Coll
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK.
| | - Mark Preston
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK
| | - José Afonso Guerra-Assunção
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK
| | - Grant Hill-Cawthorn
- Pathogen Genomics Laboratory, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia; Sydney Emerging Infections and Biosecurity Institute and School of Public Health, Sydney, NSW 2006, Australia
| | - David Harris
- Pathogen Genomics Faculty, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA Cambridge, UK
| | - João Perdigão
- Centro de Patogénese Molecular, Faculdade de Farmácia da Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Miguel Viveiros
- Grupo de Micobactérias, Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, 1349-008 Lisboa, Portugal
| | - Isabel Portugal
- Centro de Patogénese Molecular, Faculdade de Farmácia da Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Francis Drobniewski
- Centre for Immunology and Infectious Disease, Queen Mary University of London, E1 2AT London, UK
| | | | - Judith R Glynn
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK
| | - Arnab Pain
- Pathogen Genomics Laboratory, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Julian Parkhill
- Pathogen Genomics Faculty, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA Cambridge, UK
| | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK
| | - Nigel Martin
- School of Computer Science and Information Systems, Birkbeck College, WC1E 7HX London, UK
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK
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Camps C, Saini HK, Mole DR, Choudhry H, Reczko M, Guerra-Assunção JA, Tian YM, Buffa FM, Harris AL, Hatzigeorgiou AG, Enright AJ, Ragoussis J. Integrated analysis of microRNA and mRNA expression and association with HIF binding reveals the complexity of microRNA expression regulation under hypoxia. Mol Cancer 2014; 13:28. [PMID: 24517586 PMCID: PMC3928101 DOI: 10.1186/1476-4598-13-28] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [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: 09/14/2013] [Accepted: 02/05/2014] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND In mammalians, HIF is a master regulator of hypoxia gene expression through direct binding to DNA, while its role in microRNA expression regulation, critical in the hypoxia response, is not elucidated genome wide. Our aim is to investigate in depth the regulation of microRNA expression by hypoxia in the breast cancer cell line MCF-7, establish the relationship between microRNA expression and HIF binding sites, pri-miRNA transcription and microRNA processing gene expression. METHODS MCF-7 cells were incubated at 1% Oxygen for 16, 32 and 48 h. SiRNA against HIF-1α and HIF-2α were performed as previously published. MicroRNA and mRNA expression were assessed using microRNA microarrays, small RNA sequencing, gene expression microarrays and Real time PCR. The Kraken pipeline was applied for microRNA-seq analysis along with Bioconductor packages. Microarray data was analysed using Limma (Bioconductor), ChIP-seq data were analysed using Gene Set Enrichment Analysis and multiple testing correction applied in all analyses. RESULTS Hypoxia time course microRNA sequencing data analysis identified 41 microRNAs significantly up- and 28 down-regulated, including hsa-miR-4521, hsa-miR-145-3p and hsa-miR-222-5p reported in conjunction with hypoxia for the first time. Integration of HIF-1α and HIF-2α ChIP-seq data with expression data showed overall association between binding sites and microRNA up-regulation, with hsa-miR-210-3p and microRNAs of miR-27a/23a/24-2 and miR-30b/30d clusters as predominant examples. Moreover the expression of hsa-miR-27a-3p and hsa-miR-24-3p was found positively associated to a hypoxia gene signature in breast cancer. Gene expression analysis showed no full coordination between pri-miRNA and microRNA expression, pointing towards additional levels of regulation. Several transcripts involved in microRNA processing were found regulated by hypoxia, of which DICER (down-regulated) and AGO4 (up-regulated) were HIF dependent. DICER expression was found inversely correlated to hypoxia in breast cancer. CONCLUSIONS Integrated analysis of microRNA, mRNA and ChIP-seq data in a model cell line supports the hypothesis that microRNA expression under hypoxia is regulated at transcriptional and post-transcriptional level, with the presence of HIF binding sites at microRNA genomic loci associated with up-regulation. The identification of hypoxia and HIF regulated microRNAs relevant for breast cancer is important for our understanding of disease development and design of therapeutic interventions.
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Affiliation(s)
- Carme Camps
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, United Kingdom
| | - Harpreet K Saini
- EMBL—European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - David R Mole
- Henry Wellcome Building for Molecular Physiology, University of Oxford, Roosevelt Drive, Oxford, United Kingdom
| | - Hani Choudhry
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, United Kingdom
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Martin Reczko
- Institute of Molecular Oncology, Biomedical Sciences Research Center “Alexander Fleming”, 34 Fleming Street, Vari 16672, Greece
| | | | - Ya-Min Tian
- Henry Wellcome Building for Molecular Physiology, University of Oxford, Roosevelt Drive, Oxford, United Kingdom
| | - Francesca M Buffa
- Cancer Research UK Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Adrian L Harris
- Cancer Research UK Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Artemis G Hatzigeorgiou
- Institute of Molecular Oncology, Biomedical Sciences Research Center “Alexander Fleming”, 34 Fleming Street, Vari 16672, Greece
| | - Anton J Enright
- EMBL—European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Jiannis Ragoussis
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, United Kingdom
- Institute of Molecular Oncology, Biomedical Sciences Research Center “Alexander Fleming”, 34 Fleming Street, Vari 16672, Greece
- Present Address: McGill University and Genome Quebec Innovation Centre, 740 DR Penfield Ave, Montreal H3A 0G1, Canada
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Abstract
BACKGROUND In animals, microRNAs (miRNA) are important genetic regulators. Animal miRNAs appear to have expanded in conjunction with an escalation in complexity during early bilaterian evolution. Their small size and high-degree of similarity makes them challenging for phylogenetic approaches. Furthermore, genomic locations encoding miRNAs are not clearly defined in many species. A number of studies have looked at the evolution of individual miRNA families. However, we currently lack resources for large-scale analysis of miRNA evolution. RESULTS We addressed some of these issues in order to analyse the evolution of miRNAs. We perform syntenic and phylogenetic analysis for miRNAs from 80 animal species. We present synteny maps, phylogenies and functional data for miRNAs across these species. These data represent the basis of our analyses and also act as a resource for the community. CONCLUSIONS We use these data to explore the distribution of miRNAs across phylogenetic space, characterise their birth and death, and examine functional relationships between miRNAs and other genes. These data confirm a number of previously reported findings on a larger scale and also offer novel insights into the evolution of the miRNA repertoire in animals, and it's genomic organization.
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Affiliation(s)
- José Afonso Guerra-Assunção
- EMBL - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
- PDBC, Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
| | - Anton J Enright
- EMBL - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
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Parts L, Hedman ÅK, Keildson S, Knights AJ, Abreu-Goodger C, van de Bunt M, Guerra-Assunção JA, Bartonicek N, van Dongen S, Mägi R, Nisbet J, Barrett A, Rantalainen M, Nica AC, Quail MA, Small KS, Glass D, Enright AJ, Winn J, Deloukas P, Dermitzakis ET, McCarthy MI, Spector TD, Durbin R, Lindgren CM. Extent, causes, and consequences of small RNA expression variation in human adipose tissue. PLoS Genet 2012; 8:e1002704. [PMID: 22589741 PMCID: PMC3349731 DOI: 10.1371/journal.pgen.1002704] [Citation(s) in RCA: 44] [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: 02/01/2012] [Accepted: 03/27/2012] [Indexed: 12/12/2022] Open
Abstract
Small RNAs are functional molecules that modulate mRNA transcripts and have been implicated in the aetiology of several common diseases. However, little is known about the extent of their variability within the human population. Here, we characterise the extent, causes, and effects of naturally occurring variation in expression and sequence of small RNAs from adipose tissue in relation to genotype, gene expression, and metabolic traits in the MuTHER reference cohort. We profiled the expression of 15 to 30 base pair RNA molecules in subcutaneous adipose tissue from 131 individuals using high-throughput sequencing, and quantified levels of 591 microRNAs and small nucleolar RNAs. We identified three genetic variants and three RNA editing events. Highly expressed small RNAs are more conserved within mammals than average, as are those with highly variable expression. We identified 14 genetic loci significantly associated with nearby small RNA expression levels, seven of which also regulate an mRNA transcript level in the same region. In addition, these loci are enriched for variants significant in genome-wide association studies for body mass index. Contrary to expectation, we found no evidence for negative correlation between expression level of a microRNA and its target mRNAs. Trunk fat mass, body mass index, and fasting insulin were associated with more than twenty small RNA expression levels each, while fasting glucose had no significant associations. This study highlights the similar genetic complexity and shared genetic control of small RNA and mRNA transcripts, and gives a quantitative picture of small RNA expression variation in the human population. Genetic information is transmitted to the cell only through RNA molecules. A special class of RNAs is comprised of the small (up to 30 nucleotide) ones, known to be potent regulators of various cellular processes. At the same time, they have not been as widely studied as messenger RNAs—we do not know how much variation in their sequence and expression level occurs naturally in human populations or how this variability influences other traits. We measured small RNA levels and genetic variability in fat tissue from 131 individuals by high-throughput sequencing. We could associate the expression levels with genetic background of the individuals, as well as changes in metabolic traits. Surprisingly, we found no large scale influence of small RNA variation on mRNA levels, their main regulatory target. Overall, our study is the first to give a quantitative picture of the naturally occurring variation in these important regulatory molecules in human fat tissue.
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Affiliation(s)
- Leopold Parts
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Åsa K. Hedman
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Sarah Keildson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | | - Cei Abreu-Goodger
- European Bioinformatics Institute, Hinxton, United Kingdom
- National Laboratory of Genomics for Biodiversity (Langebio), Cinvestav, Irapuato, Mexico
| | - Martijn van de Bunt
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Diabetes, Endocrinology, and Metabolism, University of Oxford, Oxford, United Kingdom
| | - José Afonso Guerra-Assunção
- European Bioinformatics Institute, Hinxton, United Kingdom
- PDBC, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | | | - Reedik Mägi
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - James Nisbet
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Amy Barrett
- Oxford Centre for Diabetes, Endocrinology, and Metabolism, University of Oxford, Oxford, United Kingdom
| | - Mattias Rantalainen
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Alexandra C. Nica
- Department of Genetic Medicine and Development and Institute of Genetics and Genomics in Geneva, University of Geneva Medical School, Geneva, Switzerland
| | | | - Kerrin S. Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Daniel Glass
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | | | - John Winn
- Microsoft Research, Cambridge, United Kingdom
| | | | - Panos Deloukas
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Emmanouil T. Dermitzakis
- Department of Genetic Medicine and Development and Institute of Genetics and Genomics in Geneva, University of Geneva Medical School, Geneva, Switzerland
| | - Mark I. McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Diabetes, Endocrinology, and Metabolism, University of Oxford, Oxford, United Kingdom
| | - Timothy D. Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Richard Durbin
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- * E-mail: (RD); (CML)
| | - Cecilia M. Lindgren
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail: (RD); (CML)
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Hu M, Ayub Q, Guerra-Assunção JA, Long Q, Ning Z, Huang N, Romero IG, Mamanova L, Akan P, Liu X, Coffey AJ, Turner DJ, Swerdlow H, Burton J, Quail MA, Conrad DF, Enright AJ, Tyler-Smith C, Xue Y. Exploration of signals of positive selection derived from genotype-based human genome scans using re-sequencing data. Hum Genet 2011; 131:665-74. [PMID: 22057783 PMCID: PMC3325425 DOI: 10.1007/s00439-011-1111-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2011] [Accepted: 10/24/2011] [Indexed: 11/25/2022]
Abstract
We have investigated whether regions of the genome showing signs of positive selection in scans based on haplotype structure also show evidence of positive selection when sequence-based tests are applied, whether the target of selection can be localized more precisely, and whether such extra evidence can lead to increased biological insights. We used two tools: simulations under neutrality or selection, and experimental investigation of two regions identified by the HapMap2 project as putatively selected in human populations. Simulations suggested that neutral and selected regions should be readily distinguished and that it should be possible to localize the selected variant to within 40 kb at least half of the time. Re-sequencing of two ~300 kb regions (chr4:158Mb and chr10:22Mb) lacking known targets of selection in HapMap CHB individuals provided strong evidence for positive selection within each and suggested the micro-RNA gene hsa-miR-548c as the best candidate target in one region, and changes in regulation of the sperm protein gene SPAG6 in the other.
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Affiliation(s)
- Min Hu
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
| | - Qasim Ayub
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
| | | | - Quan Long
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
- Present Address: Gregor Mendel Institut für Molekulare Pflanzenbiologie GmbH, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Zemin Ning
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
| | - Ni Huang
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
| | - Irene Gallego Romero
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
| | - Lira Mamanova
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
| | - Pelin Akan
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
- Present Address: Science for Life Laboratory, Royal Institute of Technology, 171 65 Stockholm, Sweden
| | - Xin Liu
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
| | - Alison J. Coffey
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
| | - Daniel J. Turner
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
- Present Address: Oxford Nanopore Technologies Ltd., Oxford, UK
| | - Harold Swerdlow
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
| | - John Burton
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
| | - Michael A. Quail
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
| | - Donald F. Conrad
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
- Present Address: Department of Genetics, Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO USA
| | - Anton J. Enright
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD UK
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
| | - Yali Xue
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
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Keane TM, Goodstadt L, Danecek P, White MA, Wong K, Yalcin B, Heger A, Agam A, Slater G, Goodson M, Furlotte NA, Eskin E, Nellåker C, Whitley H, Cleak J, Janowitz D, Hernandez-Pliego P, Edwards A, Belgard TG, Oliver PL, McIntyre RE, Bhomra A, Nicod J, Gan X, Yuan W, van der Weyden L, Steward CA, Bala S, Stalker J, Mott R, Durbin R, Jackson IJ, Czechanski A, Guerra-Assunção JA, Donahue LR, Reinholdt LG, Payseur BA, Ponting CP, Birney E, Flint J, Adams DJ. Mouse genomic variation and its effect on phenotypes and gene regulation. Nature 2011; 477:289-94. [PMID: 21921910 DOI: 10.1038/nature10413] [Citation(s) in RCA: 1124] [Impact Index Per Article: 86.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 08/05/2011] [Indexed: 01/16/2023]
Abstract
We report genome sequences of 17 inbred strains of laboratory mice and identify almost ten times more variants than previously known. We use these genomes to explore the phylogenetic history of the laboratory mouse and to examine the functional consequences of allele-specific variation on transcript abundance, revealing that at least 12% of transcripts show a significant tissue-specific expression bias. By identifying candidate functional variants at 718 quantitative trait loci we show that the molecular nature of functional variants and their position relative to genes vary according to the effect size of the locus. These sequences provide a starting point for a new era in the functional analysis of a key model organism.
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Affiliation(s)
- Thomas M Keane
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
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