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Thompson CR, Torres PM, Kontogianni K, Byrne RL, Noguera SV, Luna-Muschi A, Marchi AP, Andrade PS, dos Santos Barboza A, Nishikawara M, Body R, de Vos M, Escadafal C, Adams E, Figueiredo Costa S, Cubas-Atienzar AI. Multicenter Diagnostic Evaluation of OnSite COVID-19 Rapid Test (CTK Biotech) among Symptomatic Individuals in Brazil and the United Kingdom. Microbiol Spectr 2023; 11:e0504422. [PMID: 37212699 PMCID: PMC10269675 DOI: 10.1128/spectrum.05044-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 04/17/2023] [Indexed: 05/23/2023] Open
Abstract
The COVID-19 pandemic has given rise to numerous commercially available antigen rapid diagnostic tests (Ag-RDTs). To generate and to share accurate and independent data with the global community requires multisite prospective diagnostic evaluations of Ag-RDTs. This report describes the clinical evaluation of the OnSite COVID-19 rapid test (CTK Biotech, CA, USA) in Brazil and the United Kingdom. A total of 496 paired nasopharyngeal (NP) swabs were collected from symptomatic health care workers at Hospital das Clínicas in São Paulo, Brazil, and 211 NP swabs were collected from symptomatic participants at a COVID-19 drive-through testing site in Liverpool, United Kingdom. Swabs were analyzed by Ag-RDT, and results were compared to quantitative reverse transcriptase PCR (RT-qPCR). The clinical sensitivity of the OnSite COVID-19 rapid test in Brazil was 90.3% (95% confidence interval [CI], 75.1 to 96.7%) and in the United Kingdom was 75.3% (95% CI, 64.6 to 83.6%). The clinical specificity in Brazil was 99.4% (95% CI, 98.1 to 99.8%) and in the United Kingdom was 95.5% (95% CI, 90.6 to 97.9%). Concurrently, analytical evaluation of the Ag-RDT was assessed using direct culture supernatant of SARS-CoV-2 strains from wild-type (WT), Alpha, Delta, Gamma, and Omicron lineages. This study provides comparative performance of an Ag-RDT across two different settings, geographical areas, and populations. Overall, the OnSite Ag-RDT demonstrated a lower clinical sensitivity than claimed by the manufacturer. The sensitivity and specificity from the Brazil study fulfilled the performance criteria determined by the World Health Organization, but the performance obtained from the UK study failed to do. Further evaluation of Ag-RDTs should include harmonized protocols between laboratories to facilitate comparison between settings. IMPORTANCE Evaluating rapid diagnostic tests in diverse populations is essential to improving diagnostic responses as it gives an indication of the accuracy in real-world scenarios. In the case of rapid diagnostic testing within this pandemic, lateral flow tests that meet the minimum requirements for sensitivity and specificity can play a key role in increasing testing capacity, allowing timely clinical management of those infected, and protecting health care systems. This is particularly valuable in settings where access to the test gold standard is often restricted.
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Affiliation(s)
- Caitlin R. Thompson
- Liverpool School of Tropical Medicine, Centre for Drugs and Diagnostics, Liverpool, United Kingdom
| | - Pablo Muñoz Torres
- LIM-49, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Konstantina Kontogianni
- Liverpool School of Tropical Medicine, Centre for Drugs and Diagnostics, Liverpool, United Kingdom
| | - Rachel L. Byrne
- Liverpool School of Tropical Medicine, Centre for Drugs and Diagnostics, Liverpool, United Kingdom
| | - LSTM Diagnostic group
- Liverpool School of Tropical Medicine, Centre for Drugs and Diagnostics, Liverpool, United Kingdom
- LIM-49, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Department of Epidemiology, School of Public Health of University of São Paulo, São Paulo, Brazil
- Centro de atendimento ao colaborador, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Divisão de Laboratório Central, Hospital das Clinicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- FIND, Geneva, Switzerland
- Manchester University NHS Foundation Trust, Manchester, United Kingdom
- Global Access Diagnostics, Thurleigh, Bedfordshire, United Kingdom
| | - Saidy Vásconez Noguera
- LIM-49, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Alessandra Luna-Muschi
- LIM-49, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Ana Paula Marchi
- LIM-49, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Pâmela S. Andrade
- Department of Epidemiology, School of Public Health of University of São Paulo, São Paulo, Brazil
| | - Antonio dos Santos Barboza
- Centro de atendimento ao colaborador, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Marli Nishikawara
- Centro de atendimento ao colaborador, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - CONDOR steering group
- Liverpool School of Tropical Medicine, Centre for Drugs and Diagnostics, Liverpool, United Kingdom
- LIM-49, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Department of Epidemiology, School of Public Health of University of São Paulo, São Paulo, Brazil
- Centro de atendimento ao colaborador, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Divisão de Laboratório Central, Hospital das Clinicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- FIND, Geneva, Switzerland
- Manchester University NHS Foundation Trust, Manchester, United Kingdom
- Global Access Diagnostics, Thurleigh, Bedfordshire, United Kingdom
| | - Richard Body
- Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | | | - Camille Escadafal
- Divisão de Laboratório Central, Hospital das Clinicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Emily Adams
- Liverpool School of Tropical Medicine, Centre for Drugs and Diagnostics, Liverpool, United Kingdom
- Global Access Diagnostics, Thurleigh, Bedfordshire, United Kingdom
| | - Silvia Figueiredo Costa
- LIM-49, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Ana I. Cubas-Atienzar
- Liverpool School of Tropical Medicine, Centre for Drugs and Diagnostics, Liverpool, United Kingdom
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2
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Barnett SE, Kenyani J, Tripari M, Butt Z, Grosman R, Querques F, Shaw L, Silva LC, Goate Z, Marciniak SJ, Rassl DM, Jackson R, Lian LY, Szlosarek PW, Sacco JJ, Coulson JM. BAP1 Loss Is Associated with Higher ASS1 Expression in Epithelioid Mesothelioma: Implications for Therapeutic Stratification. Mol Cancer Res 2023; 21:411-427. [PMID: 36669126 PMCID: PMC10150242 DOI: 10.1158/1541-7786.mcr-22-0635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 12/20/2022] [Accepted: 01/19/2023] [Indexed: 01/21/2023]
Abstract
The nuclear deubiquitylase BRCA1-associated protein 1 (BAP1) is frequently inactivated in malignant pleural mesothelioma (MPM) and germline BAP1 mutation predisposes to cancers including MPM. To explore the influence on cell physiology and drug sensitivity, we sequentially edited a predisposition mutation (w-) and a promoter trap (KO) into human mesothelial cells. BAP1w-/KO MeT5A cells express less BAP1 protein and phenocopy key aspects of BAP1 loss in MPM. Stable isotope labeling with amino acids in cell culture-mass spectrometry revealed evidence of metabolic adaptation, with concomitant alteration of cellular metabolites. In MeT5A, BAP1 deficiency reduces glycolytic enzyme levels but increases enzymes involved in the tricarboxylic acid cycle and anaplerotic pathways. Notably both argininosuccinate synthase 1 (ASS1), essential for cellular synthesis of arginine, and its substrate aspartate, are elevated in BAP1w-/KO MeT5A cells. Likewise, ASS1 expression is higher in BAP1-altered MPM cell lines, and inversely correlates with BAP1 in The Cancer Genome Atlas MESO dataset. Elevated ASS1 is also evident by IHC staining in epithelioid MPM lacking nuclear BAP1 expression, with improved survival among patients with BAP1-negative/ASS1-expressing tumors. Alterations in arginine metabolism may sensitize cells to metabolic drugs and we find that BAP1-negative/ASS1-expressing MPM cell lines are more sensitive to ASS1 inhibition, although not to inhibition of purine synthesis by mizoribine. Importantly, BAP1w-/KO MeT5A become desensitized to arginine deprivation by pegylated arginine deiminase (ADI-PEG20), phenocopying BAP1-negative/ASS1-expressing MPM cell lines. IMPLICATIONS Our data reveal an interrelationship between BAP1 and arginine metabolism, providing a potential means of identifying patients with epithelioid MPM likely to benefit from ADI-PEG20.
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Affiliation(s)
- Sarah E. Barnett
- Molecular Physiology and Cell Signalling, University of Liverpool, Liverpool, United Kingdom
| | - Jenna Kenyani
- Molecular Physiology and Cell Signalling, University of Liverpool, Liverpool, United Kingdom
| | - Martina Tripari
- Molecular Physiology and Cell Signalling, University of Liverpool, Liverpool, United Kingdom
| | - Zohra Butt
- Molecular Physiology and Cell Signalling, University of Liverpool, Liverpool, United Kingdom
| | - Rudi Grosman
- Biochemistry and Systems Biology, University of Liverpool, Liverpool, United Kingdom
| | - Francesca Querques
- Molecular Physiology and Cell Signalling, University of Liverpool, Liverpool, United Kingdom
| | - Liam Shaw
- Molecular Physiology and Cell Signalling, University of Liverpool, Liverpool, United Kingdom
| | - Luisa C. Silva
- Molecular Physiology and Cell Signalling, University of Liverpool, Liverpool, United Kingdom
| | - Zoe Goate
- Molecular Physiology and Cell Signalling, University of Liverpool, Liverpool, United Kingdom
| | - Stefan J. Marciniak
- Cambridge Institute for Medical Research, Cambridge, United Kingdom
- Papworth Hospital NHS Foundation Trust, Cambridge, United Kingdom
| | - Doris M. Rassl
- Papworth Hospital NHS Foundation Trust, Cambridge, United Kingdom
| | - Richard Jackson
- Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, United Kingdom
| | - Lu-Yun Lian
- Biochemistry and Systems Biology, University of Liverpool, Liverpool, United Kingdom
| | - Peter W. Szlosarek
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Joseph J. Sacco
- Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Clatterbridge Cancer Centre NHS Foundation Trust, Wirral, United Kingdom
| | - Judy M. Coulson
- Molecular Physiology and Cell Signalling, University of Liverpool, Liverpool, United Kingdom
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3
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Shrine N, Izquierdo AG, Chen J, Packer R, Hall RJ, Guyatt AL, Batini C, Thompson RJ, Pavuluri C, Malik V, Hobbs BD, Moll M, Kim W, Tal-Singer R, Bakke P, Fawcett KA, John C, Coley K, Piga NN, Pozarickij A, Lin K, Millwood IY, Chen Z, Li L, Wijnant SRA, Lahousse L, Brusselle G, Uitterlinden AG, Manichaikul A, Oelsner EC, Rich SS, Barr RG, Kerr SM, Vitart V, Brown MR, Wielscher M, Imboden M, Jeong A, Bartz TM, Gharib SA, Flexeder C, Karrasch S, Gieger C, Peters A, Stubbe B, Hu X, Ortega VE, Meyers DA, Bleecker ER, Gabriel SB, Gupta N, Smith AV, Luan J, Zhao JH, Hansen AF, Langhammer A, Willer C, Bhatta L, Porteous D, Smith BH, Campbell A, Sofer T, Lee J, Daviglus ML, Yu B, Lim E, Xu H, O'Connor GT, Thareja G, Albagha OME, Suhre K, Granell R, Faquih TO, Hiemstra PS, Slats AM, Mullin BH, Hui J, James A, Beilby J, Patasova K, Hysi P, Koskela JT, Wyss AB, Jin J, Sikdar S, Lee M, May-Wilson S, Pirastu N, Kentistou KA, Joshi PK, Timmers PRHJ, Williams AT, Free RC, Wang X, Morrison JL, Gilliland FD, Chen Z, Wang CA, Foong RE, Harris SE, Taylor A, Redmond P, Cook JP, Mahajan A, Lind L, Palviainen T, Lehtimäki T, Raitakari OT, Kaprio J, Rantanen T, Pietiläinen KH, Cox SR, Pennell CE, Hall GL, Gauderman WJ, Brightling C, Wilson JF, Vasankari T, Laitinen T, Salomaa V, Mook-Kanamori DO, Timpson NJ, Zeggini E, Dupuis J, Hayward C, Brumpton B, Langenberg C, Weiss S, Homuth G, Schmidt CO, Probst-Hensch N, Jarvelin MR, Morrison AC, Polasek O, Rudan I, Lee JH, Sayers I, Rawlins EL, Dudbridge F, Silverman EK, Strachan DP, Walters RG, Morris AP, London SJ, Cho MH, Wain LV, Hall IP, Tobin MD. Multi-ancestry genome-wide association analyses improve resolution of genes and pathways influencing lung function and chronic obstructive pulmonary disease risk. Nat Genet 2023; 55:410-422. [PMID: 36914875 PMCID: PMC10011137 DOI: 10.1038/s41588-023-01314-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [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: 05/12/2022] [Accepted: 01/25/2023] [Indexed: 03/16/2023]
Abstract
Lung-function impairment underlies chronic obstructive pulmonary disease (COPD) and predicts mortality. In the largest multi-ancestry genome-wide association meta-analysis of lung function to date, comprising 580,869 participants, we identified 1,020 independent association signals implicating 559 genes supported by ≥2 criteria from a systematic variant-to-gene mapping framework. These genes were enriched in 29 pathways. Individual variants showed heterogeneity across ancestries, age and smoking groups, and collectively as a genetic risk score showed strong association with COPD across ancestry groups. We undertook phenome-wide association studies for selected associated variants as well as trait and pathway-specific genetic risk scores to infer possible consequences of intervening in pathways underlying lung function. We highlight new putative causal variants, genes, proteins and pathways, including those targeted by existing drugs. These findings bring us closer to understanding the mechanisms underlying lung function and COPD, and should inform functional genomics experiments and potentially future COPD therapies.
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Affiliation(s)
- Nick Shrine
- Department of Population Health Sciences, University of Leicester, Leicester, UK.
| | - Abril G Izquierdo
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Jing Chen
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Richard Packer
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Robert J Hall
- Division of Respiratory Medicine and NIHR Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Anna L Guyatt
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Chiara Batini
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- Leicester National Institute for Health and Care Research, Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Rebecca J Thompson
- Division of Respiratory Medicine and NIHR Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Chandan Pavuluri
- Channing Division of Network Medicine, Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Vidhi Malik
- Channing Division of Network Medicine, Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Brian D Hobbs
- Channing Division of Network Medicine, Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Matthew Moll
- Channing Division of Network Medicine, Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Wonji Kim
- Channing Division of Network Medicine, Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Per Bakke
- Department of Clinical Science, Unversity of Bergen, Bergen, Norway
| | - Katherine A Fawcett
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Catherine John
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- Leicester National Institute for Health and Care Research, Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Kayesha Coley
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Noemi Nicole Piga
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Alfred Pozarickij
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Kuang Lin
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Iona Y Millwood
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, University of Oxford, Oxford, UK
| | - Zhengming Chen
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, University of Oxford, Oxford, UK
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Sara R A Wijnant
- Department of Respiratory Diseases, Ghent Universital Hospital, Ghent, Belgium
- Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
- Department of Epidemiology, Eramus Medical Center, Rotterdam, The Netherlands
| | - Lies Lahousse
- Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
- Department of Epidemiology, Eramus Medical Center, Rotterdam, The Netherlands
| | - Guy Brusselle
- Department of Respiratory Diseases, Ghent Universital Hospital, Ghent, Belgium
- Department of Epidemiology, Eramus Medical Center, Rotterdam, The Netherlands
| | - Andre G Uitterlinden
- Department of Internal Medicine, Eramus Medical Center, Rotterdam, The Netherlands
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Elizabeth C Oelsner
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - R Graham Barr
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Shona M Kerr
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Veronique Vitart
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Michael R Brown
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Matthias Wielscher
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Medea Imboden
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- Department of Public Health, University of Basel, Basel, Switzerland
| | - Ayoung Jeong
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- Department of Public Health, University of Basel, Basel, Switzerland
| | - Traci M Bartz
- Cardiovascular Health Research Unit, Departments of Medicine and Biostatistics, University of Washington, Seattle, WA, USA
| | - Sina A Gharib
- Computational Medicine Core, Center for Lung Biology, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Claudia Flexeder
- Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich, Munich, Germany
- Comprehensive Pneumology Center Munich (CPC-M), German Center for Lung Research (DZL), Munich, Germany
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Stefan Karrasch
- Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich, Munich, Germany
- Comprehensive Pneumology Center Munich (CPC-M), German Center for Lung Research (DZL), Munich, Germany
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Christian Gieger
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- Institute for Medical Information Processing, Biometry and Epidemiology, Medical Faculty, Ludwig Maximilian University, Munich, Germany
| | - Beate Stubbe
- Department of Internal Medicine B-Cardiology, Intensive Care, Pulmonary Medicine and Infectious Diseases, University Medicine Greifswald, Greifswald, Germany
| | - Xiaowei Hu
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Victor E Ortega
- Division of Respiratory Medicine, Department of Internal Medicine, Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | | | | | | | - Namrata Gupta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Albert Vernon Smith
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Jian'an Luan
- MRC Epidemiology Unit, Institute of Metabolic Science, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Jing-Hua Zhao
- Department of Public and Primary Care, Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Ailin F Hansen
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Arnulf Langhammer
- HUNT Research Centre, Department of Public Health and Nursing, NTNU Norwegian University of Science and Technology, Levanger, Norway
- Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
| | - Cristen Willer
- Division of Cardiology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Laxmi Bhatta
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - David Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Blair H Smith
- Division of Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Tamar Sofer
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jiwon Lee
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
| | - Martha L Daviglus
- Institute for Minority Health Research, University of Illinois at Chicago, Chicago, IL, USA
| | - Bing Yu
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Elise Lim
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Hanfei Xu
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - George T O'Connor
- Pulmonary Center, School of Medicine, Boston University, Boston, MA, USA
| | - Gaurav Thareja
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
| | - Omar M E Albagha
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Center for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Karsten Suhre
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
- Department of Biophysics and Physiology, Weill Cornell Medicine, New York, NY, USA
| | - Raquel Granell
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Tariq O Faquih
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Pieter S Hiemstra
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
| | - Annelies M Slats
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
| | - Benjamin H Mullin
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- School of Biomedical Sciences, University of Western Australia, Crawley, Western Australia, Australia
| | - Jennie Hui
- Busselton Population Medical Research Institute, QEII Medical Centre, Nedlands, Western Australia, Australia
- School of Population and Global Health, University of Western Australia, Crawley, Western Australia, Australia
- PathWest Laboratory Medicine of WA, Nedlands, Western Australia, Australia
| | - Alan James
- Busselton Population Medical Research Institute, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - John Beilby
- School of Biomedical Sciences, University of Western Australia, Crawley, Western Australia, Australia
- Busselton Population Medical Research Institute, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Karina Patasova
- Department of Twin Research and Genetic Epidemiology, King's College London School of Medicine, London, UK
- Division of Respiratory Medicine, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Pirro Hysi
- Department of Twin Research and Genetic Epidemiology, King's College London School of Medicine, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
| | - Jukka T Koskela
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Annah B Wyss
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | | | - Sinjini Sikdar
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
- Department of Mathematics and Statistics, Old Dominion University, Norfolk, VA, USA
| | - Mikyeong Lee
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Sebastian May-Wilson
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Nicola Pirastu
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Katherine A Kentistou
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
- Centre for Cardiovascular Sciences, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Paul R H J Timmers
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Alexander T Williams
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Robert C Free
- Leicester National Institute for Health and Care Research, Biomedical Research Centre, Glenfield Hospital, Leicester, UK
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Xueyang Wang
- Leicester National Institute for Health and Care Research, Biomedical Research Centre, Glenfield Hospital, Leicester, UK
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - John L Morrison
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Frank D Gilliland
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Zhanghua Chen
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Carol A Wang
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Rachel E Foong
- Wal-yan Respiratory Research Centre, Telethon Kids Institute, Perth, Western Australia, Australia
- School of Allied Health, Faculty of Health Sciences, Curtin University, Perth, Western Australia, Australia
| | - Sarah E Harris
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Adele Taylor
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Paul Redmond
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - James P Cook
- Department of Health Data Science, University of Liverpool, Liverpool, UK
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Genentech, South San Francisco, CA, USA
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Teemu Palviainen
- Institute for Molecular Medicine Finland-FIMM, University of Helsinki, Helsinki, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Olli T Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland-FIMM, University of Helsinki, Helsinki, Finland
| | - Taina Rantanen
- Faculty of Sport and Health Sciences, University of Jyvaskyla, Jyvaskyla, Finland
| | - Kirsi H Pietiläinen
- Obesity Research Unit, Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Obesity and Abdominal Centers, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Simon R Cox
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Craig E Pennell
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, Newcastle, New South Wales, Australia
- Department of Maternity and Gynaecology, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Graham L Hall
- Wal-yan Respiratory Research Centre, Telethon Kids Institute, Perth, Western Australia, Australia
- School of Allied Health, Faculty of Health Sciences, Curtin University, Perth, Western Australia, Australia
| | - W James Gauderman
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Chris Brightling
- Leicester National Institute for Health and Care Research, Biomedical Research Centre, Glenfield Hospital, Leicester, UK
- Department of Infection, Inflammation and Immunity, Institute for Lung Health, University of Leicester, Leicester, UK
| | - James F Wilson
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Tuula Vasankari
- FILHA-Finnish Lung Health Association, Helsinki, Finland
- Department of Respiratory Diseases and Allergology, University of Turku, Turku, Finland
| | - Tarja Laitinen
- Administration Center, Tampere University Hospital and University of Tampere, Tampere, Finland
| | - Veikko Salomaa
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, The Netherlands
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- ALSPAC, Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Eleftheria Zeggini
- Wellcome Sanger Institute, Cambridge, UK
- Institute of Translational Genomics, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- Technical University of Munich (TUM) and Klinikum Rechts der Isar, TUM School of Medicine, Munich, Germany
| | - Josée Dupuis
- Department of Epidemiology, Biostatistics, and Occupational Health, School of Population and Global Health, McGill University, Montreal, Quebec, Canada
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Ben Brumpton
- HUNT Research Centre, Department of Public Health and Nursing, NTNU Norwegian University of Science and Technology, Levanger, Norway
- Clinic of Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK
- Computational Medicine, Berlin Institute of Health at Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Stefan Weiss
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Carsten Oliver Schmidt
- Institute for Community Medicine, SHIP-Clinical Epidemiological Research, University Medicine Greifswald, Greifswald, Germany
| | - Nicole Probst-Hensch
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- Department of Public Health, University of Basel, Basel, Switzerland
| | - Marjo-Riitta Jarvelin
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Unit of Primary Health Care, Oulu University Hospital, OYS, Oulu, Finland
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ozren Polasek
- School of Medicine, University of Split, Split, Croatia
| | - Igor Rudan
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Joo-Hyeon Lee
- Jeffrey Cheah Biomedical Centre, Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Ian Sayers
- Division of Respiratory Medicine and NIHR Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Emma L Rawlins
- Wellcome Trust-CRUK Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Frank Dudbridge
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Edwin K Silverman
- Channing Division of Network Medicine, Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - David P Strachan
- Population Health Research Institute, St George's University of London, London, UK
| | - Robin G Walters
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, University of Oxford, Oxford, UK
| | - Andrew P Morris
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Louise V Wain
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- Leicester National Institute for Health and Care Research, Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Ian P Hall
- Division of Respiratory Medicine and NIHR Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Martin D Tobin
- Department of Population Health Sciences, University of Leicester, Leicester, UK.
- Leicester National Institute for Health and Care Research, Biomedical Research Centre, Glenfield Hospital, Leicester, UK.
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4
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Hanley CJ, Waise S, Ellis MJ, Lopez MA, Pun WY, Taylor J, Parker R, Kimbley LM, Chee SJ, Shaw EC, West J, Alzetani A, Woo E, Ottensmeier CH, Rose-Zerilli MJJ, Thomas GJ. Single-cell analysis reveals prognostic fibroblast subpopulations linked to molecular and immunological subtypes of lung cancer. Nat Commun 2023; 14:387. [PMID: 36720863 PMCID: PMC9889778 DOI: 10.1038/s41467-023-35832-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 01/04/2023] [Indexed: 02/01/2023] Open
Abstract
Fibroblasts are poorly characterised cells that variably impact tumour progression. Here, we use single cell RNA-sequencing, multiplexed immunohistochemistry and digital cytometry (CIBERSORTx) to identify and characterise three major fibroblast subpopulations in human non-small cell lung cancer: adventitial, alveolar and myofibroblasts. Alveolar and adventitial fibroblasts (enriched in control tissue samples) localise to discrete spatial niches in histologically normal lung tissue and indicate improved overall survival rates when present in lung adenocarcinomas (LUAD). Trajectory inference identifies three phases of control tissue fibroblast activation, leading to myofibroblast enrichment in tumour samples: initial upregulation of inflammatory cytokines, followed by stress-response signalling and ultimately increased expression of fibrillar collagens. Myofibroblasts correlate with poor overall survival rates in LUAD, associated with loss of epithelial differentiation, TP53 mutations, proximal molecular subtypes and myeloid cell recruitment. In squamous carcinomas myofibroblasts were not prognostic despite being transcriptomically equivalent. These findings have important implications for developing fibroblast-targeting strategies for cancer therapy.
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Affiliation(s)
- Christopher J Hanley
- School of Cancer Sciences, University of Southampton, Southampton, SO16 6YD, UK.
- Cancer Research UK and NIHR Southampton Experimental Cancer Medicine Centre, Southampton, SO16 6YD, UK.
| | - Sara Waise
- School of Cancer Sciences, University of Southampton, Southampton, SO16 6YD, UK
| | - Matthew J Ellis
- School of Cancer Sciences, University of Southampton, Southampton, SO16 6YD, UK
| | - Maria A Lopez
- Department of Histopathology, University Hospital Southampton NHS Foundation Trust, Southampton, SO16 6YD, UK
| | - Wai Y Pun
- Department of Histopathology, University Hospital Southampton NHS Foundation Trust, Southampton, SO16 6YD, UK
| | - Julian Taylor
- Department of Histopathology, University Hospital Southampton NHS Foundation Trust, Southampton, SO16 6YD, UK
| | - Rachel Parker
- School of Cancer Sciences, University of Southampton, Southampton, SO16 6YD, UK
| | - Lucy M Kimbley
- School of Cancer Sciences, University of Southampton, Southampton, SO16 6YD, UK
| | - Serena J Chee
- School of Cancer Sciences, University of Southampton, Southampton, SO16 6YD, UK
- Institute of Systems, Molecular and Integrative Biology (ISMIB) and Liverpool Experimental Cancer Medicines Centre, University of Liverpool, Liverpool, L69 7BE, UK
| | - Emily C Shaw
- Department of Histopathology, University Hospital Southampton NHS Foundation Trust, Southampton, SO16 6YD, UK
| | - Jonathan West
- School of Cancer Sciences, University of Southampton, Southampton, SO16 6YD, UK
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Aiman Alzetani
- Department of Thoracic surgery, University Hospital Southampton NHS Foundation Trust, Southampton, SO16 6YD, UK
| | - Edwin Woo
- Department of Thoracic surgery, University Hospital Southampton NHS Foundation Trust, Southampton, SO16 6YD, UK
| | - Christian H Ottensmeier
- School of Cancer Sciences, University of Southampton, Southampton, SO16 6YD, UK
- Cancer Research UK and NIHR Southampton Experimental Cancer Medicine Centre, Southampton, SO16 6YD, UK
- Institute of Systems, Molecular and Integrative Biology (ISMIB) and Liverpool Experimental Cancer Medicines Centre, University of Liverpool, Liverpool, L69 7BE, UK
| | - Matthew J J Rose-Zerilli
- School of Cancer Sciences, University of Southampton, Southampton, SO16 6YD, UK
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Gareth J Thomas
- School of Cancer Sciences, University of Southampton, Southampton, SO16 6YD, UK.
- Cancer Research UK and NIHR Southampton Experimental Cancer Medicine Centre, Southampton, SO16 6YD, UK.
- Department of Histopathology, University Hospital Southampton NHS Foundation Trust, Southampton, SO16 6YD, UK.
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5
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Subramanian A, Nirantharakumar K, Hughes S, Myles P, Williams T, Gokhale KM, Taverner T, Chandan JS, Brown K, Simms-Williams N, Shah AD, Singh M, Kidy F, Okoth K, Hotham R, Bashir N, Cockburn N, Lee SI, Turner GM, Gkoutos GV, Aiyegbusi OL, McMullan C, Denniston AK, Sapey E, Lord JM, Wraith DC, Leggett E, Iles C, Marshall T, Price MJ, Marwaha S, Davies EH, Jackson LJ, Matthews KL, Camaradou J, Calvert M, Haroon S. Symptoms and risk factors for long COVID in non-hospitalized adults. Nat Med 2022; 28:1706-1714. [PMID: 35879616 PMCID: PMC9388369 DOI: 10.1038/s41591-022-01909-w] [Citation(s) in RCA: 327] [Impact Index Per Article: 163.5] [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: 02/09/2022] [Accepted: 06/21/2022] [Indexed: 01/11/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection is associated with a range of persistent symptoms impacting everyday functioning, known as post-COVID-19 condition or long COVID. We undertook a retrospective matched cohort study using a UK-based primary care database, Clinical Practice Research Datalink Aurum, to determine symptoms that are associated with confirmed SARS-CoV-2 infection beyond 12 weeks in non-hospitalized adults and the risk factors associated with developing persistent symptoms. We selected 486,149 adults with confirmed SARS-CoV-2 infection and 1,944,580 propensity score-matched adults with no recorded evidence of SARS-CoV-2 infection. Outcomes included 115 individual symptoms, as well as long COVID, defined as a composite outcome of 33 symptoms by the World Health Organization clinical case definition. Cox proportional hazards models were used to estimate adjusted hazard ratios (aHRs) for the outcomes. A total of 62 symptoms were significantly associated with SARS-CoV-2 infection after 12 weeks. The largest aHRs were for anosmia (aHR 6.49, 95% CI 5.02-8.39), hair loss (3.99, 3.63-4.39), sneezing (2.77, 1.40-5.50), ejaculation difficulty (2.63, 1.61-4.28) and reduced libido (2.36, 1.61-3.47). Among the cohort of patients infected with SARS-CoV-2, risk factors for long COVID included female sex, belonging to an ethnic minority, socioeconomic deprivation, smoking, obesity and a wide range of comorbidities. The risk of developing long COVID was also found to be increased along a gradient of decreasing age. SARS-CoV-2 infection is associated with a plethora of symptoms that are associated with a range of sociodemographic and clinical risk factors.
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Affiliation(s)
| | - Krishnarajah Nirantharakumar
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK.
- Midlands Health Data Research UK, Birmingham, UK.
- DEMAND Hub, University of Birmingham, Birmingham, UK.
| | - Sarah Hughes
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- Centre for Patient-Reported Outcomes Research, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- National Institute for Health and Care Research (NIHR) Applied Research Collaboration (ARC) - West Midlands, Birmingham, UK
- Birmingham Health Partners Centre for Regulatory Science and Innovation, University of Birmingham, Birmingham, UK
- NIHR Birmingham-Oxford Blood and Transplant Research Unit (BTRU) in Precision Transplant and Cellular Therapeutics, University of Birmingham, Birmingham, UK
| | - Puja Myles
- Clinical Practice Research Datalink, Medicines and Healthcare products Regulatory Agency, London, UK
| | - Tim Williams
- Clinical Practice Research Datalink, Medicines and Healthcare products Regulatory Agency, London, UK
| | - Krishna M Gokhale
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Tom Taverner
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Joht Singh Chandan
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Kirsty Brown
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- School of Sport, Exercise and Rehabilitation Sciences, University of Birmingham, Birmingham, UK
| | | | - Anoop D Shah
- Institute of Health Informatics, Faculty of Population Health Sciences, University College London, London, UK
| | - Megha Singh
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Farah Kidy
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Kelvin Okoth
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Richard Hotham
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Nasir Bashir
- School of Oral and Dental Sciences, University of Bristol, Bristol, UK
| | - Neil Cockburn
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Siang Ing Lee
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Grace M Turner
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- Centre for Patient-Reported Outcomes Research, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- NIHR Surgical Reconstruction and Microbiology Research Centre, University Hospital Birmingham and University of Birmingham, Birmingham, UK
| | - Georgios V Gkoutos
- Midlands Health Data Research UK, Birmingham, UK
- DEMAND Hub, University of Birmingham, Birmingham, UK
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospital Birmingham and University of Birmingham, Birmingham, UK
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Olalekan Lee Aiyegbusi
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- Centre for Patient-Reported Outcomes Research, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- National Institute for Health and Care Research (NIHR) Applied Research Collaboration (ARC) - West Midlands, Birmingham, UK
- Birmingham Health Partners Centre for Regulatory Science and Innovation, University of Birmingham, Birmingham, UK
- NIHR Birmingham-Oxford Blood and Transplant Research Unit (BTRU) in Precision Transplant and Cellular Therapeutics, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospital Birmingham and University of Birmingham, Birmingham, UK
| | - Christel McMullan
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- Centre for Patient-Reported Outcomes Research, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- NIHR Birmingham-Oxford Blood and Transplant Research Unit (BTRU) in Precision Transplant and Cellular Therapeutics, University of Birmingham, Birmingham, UK
- NIHR Surgical Reconstruction and Microbiology Research Centre, University Hospital Birmingham and University of Birmingham, Birmingham, UK
- Centre for Trauma Science Research, University of Birmingham, Birmingham, UK
| | - Alastair K Denniston
- Midlands Health Data Research UK, Birmingham, UK
- DEMAND Hub, University of Birmingham, Birmingham, UK
- Centre for Patient-Reported Outcomes Research, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- Birmingham Health Partners Centre for Regulatory Science and Innovation, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospital Birmingham and University of Birmingham, Birmingham, UK
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Elizabeth Sapey
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
- MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
- PIONEER HDR-UK Data Hub in acute care, University of Birmingham, Birmingham, UK
| | - Janet M Lord
- NIHR Surgical Reconstruction and Microbiology Research Centre, University Hospital Birmingham and University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospital Birmingham and University of Birmingham, Birmingham, UK
- MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
- UK SPINE, University of Birmingham, Birmingham, UK
| | - David C Wraith
- NIHR Birmingham Biomedical Research Centre, University Hospital Birmingham and University of Birmingham, Birmingham, UK
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Edward Leggett
- Clinical Practice Research Datalink, Medicines and Healthcare products Regulatory Agency, London, UK
| | - Clare Iles
- Clinical Practice Research Datalink, Medicines and Healthcare products Regulatory Agency, London, UK
| | - Tom Marshall
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Malcolm J Price
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospital Birmingham and University of Birmingham, Birmingham, UK
| | - Steven Marwaha
- Institute for Mental Health, University of Birmingham, Birmingham, UK
- Birmingham and Solihull Mental Health NHS Foundation Trust, Birmingham, UK
| | | | - Louise J Jackson
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | | | | | - Melanie Calvert
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- Midlands Health Data Research UK, Birmingham, UK
- DEMAND Hub, University of Birmingham, Birmingham, UK
- Centre for Patient-Reported Outcomes Research, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- National Institute for Health and Care Research (NIHR) Applied Research Collaboration (ARC) - West Midlands, Birmingham, UK
- Birmingham Health Partners Centre for Regulatory Science and Innovation, University of Birmingham, Birmingham, UK
- NIHR Birmingham-Oxford Blood and Transplant Research Unit (BTRU) in Precision Transplant and Cellular Therapeutics, University of Birmingham, Birmingham, UK
- NIHR Surgical Reconstruction and Microbiology Research Centre, University Hospital Birmingham and University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospital Birmingham and University of Birmingham, Birmingham, UK
- PIONEER HDR-UK Data Hub in acute care, University of Birmingham, Birmingham, UK
| | - Shamil Haroon
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
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6
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Obacz J, Yung H, Shamseddin M, Linnane E, Liu X, Azad AA, Rassl DM, Fairen-Jimenez D, Rintoul RC, Nikolić MZ, Marciniak SJ. Biological basis for novel mesothelioma therapies. Br J Cancer 2021; 125:1039-1055. [PMID: 34226685 PMCID: PMC8505556 DOI: 10.1038/s41416-021-01462-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 05/13/2021] [Accepted: 06/02/2021] [Indexed: 02/06/2023] Open
Abstract
Mesothelioma is an aggressive cancer that is associated with exposure to asbestos. Although asbestos is banned in several countries, including the UK, an epidemic of mesothelioma is predicted to affect middle-income countries during this century owing to their heavy consumption of asbestos. The prognosis for patients with mesothelioma is poor, reflecting a failure of conventional chemotherapy that has ultimately resulted from an inadequate understanding of its biology. However, recent work has revolutionised the study of mesothelioma, identifying genetic and pathophysiological vulnerabilities, including the loss of tumour suppressors, epigenetic dysregulation and susceptibility to nutrient stress. We discuss how this knowledge, combined with advances in immunotherapy, is enabling the development of novel targeted therapies.
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Affiliation(s)
- Joanna Obacz
- Cambridge Institute for Medical Research, Keith Peters Building, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Henry Yung
- UCL Respiratory, Division of Medicine Rayne Institute, University College London, London, UK
| | - Marie Shamseddin
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Saffron Walden, UK
| | - Emily Linnane
- Adsorption & Advanced Materials Laboratory, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Xiewen Liu
- Adsorption & Advanced Materials Laboratory, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Arsalan A Azad
- Cambridge Institute for Medical Research, Keith Peters Building, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Doris M Rassl
- Department of Histopathology, Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK
| | - David Fairen-Jimenez
- Adsorption & Advanced Materials Laboratory, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Robert C Rintoul
- Department of Oncology, University of Cambridge, Cambridge, UK
- Department of Thoracic Oncology, Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK
| | - Marko Z Nikolić
- UCL Respiratory, Division of Medicine Rayne Institute, University College London, London, UK
| | - Stefan J Marciniak
- Cambridge Institute for Medical Research, Keith Peters Building, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK.
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.
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7
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Grosso S, Marini A, Gyuraszova K, Voorde JV, Sfakianos A, Garland GD, Tenor AR, Mordue R, Chernova T, Morone N, Sereno M, Smith CP, Officer L, Farahmand P, Rooney C, Sumpton D, Das M, Teodósio A, Ficken C, Martin MG, Spriggs RV, Sun XM, Bushell M, Sansom OJ, Murphy D, MacFarlane M, Le Quesne JPC, Willis AE. The pathogenesis of mesothelioma is driven by a dysregulated translatome. Nat Commun 2021; 12:4920. [PMID: 34389715 PMCID: PMC8363647 DOI: 10.1038/s41467-021-25173-7] [Citation(s) in RCA: 18] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 07/25/2021] [Indexed: 12/22/2022] Open
Abstract
Malignant mesothelioma (MpM) is an aggressive, invariably fatal tumour that is causally linked with asbestos exposure. The disease primarily results from loss of tumour suppressor gene function and there are no 'druggable' driver oncogenes associated with MpM. To identify opportunities for management of this disease we have carried out polysome profiling to define the MpM translatome. We show that in MpM there is a selective increase in the translation of mRNAs encoding proteins required for ribosome assembly and mitochondrial biogenesis. This results in an enhanced rate of mRNA translation, abnormal mitochondrial morphology and oxygen consumption, and a reprogramming of metabolic outputs. These alterations delimit the cellular capacity for protein biosynthesis, accelerate growth and drive disease progression. Importantly, we show that inhibition of mRNA translation, particularly through combined pharmacological targeting of mTORC1 and 2, reverses these changes and inhibits malignant cell growth in vitro and in ex-vivo tumour tissue from patients with end-stage disease. Critically, we show that these pharmacological interventions prolong survival in animal models of asbestos-induced mesothelioma, providing the basis for a targeted, viable therapeutic option for patients with this incurable disease.
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Affiliation(s)
- Stefano Grosso
- MRC Toxicology Unit, Gleeson Building, University of Cambridge, Cambridge, UK
| | - Alberto Marini
- MRC Toxicology Unit, Gleeson Building, University of Cambridge, Cambridge, UK
| | - Katarina Gyuraszova
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- Cancer Research UK Beatson Institute, Garscube Estate, Bearsden, UK
| | | | | | - Gavin D Garland
- MRC Toxicology Unit, Gleeson Building, University of Cambridge, Cambridge, UK
| | - Angela Rubio Tenor
- MRC Toxicology Unit, Gleeson Building, University of Cambridge, Cambridge, UK
| | - Ryan Mordue
- MRC Toxicology Unit, Gleeson Building, University of Cambridge, Cambridge, UK
| | - Tanya Chernova
- MRC Toxicology Unit, Gleeson Building, University of Cambridge, Cambridge, UK
| | - Nobu Morone
- MRC Toxicology Unit, Gleeson Building, University of Cambridge, Cambridge, UK
| | - Marco Sereno
- MRC Toxicology Unit, Gleeson Building, University of Cambridge, Cambridge, UK
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Claire P Smith
- MRC Toxicology Unit, Gleeson Building, University of Cambridge, Cambridge, UK
| | - Leah Officer
- MRC Toxicology Unit, Gleeson Building, University of Cambridge, Cambridge, UK
| | - Pooyeh Farahmand
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- Cancer Research UK Beatson Institute, Garscube Estate, Bearsden, UK
| | - Claire Rooney
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- Cancer Research UK Beatson Institute, Garscube Estate, Bearsden, UK
| | - David Sumpton
- Cancer Research UK Beatson Institute, Garscube Estate, Bearsden, UK
| | - Madhumita Das
- MRC Toxicology Unit, Gleeson Building, University of Cambridge, Cambridge, UK
| | - Ana Teodósio
- MRC Toxicology Unit, Gleeson Building, University of Cambridge, Cambridge, UK
| | - Catherine Ficken
- MRC Toxicology Unit, Gleeson Building, University of Cambridge, Cambridge, UK
| | - Maria Guerra Martin
- MRC Toxicology Unit, Gleeson Building, University of Cambridge, Cambridge, UK
| | - Ruth V Spriggs
- MRC Toxicology Unit, Gleeson Building, University of Cambridge, Cambridge, UK
| | - Xiao-Ming Sun
- MRC Toxicology Unit, Gleeson Building, University of Cambridge, Cambridge, UK
| | - Martin Bushell
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- Cancer Research UK Beatson Institute, Garscube Estate, Bearsden, UK
| | - Owen J Sansom
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- Cancer Research UK Beatson Institute, Garscube Estate, Bearsden, UK
| | - Daniel Murphy
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.
| | - Marion MacFarlane
- MRC Toxicology Unit, Gleeson Building, University of Cambridge, Cambridge, UK.
| | - John P C Le Quesne
- MRC Toxicology Unit, Gleeson Building, University of Cambridge, Cambridge, UK.
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.
- Cancer Research UK Beatson Institute, Garscube Estate, Bearsden, UK.
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK.
- Glenfield Hospital, Groby Road, University Hospitals Leicester NHS Trust Leicester, Leicester, UK.
| | - Anne E Willis
- MRC Toxicology Unit, Gleeson Building, University of Cambridge, Cambridge, UK.
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8
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Zhang M, Luo JL, Sun Q, Harber J, Dawson AG, Nakas A, Busacca S, Sharkey AJ, Waller D, Sheaff MT, Richards C, Wells-Jordan P, Gaba A, Poile C, Baitei EY, Bzura A, Dzialo J, Jama M, Le Quesne J, Bajaj A, Martinson L, Shaw JA, Pritchard C, Kamata T, Kuse N, Brannan L, De Philip Zhang P, Yang H, Griffiths G, Wilson G, Swanton C, Dudbridge F, Hollox EJ, Fennell DA. Clonal architecture in mesothelioma is prognostic and shapes the tumour microenvironment. Nat Commun 2021; 12:1751. [PMID: 33741915 PMCID: PMC7979861 DOI: 10.1038/s41467-021-21798-w] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 02/04/2021] [Indexed: 01/31/2023] Open
Abstract
Malignant Pleural Mesothelioma (MPM) is typically diagnosed 20-50 years after exposure to asbestos and evolves along an unknown evolutionary trajectory. To elucidate this path, we conducted multi-regional exome sequencing of 90 tumour samples from 22 MPMs acquired at surgery. Here we show that exomic intratumour heterogeneity varies widely across the cohort. Phylogenetic tree topology ranges from linear to highly branched, reflecting a steep gradient of genomic instability. Using transfer learning, we detect repeated evolution, resolving 5 clusters that are prognostic, with temporally ordered clonal drivers. BAP1/-3p21 and FBXW7/-chr4 events are always early clonal. In contrast, NF2/-22q events, leading to Hippo pathway inactivation are predominantly late clonal, positively selected, and when subclonal, exhibit parallel evolution indicating an evolutionary constraint. Very late somatic alteration of NF2/22q occurred in one patient 12 years after surgery. Clonal architecture and evolutionary clusters dictate MPM inflammation and immune evasion. These results reveal potentially drugable evolutionary bottlenecking in MPM, and an impact of clonal architecture on shaping the immune landscape, with potential to dictate the clinical response to immune checkpoint inhibition.
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Affiliation(s)
- Min Zhang
- Novogene Co., Ltd, Building 301, Beijing, China
| | - Jin-Li Luo
- Bioinformatics and Biostatistics Support Hub, University of Leicester, Leicester, UK
| | | | - James Harber
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Alan G Dawson
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Department of Cardiothoracic Surgery, Glenfield Hospital, Leicester, UK
| | - Apostolos Nakas
- Department of Cardiothoracic Surgery, Glenfield Hospital, Leicester, UK
| | - Sara Busacca
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | | | - David Waller
- Barts Health NHS Trust, The Royal London Hospital, London, UK
| | | | - Cathy Richards
- Department of Pathology, Leicester Royal Infirmary, Infirmary Square, Leicester, Leicestershire, UK
| | - Peter Wells-Jordan
- Department of Pathology, Leicester Royal Infirmary, Infirmary Square, Leicester, Leicestershire, UK
| | - Aarti Gaba
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Charlotte Poile
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Essa Y Baitei
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Aleksandra Bzura
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Joanna Dzialo
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Maymun Jama
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - John Le Quesne
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Bearsden, UK
| | - Amrita Bajaj
- Department of Radiology, Glenfield Hospital, Leicester, UK
| | - Luke Martinson
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Jacqui A Shaw
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Catrin Pritchard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Tamihiro Kamata
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Nathaniel Kuse
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Lee Brannan
- Department of Health Sciences, University of Leicester, Leicester, UK
| | | | - Hongji Yang
- Department of Informatics, University of Leicester, Leicester, UK
| | - Gareth Griffiths
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | | | | | - Frank Dudbridge
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Edward J Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Dean A Fennell
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.
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9
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Yao L, Conforti F, Hill C, Bell J, Drawater L, Li J, Liu D, Xiong H, Alzetani A, Chee SJ, Marshall BG, Fletcher SV, Hancock D, Coldwell M, Yuan X, Ottensmeier CH, Downward J, Collins JE, Ewing RM, Richeldi L, Skipp P, Jones MG, Davies DE, Wang Y. Paracrine signalling during ZEB1-mediated epithelial-mesenchymal transition augments local myofibroblast differentiation in lung fibrosis. Cell Death Differ 2019; 26:943-957. [PMID: 30050057 PMCID: PMC6252080 DOI: 10.1038/s41418-018-0175-7] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [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: 05/08/2018] [Revised: 07/03/2018] [Accepted: 07/09/2018] [Indexed: 01/06/2023] Open
Abstract
The contribution of epithelial-mesenchymal transition (EMT) to human lung fibrogenesis is controversial. Here we provide evidence that ZEB1-mediated EMT in human alveolar epithelial type II (ATII) cells contributes to the development of lung fibrosis by paracrine signalling to underlying fibroblasts. Activation of EGFR-RAS-ERK signalling in ATII cells induced EMT via ZEB1. ATII cells had extremely low extracellular matrix gene expression even after induction of EMT, however conditioned media from ATII cells undergoing RAS-induced EMT augmented TGFβ-induced profibrogenic responses in lung fibroblasts. This epithelial-mesenchymal crosstalk was controlled by ZEB1 via the expression of tissue plasminogen activator (tPA). In human fibrotic lung tissue, nuclear ZEB1 expression was detected in alveolar epithelium adjacent to sites of extracellular matrix (ECM) deposition, suggesting that ZEB1-mediated paracrine signalling has the potential to contribute to early fibrotic changes in the lung interstitium. Targeting this novel ZEB1 regulatory axis may be a viable strategy for the treatment of pulmonary fibrosis.
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Affiliation(s)
- Liudi Yao
- Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Franco Conforti
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, SO16 6YD, UK
| | - Charlotte Hill
- Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Joseph Bell
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| | - Leena Drawater
- Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Juanjuan Li
- Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Dian Liu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Hua Xiong
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Aiman Alzetani
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
- Department of Thoracic Surgery, University Hospital Southampton, Southampton, SO16 6YD, UK
| | - Serena J Chee
- University Hospital Southampton, Southampton, SO16 6YD, UK
- Cancer Sciences & NIHR and CRUK Experimental Cancer Sciences Unit, University of Southampton, Southampton, SO16 6YD, UK
| | - Ben G Marshall
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, SO16 6YD, UK
- University Hospital Southampton, Southampton, SO16 6YD, UK
| | - Sophie V Fletcher
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, SO16 6YD, UK
- University Hospital Southampton, Southampton, SO16 6YD, UK
| | - David Hancock
- Oncogene Biology, The Francis Crick Institute, London, NW1 1AT, UK
| | - Mark Coldwell
- Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Xianglin Yuan
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Christian H Ottensmeier
- Cancer Sciences & NIHR and CRUK Experimental Cancer Sciences Unit, University of Southampton, Southampton, SO16 6YD, UK
| | - Julian Downward
- Oncogene Biology, The Francis Crick Institute, London, NW1 1AT, UK
| | - Jane E Collins
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| | - Rob M Ewing
- Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Luca Richeldi
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, SO16 6YD, UK
- Unità Operativa Complessa di Pneumologia, Università Cattolica del Sacro Cuore, Fondazione Policlinico A. Gemelli, Rome, Italy
| | - Paul Skipp
- Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- Centre for Proteomic Research, Institute for Life Sciences University of Southampton, Southampton, SO17 1BJ, UK
| | - Mark G Jones
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, SO16 6YD, UK
| | - Donna E Davies
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK.
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, SO16 6YD, UK.
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
| | - Yihua Wang
- Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
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