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Vilà-González M, Pinte L, Fradique R, Causa E, Kool H, Rodrat M, Morell CM, Al-Thani M, Porter L, Guo W, Maeshima R, Hart SL, McCaughan F, Granata A, Sheppard DN, Floto RA, Rawlins EL, Cicuta P, Vallier L. In vitro platform to model the function of ionocytes in the human airway epithelium. Respir Res 2024; 25:180. [PMID: 38664797 PMCID: PMC11045446 DOI: 10.1186/s12931-024-02800-7] [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: 09/03/2023] [Accepted: 04/01/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Pulmonary ionocytes have been identified in the airway epithelium as a small population of ion transporting cells expressing high levels of CFTR (cystic fibrosis transmembrane conductance regulator), the gene mutated in cystic fibrosis. By providing an infinite source of airway epithelial cells (AECs), the use of human induced pluripotent stem cells (hiPSCs) could overcome some challenges of studying ionocytes. However, the production of AEC epithelia containing ionocytes from hiPSCs has proven difficult. Here, we present a platform to produce hiPSC-derived AECs (hiPSC-AECs) including ionocytes and investigate their role in the airway epithelium. METHODS hiPSCs were differentiated into lung progenitors, which were expanded as 3D organoids and matured by air-liquid interface culture as polarised hiPSC-AEC epithelia. Using CRISPR/Cas9 technology, we generated a hiPSCs knockout (KO) for FOXI1, a transcription factor that is essential for ionocyte specification. Differences between FOXI1 KO hiPSC-AECs and their wild-type (WT) isogenic controls were investigated by assessing gene and protein expression, epithelial composition, cilia coverage and motility, pH and transepithelial barrier properties. RESULTS Mature hiPSC-AEC epithelia contained basal cells, secretory cells, ciliated cells with motile cilia, pulmonary neuroendocrine cells (PNECs) and ionocytes. There was no difference between FOXI1 WT and KO hiPSCs in terms of their capacity to differentiate into airway progenitors. However, FOXI1 KO led to mature hiPSC-AEC epithelia without ionocytes with reduced capacity to produce ciliated cells. CONCLUSION Our results suggest that ionocytes could have role beyond transepithelial ion transport by regulating epithelial properties and homeostasis in the airway epithelium.
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Affiliation(s)
- Marta Vilà-González
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK.
- Cell Therapy and Tissue Engineering Group, Research Institute of Health Sciences (IUNICS), University of Balearic Islands, Palma, 07122, Spain.
- Health Research Institute of the Balearic Islands (IdISBa), Palma, 07120, Spain.
| | - Laetitia Pinte
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Ricardo Fradique
- Department of Physics, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Erika Causa
- Department of Physics, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Heleen Kool
- Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Mayuree Rodrat
- School of Physiology, Pharmacology and Neuroscience, Biomedical Sciences Building, University of Bristol, University Walk, Bristol, BS8 1TD, UK
- Center of Research and Development for Biomedical Instrumentation, Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Carola Maria Morell
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
- IRCCS Humanitas Research Hospital, via Manzoni 56, Rozzano, Milan, 20089, Italy
| | - Maha Al-Thani
- Department of Clinical Neurosciences, Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Papworth Road, Cambridge, CB2 0BB, UK
| | - Linsey Porter
- Department of Medicine, Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Papworth Road, Cambridge, CB2 0BB, UK
| | - Wenrui Guo
- Department of Medicine, Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Papworth Road, Cambridge, CB2 0BB, UK
| | - Ruhina Maeshima
- Genetics and Genome Medicine Department, UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
| | - Stephen L Hart
- Genetics and Genome Medicine Department, UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
| | - Frank McCaughan
- Department of Medicine, Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Papworth Road, Cambridge, CB2 0BB, UK
| | - Alessandra Granata
- Department of Clinical Neurosciences, Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Papworth Road, Cambridge, CB2 0BB, UK
| | - David N Sheppard
- School of Physiology, Pharmacology and Neuroscience, Biomedical Sciences Building, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - R Andres Floto
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, CB2 0QH, UK
- Cambridge Centre for Lung Infection, Royal Papworth Hospital NHS Foundation Trust, Cambridge, CB2 0AY, UK
| | - Emma L Rawlins
- Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Pietro Cicuta
- Department of Physics, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Ludovic Vallier
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK.
- BIH Center for Regenerative Therapies, Berlin Institute of Health at Charité, Augustenburger Platz 1, 13353, Berlin, DE, Germany.
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany.
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Barron SL, Oldroyd SV, Saez J, Chernaik A, Guo W, McCaughan F, Bulmer D, Owens RM. A Conformable Organic Electronic Device for Monitoring Epithelial Integrity at the Air Liquid Interface. Adv Mater 2024; 36:e2306679. [PMID: 38061027 DOI: 10.1002/adma.202306679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 11/27/2023] [Indexed: 02/23/2024]
Abstract
Air liquid interfaced (ALI) epithelial barriers are essential for homeostatic functions such as nutrient transport and immunological protection. Dysfunction of such barriers are implicated in a variety of autoimmune and inflammatory disorders and, as such, sensors capable of monitoring barrier health are integral for disease modelling, diagnostics and drug screening applications. To date, gold-standard electrical methods for detecting barrier resistance require rigid electrodes bathed in an electrolyte, which limits compatibility with biological architectures and is non-physiological for ALI. This work presents a flexible all-planar electronic device capable of monitoring barrier formation and perturbations in human respiratory and intestinal cells at ALI. By interrogating patient samples with electrochemical impedance spectroscopy and simple equivalent circuit models, disease-specific and patient-specific signatures are uncovered. Device readouts are validated against commercially available chopstick electrodes and show greater conformability, sensitivity and biocompatibility. The effect of electrode size on sensing efficiency is investigated and a cut-off sensing area is established, which is one order of magnitude smaller than previously reported. This work provides the first steps in creating a physiologically relevant sensor capable of mapping local and real-time changes of epithelial barrier function at ALI, which will have broad applications in toxicology and drug screening applications.
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Affiliation(s)
- Sarah L Barron
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
| | - Sophie V Oldroyd
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
| | - Janire Saez
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
- Microfluidics Cluster, BIOMICs Microfluidics Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, CP 01006, Spain
- Basque Foundation for Science, IKERBASQUE, Bilbao, Spain
- Bioaraba Health Research Institute, Microfluidics Cluster UPV/EHU, Vitoria-Gasteiz, 01009, Spain
| | - Alice Chernaik
- Department of Medicine, Addenbrookes Hospital, University of Cambridge, Cambridge, CB2 2QQ, UK
| | - Wenrui Guo
- Department of Medicine, Addenbrookes Hospital, University of Cambridge, Cambridge, CB2 2QQ, UK
| | - Frank McCaughan
- Department of Medicine, Addenbrookes Hospital, University of Cambridge, Cambridge, CB2 2QQ, UK
| | - David Bulmer
- Department of Pharmacology, University of Cambridge, Cambridge, CB2 1PD, UK
| | - Róisín M Owens
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
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Favara DM, Verissimo T, McCaughan F. Cell-free DNA Testing in Lung Cancer Patients Improves National Health Service Real-world Result Turnaround Time and Treatment Initiation for Tumours with Targetable Alterations by 4 Weeks. Clin Oncol (R Coll Radiol) 2024; 36:129-131. [PMID: 38044195 DOI: 10.1016/j.clon.2023.11.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 11/16/2023] [Indexed: 12/05/2023]
Affiliation(s)
- D M Favara
- Oncology Department, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Department of Oncology, University of Cambridge, Cambridge, UK
| | - T Verissimo
- Oncology Department, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - F McCaughan
- Respiratory Department, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
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Porter LM, Guo W, Crozier TWM, Greenwood EJD, Ortmann B, Kottmann D, Nathan JA, Mahadeva R, Lehner PJ, McCaughan F. Cigarette smoke preferentially induces full length ACE2 expression in differentiated primary human airway cultures but does not alter the efficiency of cellular SARS-CoV-2 infection. Heliyon 2023; 9:e14383. [PMID: 36938474 PMCID: PMC10005841 DOI: 10.1016/j.heliyon.2023.e14383] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 03/12/2023] Open
Abstract
Cigarette smoking has many serious negative health consequences. The relationship between smoking and SARS-CoV-2 infection is controversial, specifically whether smokers are at increased risk of infection. We investigated the impact of cigarette smoke on ACE2 isoform expression and SARS-CoV-2 infection in differentiated primary human bronchial epithelial cells at the air-liquid-interface (ALI). We assessed the expression of ACE2 in response to CSE and therapeutics reported to modulate ACE2. We exposed ALI cultures to cigarette smoke extract (CSE) and then infected them with SARS-CoV-2. We measured cellular infection using flow cytometry and whole-transwell immunofluorescence. We found that CSE increased expression of full-length ACE2 (flACE2) but did not alter the expression of a Type I-interferon sensitive truncated isoform (dACE2) that lacks the capacity to bind SARS-CoV-2. CSE did not have a significant impact on key mediators of the innate immune response. Importantly, we show that, despite the increase in flACE2, CSE did not alter airway cell infection after CSE exposure. We found that nicotine does not significantly alter flACE2 expression but that NRF2 agonists do lead to an increase in flACE2 expression. This increase was not associated with an increase in SARS-CoV-2 infection. Our results are consistent with the epidemiological data suggesting that current smokers do not have an excess of SARS-CoV-2 infection. but that those with chronic respiratory or cardiovascular disease are more vulnerable to severe COVID-19. They suggest that, in differentiated conducting airway cells, flACE2 expression levels may not limit airway SARS-CoV-2 infection.
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Affiliation(s)
- Linsey M. Porter
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, CB2 OQQ, UK
| | - Wenrui Guo
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, CB2 OQQ, UK
| | - Thomas WM. Crozier
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Department of Medicine, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Edward JD. Greenwood
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Department of Medicine, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Brian Ortmann
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Department of Medicine, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Daniel Kottmann
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, CB2 OQQ, UK
| | - James A. Nathan
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Department of Medicine, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Ravindra Mahadeva
- Cambridge University Hospitals NHS Foundation Trust, University of Cambridge, Addenbrookes Hospital, Cambridge, CB2 OQQ, UK
| | - Paul J. Lehner
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Department of Medicine, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Frank McCaughan
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, CB2 OQQ, UK
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Hardt K, Vandebosch A, Sadoff J, Le Gars M, Truyers C, Lowson D, Van Dromme I, Vingerhoets J, Kamphuis T, Scheper G, Ruiz-Guiñazú J, Faust SN, Spinner CD, Schuitemaker H, Van Hoof J, Douoguih M, Struyf F, Albertson TE, Sandrock C, Lee JS, Looney MR, Tapson VF, Wiysonge CS, Velarde LHA, Backenroth D, Bhushanan J, Brandenburg B, Cárdenas V, Chen B, Chen F, Chetty P, Chu PL, Cooper K, Custers J, Delanghe H, Duca A, Henrick T, Juraszek J, Nalpas C, Peeters M, Pinheiro J, Roels S, Ryser MF, Salas J, Santoro Matias S, Scheys I, Shetty P, Shukarev G, Stoddard J, Talloen W, Tran N, Vaissiere N, van Son-Palmen E, Xu J, Goecker EA, Greninger AL, Jerome KR, Roychoudhury P, Takuva SG, Accini Mendoza JL, Achtyes E, Ahsan H, Alhatemi A, Allen N, Arribas JR, Bahrami G, Bailon L, Bajwa A, Baker J, Baron M, Benet S, Berdaï D, Berger P, Bertoch T, Bethune C, Bevilacqua S, Biagioni Santos MS, Binnian I, Bisnauthsing K, Boivin JM, Bollen H, Bonnet S, Borobia AM, Botelho-Nevers E, Bright P, Britten V, Brown C, Buadi A, Buntinx E, Burgess L, Bush L, Capeding MR, Carr QO, Carrasco Mas A, Catala H, Cathie K, Caudill TS, Cereto Castro F, Chau K, Chavoustie S, Chowdhury M, Chronos N, Cicconi P, Cifuentes L, Cobo SM, Collins H, Colton H, Cuaño CRG, D'Onofrio V, Dargan P, Darton T, Deane P, Del Pozo JL, Derdelinckx I, Desai A, Dever M, Díaz-Pollán B, DiBuono M, Doust M, Duncan C, Echave-Sustaeta JM, Eder F, Ellis K, Elzi S, Emmett S, Engelbrecht J, Evans M, Farah T, Felton T, Ferreira JP, Floutier C, Flume P, Ford S, Fragoso V, Freedman A, Frentiu E, Galloway C, Galtier F, Garcia Diaz J, García García I, Garcia A, Gardener Z, Gauteul P, Geller S, Gibson A, Gillet C, Girerd N, Girodet PO, Gler MT, Glover R, Go HDD, Gokani K, Gonthier D, Green C, Greenberg R, Griffin C, Grobbelaar C, Guancia A, Hakkarainen G, Harris J, Hassman M, Heimer D, Hellstrom-Louw E, Herades Y, Holroyd C, Hussen N, Isidro MGD, Jackson Y, Jain M, João Filho EC, Johnson D, Jones B, Joseph N, Jumeras A, Junquera P, Kellett-Wright J, Kennedy P, Kilgore PE, Kim K, Kimmel M, Konis G, Kutner M, Lacombe K, Launay O, Lazarus R, Lederman S, Lefebvre G, Lennon Collins K, Leroux-Roels I, Lim KWO, Lins M, Liu E, Llewelyn M, Mahomed A, Maia BP, Marín-Candon A, Martínez-Gómez X, Martinot JB, Mazzella A, McCaughan F, McCormack L, McGettigan J, Mehra P, Mejeur R, Miller V, Mills A, Molto Marhuenda J, Moodley P, Mora-Rillo M, Mothe B, Mullan D, Munro A, Myers P, Nell J, Newman Lobato Souza T, O'Halloran JA, Ochoa Mazarro MD, Oliver A, Onate Gutierrez JM, Ortega J, Oshita M, Otero Romero S, Overcash JS, Owens D, Packham A, Paiva de Sousa L, Palfreeman A, Pallares CJ, Patel R, Patel S, Pelkey L, Peluso D, Penciu F, Pinto SJ, Pounds K, Pouzar J, Pragalos A, Presti R, Price D, Qureshi E, Ramalho Madruga JV, Ramesh M, Rankin B, Razat B, Riegel Santos B, Riesenberg R, Riffer E, Roche S, Rose K, Rosellini P, Rossignol P, Safirstein B, Salazar H, Sanchez Vallejo G, Santhosh S, Seco-Meseguer E, Seep M, Sherry E, Short P, Soentjens P, Solis J, Soriano Viladomiu A, Sorli C, Spangenthal S, Spence N, Stephenson E, Strout C, Surowitz R, Taladua KM, Tellalian D, Thalamas C, Thiriphoo N, Thomas J, Thomas N, Trout G, Urroz M, Veekmans B, Veekmans L, Villalobos REM, Webster B, White A, Williams G, Williams H, Wilson B, Winston A, Wiselka M, Zervos M. Efficacy, safety, and immunogenicity of a booster regimen of Ad26.COV2.S vaccine against COVID-19 (ENSEMBLE2): results of a randomised, double-blind, placebo-controlled, phase 3 trial. Lancet Infect Dis 2022; 22:1703-1715. [PMID: 36113538 PMCID: PMC9639796 DOI: 10.1016/s1473-3099(22)00506-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 01/07/2023]
Abstract
BACKGROUND Despite the availability of effective vaccines against COVID-19, booster vaccinations are needed to maintain vaccine-induced protection against variant strains and breakthrough infections. This study aimed to investigate the efficacy, safety, and immunogenicity of the Ad26.COV2.S vaccine (Janssen) as primary vaccination plus a booster dose. METHODS ENSEMBLE2 is a randomised, double-blind, placebo-controlled, phase 3 trial including crossover vaccination after emergency authorisation of COVID-19 vaccines. Adults aged at least 18 years without previous COVID-19 vaccination at public and private medical practices and hospitals in Belgium, Brazil, Colombia, France, Germany, the Philippines, South Africa, Spain, the UK, and the USA were randomly assigned 1:1 via a computer algorithm to receive intramuscularly administered Ad26.COV2.S as a primary dose plus a booster dose at 2 months or two placebo injections 2 months apart. The primary endpoint was vaccine efficacy against the first occurrence of molecularly confirmed moderate to severe-critical COVID-19 with onset at least 14 days after booster vaccination, which was assessed in participants who received two doses of vaccine or placebo, were negative for SARS-CoV-2 by PCR at baseline and on serology at baseline and day 71, had no major protocol deviations, and were at risk of COVID-19 (ie, had no PCR-positive result or discontinued the study before day 71). Safety was assessed in all participants; reactogenicity, in terms of solicited local and systemic adverse events, was assessed as a secondary endpoint in a safety subset (approximately 6000 randomly selected participants). The trial is registered with ClinicalTrials.gov, NCT04614948, and is ongoing. FINDINGS Enrolment began on Nov 16, 2020, and the primary analysis data cutoff was June 25, 2021. From 34 571 participants screened, the double-blind phase enrolled 31 300 participants, 14 492 of whom received two doses (7484 in the Ad26.COV2.S group and 7008 in the placebo group) and 11 639 of whom were eligible for inclusion in the assessment of the primary endpoint (6024 in the Ad26.COV2.S group and 5615 in the placebo group). The median (IQR) follow-up post-booster vaccination was 36·0 (15·0-62·0) days. Vaccine efficacy was 75·2% (adjusted 95% CI 54·6-87·3) against moderate to severe-critical COVID-19 (14 cases in the Ad26.COV2.S group and 52 cases in the placebo group). Most cases were due to the variants alpha (B.1.1.7) and mu (B.1.621); endpoints for the primary analysis accrued from Nov 16, 2020, to June 25, 2021, before the global dominance of delta (B.1.617.2) or omicron (B.1.1.529). The booster vaccine exhibited an acceptable safety profile. The overall frequencies of solicited local and systemic adverse events (evaluated in the safety subset, n=6067) were higher among vaccine recipients than placebo recipients after the primary and booster doses. The frequency of solicited adverse events in the Ad26.COV2.S group were similar following the primary and booster vaccinations (local adverse events, 1676 [55·6%] of 3015 vs 896 [57·5%] of 1559, respectively; systemic adverse events, 1764 [58·5%] of 3015 vs 821 [52·7%] of 1559, respectively). Solicited adverse events were transient and mostly grade 1-2 in severity. INTERPRETATION A homologous Ad26.COV2.S booster administered 2 months after primary single-dose vaccination in adults had an acceptable safety profile and was efficacious against moderate to severe-critical COVID-19. Studies assessing efficacy against newer variants and with longer follow-up are needed. FUNDING Janssen Research & Development.
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Affiliation(s)
- Karin Hardt
- Janssen Research & Development, Beerse, Belgium
| | | | | | | | | | - David Lowson
- Janssen Research & Development, High Wycombe, UK
| | | | | | | | - Gert Scheper
- Janssen Vaccines & Prevention, Leiden, Netherlands
| | | | - Saul N Faust
- NIHR Southampton Clinical Research Facility and Biomedical Research Centre, Southampton, UK; Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
| | | | | | | | | | - Frank Struyf
- Janssen Research & Development, Beerse, Belgium.
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Guo W, Porter LM, Crozier TWM, Coates M, Jha A, McKie M, Nathan JA, Lehner PJ, Greenwood EJD, McCaughan F. Topical TMPRSS2 inhibition prevents SARS-CoV-2 infection in differentiated human airway cultures. Life Sci Alliance 2022; 5:5/4/e202101116. [PMID: 35110354 PMCID: PMC8814636 DOI: 10.26508/lsa.202101116] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 05/09/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND There are limited effective prophylactic/early treatments for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Viral entry requires spike protein binding to the angiotensin-converting enzyme-2 receptor and cleavage by transmembrane serine protease 2 (TMPRSS2), a cell surface serine protease. Targeting of TMPRSS2 by either androgen blockade or direct inhibition is in clinical trials in early SARS-CoV-2 infection. METHODS We used differentiated primary human airway epithelial cells at the air-liquid interface to test the impact of targeting TMPRSS2 on the prevention of SARS-CoV-2 infection. RESULTS We first modelled the systemic delivery of compounds. Enzalutamide, an oral androgen receptor antagonist, had no impact on SARS-CoV-2 infection. By contrast, camostat mesylate, an orally available serine protease inhibitor, blocked SARS-CoV-2 entry. However, oral camostat is rapidly metabolised in the circulation, with poor airway bioavailability. We therefore modelled local airway administration by applying camostat to the apical surface of differentiated airway cultures. We demonstrated that a brief exposure to topical camostat effectively restricts SARS-CoV-2 infection. CONCLUSION These experiments demonstrate a potential therapeutic role for topical camostat for pre- or post-exposure prophylaxis of SARS-CoV-2, which can now be evaluated in a clinical trial.
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Affiliation(s)
- Wenrui Guo
- Department of Medicine, Addenbrookes Hospital, University of Cambridge, Cambridge, UK
| | - Linsey M Porter
- Department of Medicine, Addenbrookes Hospital, University of Cambridge, Cambridge, UK
| | - Thomas WM Crozier
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Matthew Coates
- Department of Medicine, Addenbrookes Hospital, University of Cambridge, Cambridge, UK
| | - Akhilesh Jha
- Department of Medicine, Addenbrookes Hospital, University of Cambridge, Cambridge, UK
| | - Mikel McKie
- Medical Research Council, Biostatistic Unit, Cambridge, UK
| | - James A Nathan
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Paul J Lehner
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Edward JD Greenwood
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK,
| | - Frank McCaughan
- Department of Medicine, Addenbrookes Hospital, University of Cambridge, Cambridge, UK
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7
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Crozier TWM, Greenwood EJD, Williamson JC, Guo W, Porter LM, Gabaev I, Teixeira-Silva A, Grice GL, Wickenhagen A, Stanton RJ, Wang ECY, Wilson SJ, Matheson NJ, Nathan JA, McCaughan F, Lehner PJ. Quantitative proteomic analysis of SARS-CoV-2 infection of primary human airway ciliated cells and lung epithelial cells demonstrates the effectiveness of SARS-CoV-2 innate immune evasion. Wellcome Open Res 2022; 7:224. [PMID: 36483314 PMCID: PMC9706147 DOI: 10.12688/wellcomeopenres.17946.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2022] [Indexed: 02/02/2023] Open
Abstract
Background: Quantitative proteomics is able to provide a comprehensive, unbiased description of changes to cells caused by viral infection, but interpretation may be complicated by differential changes in infected and uninfected 'bystander' cells, or the use of non-physiological cellular models. Methods: In this paper, we use fluorescence-activated cell sorting (FACS) and quantitative proteomics to analyse cell-autonomous changes caused by authentic SARS-CoV-2 infection of respiratory epithelial cells, the main target of viral infection in vivo. First, we determine the relative abundance of proteins in primary human airway epithelial cells differentiated at the air-liquid interface (basal, secretory and ciliated cells). Next, we specifically characterise changes caused by SARS-CoV-2 infection of ciliated cells. Finally, we compare temporal proteomic changes in infected and uninfected 'bystander' Calu-3 lung epithelial cells and compare infection with B.29 and B.1.1.7 (Alpha) variants. Results: Amongst 5,709 quantified proteins in primary human airway ciliated cells, the abundance of 226 changed significantly in the presence of SARS-CoV-2 infection (q <0.05 and >1.5-fold). Notably, viral replication proceeded without inducing a type-I interferon response. Amongst 6,996 quantified proteins in Calu-3 cells, the abundance of 645 proteins changed significantly in the presence of SARS-CoV-2 infection (q < 0.05 and > 1.5-fold). In contrast to the primary cell model, a clear type I interferon (IFN) response was observed. Nonetheless, induction of IFN-inducible proteins was markedly attenuated in infected cells, compared with uninfected 'bystander' cells. Infection with B.29 and B.1.1.7 (Alpha) variants gave similar results. Conclusions: Taken together, our data provide a detailed proteomic map of changes in SARS-CoV-2-infected respiratory epithelial cells in two widely used, physiologically relevant models of infection. As well as identifying dysregulated cellular proteins and processes, the effectiveness of strategies employed by SARS-CoV-2 to avoid the type I IFN response is illustrated in both models.
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Affiliation(s)
- Thomas W M Crozier
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Edward J D Greenwood
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - James C Williamson
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Wenrui Guo
- Department of Medicine, Addenbrookes Hospital, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Linsey M Porter
- Department of Medicine, Addenbrookes Hospital, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Ildar Gabaev
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Ana Teixeira-Silva
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Guinevere L Grice
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Arthur Wickenhagen
- MRC - University of Glasgow Centre for Virus Research, Glasgow, G61 1QH, UK
| | - Richard J Stanton
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Eddie C Y Wang
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Sam J Wilson
- MRC - University of Glasgow Centre for Virus Research, Glasgow, G61 1QH, UK
| | - Nicholas J Matheson
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK.,NHS Blood and Transplant, Cambridge, CB2 0PT, UK
| | - James A Nathan
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Frank McCaughan
- Department of Medicine, Addenbrookes Hospital, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Paul J Lehner
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
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8
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Neary M, Box H, Sharp J, Tatham L, Curley P, Herriott J, Kijak E, Arshad U, Hobson JJ, Rajoli R, Pertinez H, Valentijn A, Dhaliwal K, McCaughan F, Rannard SP, Kipar A, Stewart JP, Owen A. Evaluation of intranasal nafamostat or camostat for SARS-CoV-2 chemoprophylaxis in Syrian golden hamsters. bioRxiv 2021:2021.07.08.451654. [PMID: 34268511 PMCID: PMC8282100 DOI: 10.1101/2021.07.08.451654] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Successful development of a chemoprophylaxis against SARS-CoV-2 could provide a tool for infection prevention implementable alongside vaccination programmes. Camostat and nafamostat are serine protease inhibitors that inhibit SARS-CoV-2 viral entry in vitro but have not been characterised for chemoprophylaxis in animal models. Clinically, nafamostat is limited to intravenous delivery and while camostat is orally available, both drugs have extremely short plasma half-lives. This study sought to determine whether intranasal dosing at 5 mg/kg twice daily was able to prevent airborne transmission of SARS-CoV-2 from infected to uninfected Syrian golden hamsters. SARS-CoV-2 viral RNA was above the limits of quantification in both saline- and camostat-treated hamsters 5 days after cohabitation with a SARS-CoV-2 inoculated hamster. However, intranasal nafamostat-treated hamsters remained RNA negative for the full 7 days of cohabitation. Changes in body weight over the course of the experiment were supportive of a lack of clinical symptomology in nafamostat-treated but not saline- or camostat-treated animals. These data are strongly supportive of the utility of intranasally delivered nafamostat for prevention of SARS-CoV-2 infection and further studies are underway to confirm absence of pulmonary infection and pathological changes.
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9
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Smolinska A, Jessop DS, Pappan KL, De Saedeleer A, Kang A, Martin AL, Allsworth M, Tyson C, Bos MP, Clancy M, Morel M, Cooke T, Dymond T, Harris C, Galloway J, Bresser P, Dijkstra N, Jagesar V, Savelkoul PHM, Beuken EVH, Nix WHV, Louis R, Delvaux M, Calmes D, Ernst B, Pollini S, Peired A, Guiot J, Tomassetti S, Budding AE, McCaughan F, Marciniak SJ, van der Schee MP. The SARS-CoV-2 viral load in COVID-19 patients is lower on face mask filters than on nasopharyngeal swabs. Sci Rep 2021; 11:13476. [PMID: 34188082 PMCID: PMC8242000 DOI: 10.1038/s41598-021-92665-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 06/08/2021] [Indexed: 11/22/2022] Open
Abstract
Face masks and personal respirators are used to curb the transmission of SARS-CoV-2 in respiratory droplets; filters embedded in some personal protective equipment could be used as a non-invasive sample source for applications, including at-home testing, but information is needed about whether filters are suited to capture viral particles for SARS-CoV-2 detection. In this study, we generated inactivated virus-laden aerosols of 0.3–2 microns in diameter (0.9 µm mean diameter by mass) and dispersed the aerosolized viral particles onto electrostatic face mask filters. The limit of detection for inactivated coronaviruses SARS-CoV-2 and HCoV-NL63 extracted from filters was between 10 to 100 copies/filter for both viruses. Testing for SARS-CoV-2, using face mask filters and nasopharyngeal swabs collected from hospitalized COVID-19-patients, showed that filter samples offered reduced sensitivity (8.5% compared to nasopharyngeal swabs). The low concordance of SARS-CoV-2 detection between filters and nasopharyngeal swabs indicated that number of viral particles collected on the face mask filter was below the limit of detection for all patients but those with the highest viral loads. This indicated face masks are unsuitable to replace diagnostic nasopharyngeal swabs in COVID-19 diagnosis. The ability to detect nucleic acids on face mask filters may, however, find other uses worth future investigation.
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Affiliation(s)
- Agnieszka Smolinska
- Owlstone Medical Ltd., Cambridge, Cambridgeshire, UK.,Department of Pharmacology and Toxicology, Maastricht University, Maastricht, The Netherlands
| | | | - Kirk L Pappan
- Owlstone Medical Ltd., Cambridge, Cambridgeshire, UK
| | | | - Amerjit Kang
- Owlstone Medical Ltd., Cambridge, Cambridgeshire, UK
| | | | - Max Allsworth
- Owlstone Medical Ltd., Cambridge, Cambridgeshire, UK
| | | | | | | | - Mike Morel
- Cambridge Clinical Laboratories Ltd., Cambridge, Cambridgeshire, UK
| | - Tony Cooke
- Cambridge Clinical Laboratories Ltd., Cambridge, Cambridgeshire, UK
| | - Tom Dymond
- Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, UK
| | - Claire Harris
- Department of Medicine, Addenbrooke's Hospital, Cambridge, UK.,University of Cambridge, Cambridge, UK
| | - Jacqui Galloway
- Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, UK
| | | | | | | | - Paul H M Savelkoul
- Department of Medical Microbiology, Maastricht University Medical Center, Care and Public Health Research Institute (Caphri), Maastricht, The Netherlands
| | - Erik V H Beuken
- Department of Medical Microbiology, Maastricht University Medical Center, Care and Public Health Research Institute (Caphri), Maastricht, The Netherlands
| | - Wesley H V Nix
- Department of Medical Microbiology, Maastricht University Medical Center, Care and Public Health Research Institute (Caphri), Maastricht, The Netherlands
| | - Renaud Louis
- Repiratory Department, CHU Liège, Liège, Belgium
| | | | | | - Benoit Ernst
- Repiratory Department, CHU Liège, Liège, Belgium
| | - Simona Pollini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Anna Peired
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Julien Guiot
- Repiratory Department, CHU Liège, Liège, Belgium
| | - Sara Tomassetti
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Interventional Pulmonology Unit, Careggi University Hospital, Florence, Italy
| | | | - Frank McCaughan
- Department of Medicine, Addenbrooke's Hospital, Cambridge, UK.,University of Cambridge, Cambridge, UK
| | - Stefan J Marciniak
- Department of Medicine, Addenbrooke's Hospital, Cambridge, UK.,University of Cambridge, Cambridge, UK
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10
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Han N, Hwang W, Tzelepis K, Schmerer P, Yankova E, MacMahon M, Lei W, M Katritsis N, Liu A, Felgenhauer U, Schuldt A, Harris R, Chapman K, McCaughan F, Weber F, Kouzarides T. Identification of SARS-CoV-2-induced pathways reveals drug repurposing strategies. Sci Adv 2021; 7:eabh3032. [PMID: 34193418 PMCID: PMC8245040 DOI: 10.1126/sciadv.abh3032] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 05/14/2021] [Indexed: 05/02/2023]
Abstract
The global outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) necessitates the rapid development of new therapies against coronavirus disease 2019 (COVID-19) infection. Here, we present the identification of 200 approved drugs, appropriate for repurposing against COVID-19. We constructed a SARS-CoV-2-induced protein network, based on disease signatures defined by COVID-19 multiomics datasets, and cross-examined these pathways against approved drugs. This analysis identified 200 drugs predicted to target SARS-CoV-2-induced pathways, 40 of which are already in COVID-19 clinical trials, testifying to the validity of the approach. Using artificial neural network analysis, we classified these 200 drugs into nine distinct pathways, within two overarching mechanisms of action (MoAs): viral replication (126) and immune response (74). Two drugs (proguanil and sulfasalazine) implicated in viral replication were shown to inhibit replication in cell assays. This unbiased and validated analysis opens new avenues for the rapid repurposing of approved drugs into clinical trials.
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Affiliation(s)
- Namshik Han
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK.
| | - Woochang Hwang
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | | | - Patrick Schmerer
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, Gießen 35392, Germany
| | - Eliza Yankova
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Méabh MacMahon
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
- Centre for Therapeutics Discovery, LifeArc, Stevenage, UK
| | - Winnie Lei
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Nicholas M Katritsis
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Anika Liu
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Data and Computational Sciences, GSK, London, UK
| | - Ulrike Felgenhauer
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, Gießen 35392, Germany
| | - Alison Schuldt
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Rebecca Harris
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Kathryn Chapman
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Frank McCaughan
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Friedemann Weber
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, Gießen 35392, Germany
| | - Tony Kouzarides
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge, UK
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11
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Tran S, Niyomthong P, McCaughan F, Hardavella G, Warwick G, Whitaker D, Desai S. Microwave ablation of malignant lung lesions;safety and efficacy – the King’s experience. Lung Cancer 2017. [DOI: 10.1183/1393003.congress-2017.pa4282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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12
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Correia L, Littlewood T, Evan G, McCaughan F. LSC - 2017 - Deregulated SOX2 drives a migratory signature in a novel organotypic model of bronchial dysplasia. Lung Cancer 2017. [DOI: 10.1183/1393003.congress-2017.pa3293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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13
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khan A, Hardavella G, Warwick G, McCaughan F, desai S, mulholland N, greenwood N, whitaker D. Diagnostic efficacy and safety of navigational bronchoscopy (NB) in the investigation of challenging lung lesions. Lung Cancer 2017. [DOI: 10.1183/1393003.congress-2017.pa4275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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14
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Irshad S, Flores-Borja F, Lawler K, Monypenny J, Evans R, Male V, Gordon P, Cheung A, Gazinska P, Noor F, Wong F, Grigoriadis A, Fruhwirth GO, Barber PR, Woodman N, Patel D, Rodriguez-Justo M, Owen J, Martin SG, Pinder SE, Gillett CE, Poland SP, Ameer-Beg S, McCaughan F, Carlin LM, Hasan U, Withers DR, Lane P, Vojnovic B, Quezada SA, Ellis P, Tutt ANJ, Ng T. RORγt + Innate Lymphoid Cells Promote Lymph Node Metastasis of Breast Cancers. Cancer Res 2017; 77:1083-1096. [PMID: 28082403 DOI: 10.1158/0008-5472.can-16-0598] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [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: 04/20/2016] [Revised: 12/09/2016] [Accepted: 12/10/2016] [Indexed: 11/16/2022]
Abstract
Cancer cells tend to metastasize first to tumor-draining lymph nodes, but the mechanisms mediating cancer cell invasion into the lymphatic vasculature remain little understood. Here, we show that in the human breast tumor microenvironment (TME), the presence of increased numbers of RORγt+ group 3 innate lymphoid cells (ILC3) correlates with an increased likelihood of lymph node metastasis. In a preclinical mouse model of breast cancer, CCL21-mediated recruitment of ILC3 to tumors stimulated the production of the CXCL13 by TME stromal cells, which in turn promoted ILC3-stromal interactions and production of the cancer cell motile factor RANKL. Depleting ILC3 or neutralizing CCL21, CXCL13, or RANKL was sufficient to decrease lymph node metastasis. Our findings establish a role for RORγt+ILC3 in promoting lymphatic metastasis by modulating the local chemokine milieu of cancer cells in the TME. Cancer Res; 77(5); 1083-96. ©2017 AACR.
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Affiliation(s)
- Sheeba Irshad
- Breast Cancer Now (BCN) Research Unit, King's College London, London, United Kingdom
| | - Fabian Flores-Borja
- Breast Cancer Now (BCN) Research Unit, King's College London, London, United Kingdom
- Richard Dimbleby, Randall Division & Division of Cancer Studies, King's College London, London, United Kingdom
| | - Katherine Lawler
- Richard Dimbleby, Randall Division & Division of Cancer Studies, King's College London, London, United Kingdom
- Institute for Mathematical and Molecular Biomedicine, King's College London, London, United Kingdom
| | - James Monypenny
- Richard Dimbleby, Randall Division & Division of Cancer Studies, King's College London, London, United Kingdom
| | - Rachel Evans
- Richard Dimbleby, Randall Division & Division of Cancer Studies, King's College London, London, United Kingdom
| | - Victoria Male
- Breast Cancer Now (BCN) Research Unit, King's College London, London, United Kingdom
| | - Peter Gordon
- Breast Cancer Now (BCN) Research Unit, King's College London, London, United Kingdom
- Richard Dimbleby, Randall Division & Division of Cancer Studies, King's College London, London, United Kingdom
| | - Anthony Cheung
- Richard Dimbleby, Randall Division & Division of Cancer Studies, King's College London, London, United Kingdom
| | - Patrycja Gazinska
- Breast Cancer Now (BCN) Research Unit, King's College London, London, United Kingdom
| | - Farzana Noor
- Breast Cancer Now (BCN) Research Unit, King's College London, London, United Kingdom
| | - Felix Wong
- Richard Dimbleby, Randall Division & Division of Cancer Studies, King's College London, London, United Kingdom
| | - Anita Grigoriadis
- Breast Cancer Now (BCN) Research Unit, King's College London, London, United Kingdom
| | - Gilbert O Fruhwirth
- Richard Dimbleby, Randall Division & Division of Cancer Studies, King's College London, London, United Kingdom
- Leukocyte Dynamics Group, Beatson Advanced Imaging Resource, CRUK Beatson Institute, Glasgow, United Kingdom
| | - Paul R Barber
- Gray Institute for Radiation Oncology & Biology, University of Oxford, Oxford, United Kingdom
| | - Natalie Woodman
- King's Health Partners Cancer Biobank, King's College London, London, United Kingdom
| | - Dominic Patel
- International Center for Infectiology Research, University of Lyon, Lyon, France
| | | | - Julie Owen
- King's Health Partners Cancer Biobank, King's College London, London, United Kingdom
| | - Stewart G Martin
- Division of Cancer and Stem Cells, Department of Clinical Oncology, School of Medicine, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Sarah E Pinder
- King's Health Partners Cancer Biobank, King's College London, London, United Kingdom
- Research Oncology, Division of Cancer Studies, King's College London, Guy's Hospital, London, United Kingdom
| | - Cheryl E Gillett
- King's Health Partners Cancer Biobank, King's College London, London, United Kingdom
- Research Oncology, Division of Cancer Studies, King's College London, Guy's Hospital, London, United Kingdom
| | - Simon P Poland
- Richard Dimbleby, Randall Division & Division of Cancer Studies, King's College London, London, United Kingdom
| | - Simon Ameer-Beg
- Richard Dimbleby, Randall Division & Division of Cancer Studies, King's College London, London, United Kingdom
| | - Frank McCaughan
- Department of Asthma, Allergy, and Lung Biology, King's College London, London, United Kingdom
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Leo M Carlin
- Leukocyte Dynamics Group, Beatson Advanced Imaging Resource, CRUK Beatson Institute, Glasgow, United Kingdom
| | - Uzma Hasan
- International Center for Infectiology Research, University of Lyon, Lyon, France
| | - David R Withers
- MRC Centre for Immune Regulation, Institute for Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Peter Lane
- MRC Centre for Immune Regulation, Institute for Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Borivoj Vojnovic
- Gray Institute for Radiation Oncology & Biology, University of Oxford, Oxford, United Kingdom
| | - Sergio A Quezada
- UCL Cancer Institute, Paul O'Gorman Building, University College London, London, United Kingdom
| | - Paul Ellis
- Department of Medical Oncology, Guy's and St Thomas Foundation Trust, London, United Kingdom
| | - Andrew N J Tutt
- Breast Cancer Now (BCN) Research Unit, King's College London, London, United Kingdom
- ICR, BCN Research Unit, Toby Robins Research Centre, London, United Kingdom
| | - Tony Ng
- Breast Cancer Now (BCN) Research Unit, King's College London, London, United Kingdom.
- Richard Dimbleby, Randall Division & Division of Cancer Studies, King's College London, London, United Kingdom
- UCL Cancer Institute, Paul O'Gorman Building, University College London, London, United Kingdom
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15
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Ortiz-Zapater E, Lee RW, Owen W, Weitsman G, Fruhwirth G, Dunn RG, Neat MJ, McCaughan F, Parker P, Ng T, Santis G. MET-EGFR dimerization in lung adenocarcinoma is dependent on EGFR mtations and altered by MET kinase inhibition. PLoS One 2017; 12:e0170798. [PMID: 28141869 PMCID: PMC5283661 DOI: 10.1371/journal.pone.0170798] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [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: 09/13/2016] [Accepted: 01/11/2017] [Indexed: 01/06/2023] Open
Abstract
Advanced lung cancer has poor survival with few therapies. EGFR tyrosine kinase inhibitors (TKIs) have high response rates in patients with activating EGFR mutations, but acquired resistance is inevitable. Acquisition of the EGFR T790M mutation causes over 50% of resistance; MET amplification is also common. Preclinical data suggest synergy between MET and EGFR inhibitors. We hypothesized that EGFR-MET dimerization determines response to MET inhibition, depending on EGFR mutation status, independently of MET copy number. We tested this hypothesis by generating isogenic cell lines from NCI-H1975 cells, which co-express L858R and T790M EGFR mutations, namely H1975L858R/T790M (EGFR TKI resistant); H1975L858R (sensitized) and H1975WT (wild-type). We assessed cell proliferation in vitro and tumor growth/stroma formation in derived xenograft models in response to a MET TKI (SGX523) and correlated with EGFR-MET dimerization assessed by Förster Resonance Energy Transfer (FRET). SGX523 significantly reduced H1975L858R/T790M cell proliferation, xenograft tumor growth and decreased ERK phosphorylation. The same was not seen in H1975L858R or H1975WT cells. SGX523 only reduced stroma formation in H1975L858R. SGX523 reduced EGFR-MET dimerization in H1975L858R/T790M but induced dimer formation in H1975L858R with no effect in H1975WT. Our data suggests that MET inhibition by SGX523 and EGFR-MET heterodimerisation are determined by EGFR genotype. As tumor behaviour is modulated by this interaction, this could determine treatment efficacy.
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Affiliation(s)
- Elena Ortiz-Zapater
- Division of Asthma, Allergy and Lung Biology, King's College London, Guy's Hospital, London, United Kingdom
| | - Richard W. Lee
- Division of Asthma, Allergy and Lung Biology, King's College London, Guy's Hospital, London, United Kingdom
| | - William Owen
- Division of Asthma, Allergy and Lung Biology, King's College London, Guy's Hospital, London, United Kingdom
| | - Gregory Weitsman
- Richard Dimbleby Department of Cancer Research, Randall Division of Cell and Molecular Biophysics, King’s College London, Guy's Medical School Campus, London, United Kingdom
| | - Gilbert Fruhwirth
- Department of Imaging Chemistry and Biology, Division of Imaging Science and Biomedical Engineering, King’s College London, The Rayne Institute/St. Thomas' Hospital, London, United Kingdom
| | - Robert G. Dunn
- Department of Cancer Genetics, Viapath, Guy’s and St Thomas’ NHS Foundation Trust, Guy's Hospital, London, United Kingdom
| | - Michael J. Neat
- Department of Cancer Genetics, Viapath, Guy’s and St Thomas’ NHS Foundation Trust, Guy's Hospital, London, United Kingdom
| | - Frank McCaughan
- Division of Asthma, Allergy and Lung Biology, King's College London, Guy's Hospital, London, United Kingdom
| | - Peter Parker
- Division of Cancer Studies, King’s College London, Guy's Medical School Campus, London, United Kingdom
- Protein Phosphorylation Laboratory, Francis Crick Institute, London, United Kingdom
| | - Tony Ng
- Richard Dimbleby Department of Cancer Research, Randall Division of Cell and Molecular Biophysics, King’s College London, Guy's Medical School Campus, London, United Kingdom
- Division of Cancer Studies, King’s College London, Guy's Medical School Campus, London, United Kingdom
- Breast Cancer Research Unit, King’s College London, Guy's Hospital, London, United Kingdom
- UCL Cancer Institute, Paul O' Gorman Building, University College London, London, United Kingdom
| | - George Santis
- Division of Asthma, Allergy and Lung Biology, King's College London, Guy's Hospital, London, United Kingdom
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16
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Tran S, Niyomthong P, McCaughan F, Hardavella G, Warwick G, Whitaker D, Desai S. 112: Microwave ablation of malignant lung lesions – the King's experience. Lung Cancer 2017. [DOI: 10.1016/s0169-5002(17)30162-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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17
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Galazi M, Weitsman G, Monypenny J, Coban O, Vicencio J, McCaughan F, Forster MD, Ng T. Exploring the utility of exosomal HER receptor dimerization as a resistance mechanism in NSCLC. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.e23100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Myria Galazi
- University College London, Cancer Institute, London, United Kingdom
| | | | | | - Oana Coban
- King's College London, London, United Kingdom
| | - Jose Vicencio
- University College London Cancer Institute, London, United Kingdom
| | | | - Martin David Forster
- University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Tony Ng
- Kings College London, London, United Kingdom
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18
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Abstract
Circulating tumour DNA (ctDNA) is that fraction of circulating DNA that is derived from a patient's cancer. For a number of years, patients with haematological malignancies have had their disease diagnosed or monitored using tests based on detecting specific cytological or molecular biomarkers in blood. It has long been appreciated that the more common epithelial malignancies also shed DNA into the blood and that this tumour-derived DNA generally contributes a minor percentage of the overall cell-free DNA burden in peripheral blood. The biotech revolution has transformed our ability to detect, quantify and interpret genetic events. This has led to a renewed interest in the potential of using a simple blood test to both diagnose cancer and longitudinally monitor the response to medical interventions in patients with solid organ malignancies.In this review we provide a summary of the literature to date and describe the main attributes of the current analytical approaches to ctDNA. We then focus on the potential clinical applications. There is increasing evidence to support the routine analysis of ctDNA in clinical decision-making for certain subgroups of patients with so-called hotspot mutations, particularly in lung and colorectal cancer. With continued refinement and technological progress, non-invasive molecular biomarkers including of ctDNA may be clinically useful at all stages of cancer management from diagnosis to disease progression.
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Affiliation(s)
- E. Karampini
- From the Department of Asthma, Allergy and Lung Biology, King’s College London, London SE1 9RT, UK and
| | - F. McCaughan
- From the Department of Asthma, Allergy and Lung Biology, King’s College London, London SE1 9RT, UK and
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA
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Ivey A, Hills RK, Simpson MA, Jovanovic JV, Gilkes A, Grech A, Patel Y, Bhudia N, Farah H, Mason J, Wall K, Akiki S, Griffiths M, Solomon E, McCaughan F, Linch DC, Gale RE, Vyas P, Freeman SD, Russell N, Burnett AK, Grimwade D. Assessment of Minimal Residual Disease in Standard-Risk AML. N Engl J Med 2016; 374:422-33. [PMID: 26789727 DOI: 10.1056/nejmoa1507471] [Citation(s) in RCA: 551] [Impact Index Per Article: 68.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Despite the molecular heterogeneity of standard-risk acute myeloid leukemia (AML), treatment decisions are based on a limited number of molecular genetic markers and morphology-based assessment of remission. Sensitive detection of a leukemia-specific marker (e.g., a mutation in the gene encoding nucleophosmin [NPM1]) could improve prognostication by identifying submicroscopic disease during remission. METHODS We used a reverse-transcriptase quantitative polymerase-chain-reaction assay to detect minimal residual disease in 2569 samples obtained from 346 patients with NPM1-mutated AML who had undergone intensive treatment in the National Cancer Research Institute AML17 trial. We used a custom 51-gene panel to perform targeted sequencing of 223 samples obtained at the time of diagnosis and 49 samples obtained at the time of relapse. Mutations associated with preleukemic clones were tracked by means of digital polymerase chain reaction. RESULTS Molecular profiling highlighted the complexity of NPM1-mutated AML, with segregation of patients into more than 150 subgroups, thus precluding reliable outcome prediction. The determination of minimal-residual-disease status was more informative. Persistence of NPM1-mutated transcripts in blood was present in 15% of the patients after the second chemotherapy cycle and was associated with a greater risk of relapse after 3 years of follow-up than was an absence of such transcripts (82% vs. 30%; hazard ratio, 4.80; 95% confidence interval [CI], 2.95 to 7.80; P<0.001) and a lower rate of survival (24% vs. 75%; hazard ratio for death, 4.38; 95% CI, 2.57 to 7.47; P<0.001). The presence of minimal residual disease was the only independent prognostic factor for death in multivariate analysis (hazard ratio, 4.84; 95% CI, 2.57 to 9.15; P<0.001). These results were validated in an independent cohort. On sequential monitoring of minimal residual disease, relapse was reliably predicted by a rising level of NPM1-mutated transcripts. Although mutations associated with preleukemic clones remained detectable during ongoing remission after chemotherapy, NPM1 mutations were detected in 69 of 70 patients at the time of relapse and provided a better marker of disease status. CONCLUSIONS The presence of minimal residual disease, as determined by quantitation of NPM1-mutated transcripts, provided powerful prognostic information independent of other risk factors. (Funded by Bloodwise and the National Institute for Health Research; Current Controlled Trials number, ISRCTN55675535.).
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Affiliation(s)
- Adam Ivey
- From the Molecular Oncology Unit and Cancer Genetics Laboratory, Department of Medical and Molecular Genetics, Guy's Hospital (A.I.), the Department of Medical and Molecular Genetics (M.A.S., J.V.J., E.S., D.G.) and Department of Asthma, Allergy and Respiratory Science (H.F., F.M.), Faculty of Life Sciences and Medicine, King's College London, the Department of Haematology, University College London (Y.P., D.C.L., R.E.G.), and the Innovation Department, Cancer Research UK (N.B.), London, the Experimental Cancer Medicine Centre (A. Gilkes) and Department of Haematology (R.K.H., A.K.B.), Cardiff University School of Medicine, and the Haematology Clinical Trials Unit, Cardiff University (A. Grech), Cardiff, West Midlands Regional Genetics Laboratory, Birmingham (J.M., K.W., S.A., M.G.), MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine and Department of Haematology, University of Oxford and Oxford University Hospitals NHS Trust, and the National Institute for Health Research Oxford Biomedical Research Centre (P.V.), Oxford, the Department of Clinical Immunology, University of Birmingham, Birmingham (S.D.F.), and the Centre for Clinical Haematology, Nottingham University Hospital, Nottingham (N.R.) - all in the United Kingdom
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Correia LL, Littlewood TD, Evan G, McCaughan F. Deregulated SOX2 drives dysplasia in a novel 3D organotypic model of bronchial dysplasia. J Thorac Oncol 2016. [DOI: 10.1016/j.jtho.2015.12.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Karampini E, Muhith A, Farah H, King J, Cane P, Spicer J, McCaughan F. S105 Microdroplet digital PCR for the longitudinal monitoring of circulating tumour DNA biomarkers in unselected patients with advanced lung cancer: Abstract S105 Table 1. Thorax 2015. [DOI: 10.1136/thoraxjnl-2015-207770.111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Correia LD, Farah H, Rassl DM, Rintoul RC, Sethi T, Littlewood TD, Evan GI, McCaughan F. S102 SOX2 initiates carcinogenesis in a novel organotypic model of bronchial dysplasia. Thorax 2015. [DOI: 10.1136/thoraxjnl-2015-207770.108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Pipinikas CP, Kiropoulos TS, Teixeira VH, Brown JM, Varanou A, Falzon M, Capitanio A, Bottoms SE, Carroll B, Navani N, McCaughan F, George JP, Giangreco A, Wright NA, McDonald SAC, Graham TA, Janes SM. Cell migration leads to spatially distinct but clonally related airway cancer precursors. Thorax 2014; 69:548-57. [PMID: 24550057 PMCID: PMC4033139 DOI: 10.1136/thoraxjnl-2013-204198] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [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: 07/17/2013] [Revised: 01/09/2014] [Accepted: 01/24/2014] [Indexed: 11/04/2022]
Abstract
BACKGROUND Squamous cell carcinoma of the lung is a common cancer with 95% mortality at 5 years. These cancers arise from preinvasive lesions, which have a natural history of development progressing through increasing severity of dysplasia to carcinoma in situ (CIS), and in some cases, ending in transformation to invasive carcinoma. Synchronous preinvasive lesions identified at autopsy have been previously shown to be clonally related. METHODS Using autofluorescence bronchoscopy that allows visual observation of preinvasive lesions within the upper airways, together with molecular profiling of biopsies using gene sequencing and loss-of-heterozygosity analysis from both preinvasive lesions and from intervening normal tissue, we have monitored individual lesions longitudinally and documented their visual, histological and molecular relationship. RESULTS We demonstrate that rather than forming a contiguous field of abnormal tissue, clonal CIS lesions can develop at multiple anatomically discrete sites over time. Further, we demonstrate that patients with CIS in the trachea have invariably had previous lesions that have migrated proximally, and in one case, into the other lung over a period of 12 years. CONCLUSIONS Molecular information from these unique biopsies provides for the first time evidence that field cancerisation of the upper airways can occur through cell migration rather than via local contiguous cellular expansion as previously thought. Our findings urge a clinical strategy of ablating high-grade premalignant airway lesions with subsequent attentive surveillance for recurrence in the bronchial tree.
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Affiliation(s)
| | - Theodoros S Kiropoulos
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
- Department of Respiratory Medicine, University of Thessaly School of Medicine, Larissa, Greece
| | - Vitor H Teixeira
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - James M Brown
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Aikaterini Varanou
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Mary Falzon
- Department of Pathology, University College London, London, UK
| | | | - Steven E Bottoms
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Bernadette Carroll
- Department of Thoracic Medicine, University College London Hospital, London, UK
| | - Neal Navani
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
- Department of Thoracic Medicine, University College London Hospital, London, UK
| | - Frank McCaughan
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Asthma, Allergy and Respiratory Science, King's College London, London, UK
| | - Jeremy P George
- Department of Thoracic Medicine, University College London Hospital, London, UK
| | - Adam Giangreco
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Nicholas A Wright
- Histopathology Laboratory, Cancer Research UK London Research Institute, London, UK
- Centre for Digestive Diseases, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Stuart A C McDonald
- Histopathology Laboratory, Cancer Research UK London Research Institute, London, UK
- Centre for Digestive Diseases, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Trevor A Graham
- Histopathology Laboratory, Cancer Research UK London Research Institute, London, UK
- Centre for Evolution and Cancer, UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
| | - Sam M Janes
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
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Heitmann A, Cruse G, Breen R, Santis G, Whitaker D, McCaughan F, Barker R. 50 Mediastinal staging of lung cancer at King's College Hospital – an audit over 2 years. Lung Cancer 2014. [DOI: 10.1016/s0169-5002(14)70050-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Gao F, Dua D, Pfeifer E, Farah H, Tobal K, Cane P, Spicer J, McCaughan F. 6 Microdroplet digital PCR in detecting mutational events in cell-free DNA in patients with lung cancer – a pilot study. Lung Cancer 2014. [DOI: 10.1016/s0169-5002(14)70007-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Day E, Poulogiannis G, McCaughan F, Mulholland S, Arends MJ, Ibrahim AEK, Dear PH. IRS2 is a candidate driver oncogene on 13q34 in colorectal cancer. Int J Exp Pathol 2013; 94:203-11. [PMID: 23594372 PMCID: PMC3664965 DOI: 10.1111/iep.12021] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 02/18/2013] [Indexed: 12/31/2022] Open
Abstract
Copy number alterations are frequently found in colorectal cancer (CRC), and recurrent gains or losses are likely to correspond to regions harbouring genes that promote or impede carcinogenesis respectively. Gain of chromosome 13q is common in CRC but, because the region of gain is frequently large, identification of the driver gene(s) has hitherto proved difficult. We used array comparative genomic hybridization to analyse 124 primary CRCs, demonstrating that 13q34 is a region of gain in 35% of CRCs, with focal gains in 4% and amplification in a further 1.6% of cases. To reduce the number of potential driver genes to consider, it was necessary to refine the boundaries of the narrowest copy number changes seen in this series and hence define the minimal copy region (MCR). This was performed using molecular copy-number counting, identifying IRS2 as the only complete gene, and therefore the likely driver oncogene, within the refined MCR. Analysis of available colorectal neoplasia data sets confirmed IRS2 gene gain as a common event. Furthermore, IRS2 protein and mRNA expression in colorectal neoplasia was assessed and was positively correlated with progression from normal through adenoma to carcinoma. In functional in vitro experiments, we demonstrate that deregulated expression of IRS2 activates the oncogenic PI3 kinase pathway and increases cell adhesion, both characteristics of invasive CRC cells. Together, these data identify IRS2 as a likely driver oncogene in the prevalent 13q34 region of gain/amplification and suggest that IRS2 over-expression may provide an additional mechanism of PI3 kinase pathway activation in CRC.
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Day E, Dear PH, McCaughan F. Digital PCR strategies in the development and analysis of molecular biomarkers for personalized medicine. Methods 2013; 59:101-7. [DOI: 10.1016/j.ymeth.2012.08.001] [Citation(s) in RCA: 147] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 07/30/2012] [Accepted: 08/02/2012] [Indexed: 12/18/2022] Open
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Day E, McCaughan F, Ibrahim A, Arends M, Deara P. Appearances can be deceiving – genetic heterogeneity in the colon of cancer patients. Int J Surg 2012. [DOI: 10.1016/j.ijsu.2012.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Abstract
Rearrangements of the genome can be detected by microarray methods and massively parallel sequencing, which identify copy-number alterations and breakpoint junctions, but these techniques are poorly suited to reconstructing the long-range organization of rearranged chromosomes, for example, to distinguish between translocations and insertions. The single-DNA-molecule technique HAPPY mapping is a method for mapping normal genomes that should be able to analyse genome rearrangements, i.e. deviations from a known genome map, to assemble rearrangements into a long-range map. We applied HAPPY mapping to cancer cell lines to show that it could identify rearrangement of genomic segments, even in the presence of normal copies of the genome. We could distinguish a simple interstitial deletion from a copy-number loss at an inversion junction, and detect a known translocation. We could determine whether junctions detected by sequencing were on the same chromosome, by measuring their linkage to each other, and hence map the rearrangement. Finally, we mapped an uncharacterized reciprocal translocation in the T-47D breast cancer cell line to about 2 kb and hence cloned the translocation junctions. We conclude that HAPPY mapping is a versatile tool for determining the structure of rearrangements in the human genome.
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Affiliation(s)
- Jessica C M Pole
- Hutchison/MRC Research Centre and Department of Pathology, University of Cambridge, Hills Road, Cambridge, CB2 0XZ, UK
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McCaughan F, Pipinikas CP, Janes SM, George PJ, Rabbitts PH, Dear PH. Genomic evidence of pre-invasive clonal expansion, dispersal and progression in bronchial dysplasia. J Pathol 2011; 224:153-9. [PMID: 21506132 PMCID: PMC3378694 DOI: 10.1002/path.2887] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [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: 12/29/2010] [Revised: 02/09/2011] [Accepted: 02/28/2011] [Indexed: 12/23/2022]
Abstract
The term ‘field cancerization’ is used to describe an epithelial surface that has a propensity to develop cancerous lesions, and in the case of the aerodigestive tract this is often as a result of chronic exposure to carcinogens in cigarette smoke 1, 2. The clinical endpoint is the development of multiple tumours, either simultaneously or sequentially in the same epithelial surface. The mechanisms underlying this process remain unclear; one possible explanation is that the epithelium is colonized by a clonal population of cells that are at increased risk of progression to cancer. We now address this possibility in a short case series, using individual genomic events as molecular biomarkers of clonality. In squamous lung cancer the most common genomic aberration is 3q amplification. We use a digital PCR technique to assess the clonal relationships between multiple biopsies in a longitudinal bronchoscopic study, using amplicon boundaries as markers of clonality. We demonstrate that clonality can readily be defined by these analyses and confirm that field cancerization occurs at a pre-invasive stage and that pre-invasive lesions and subsequent cancers are clonally related. We show that while the amplicon boundaries can be shared between different biopsies, the degree of 3q amplification and the internal structure of the 3q amplicon varies from lesion to lesion. Finally, in this small cohort, the degree of 3q amplification corresponds to clinical progression. Copyright © 2011 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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McCaughan F, Pole JCM, Bankier AT, Konfortov BA, Carroll B, Falzon M, Rabbitts TH, George PJ, Dear PH, Rabbitts PH. Progressive 3q amplification consistently targets SOX2 in preinvasive squamous lung cancer. Am J Respir Crit Care Med 2010; 182:83-91. [PMID: 20299530 DOI: 10.1164/rccm.201001-0005oc] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Amplification of distal 3q is the most common genomic aberration in squamous lung cancer (SQC). SQC develops in a multistage progression from normal bronchial epithelium through dysplasia to invasive disease. Identifying the key driver events in the early pathogenesis of SQC will facilitate the search for predictive molecular biomarkers and the identification of novel molecular targets for chemoprevention and therapeutic strategies. For technical reasons, previous attempts to analyze 3q amplification in preinvasive lesions have focused on small numbers of predetermined candidate loci rather than an unbiased survey of copy-number variation. OBJECTIVES To perform a detailed analysis of the 3q amplicon in bronchial dysplasia of different histological grades. METHODS We use molecular copy-number counting (MCC) to analyze the structure of chromosome 3 in 19 preinvasive bronchial biopsy specimens from 15 patients and sequential biopsy specimens from 3 individuals. MEASUREMENTS AND MAIN RESULTS We demonstrate that no low-grade lesions, but all high-grade lesions, have 3q amplification. None of seven low-grade lesions progressed clinically, whereas 8 of 10 patients with high-grade disease progressed to cancer. We identify a minimum commonly amplified region on chromosome 3 consisting of 17 genes, including 2 known oncogenes, SOX2 and PIK3CA. We confirm that both genes are amplified in all high-grade dysplastic lesions tested. We further demonstrate, in three individuals, that the clinical progression of high-grade preinvasive disease is associated with incremental amplification of SOX2, suggesting this promotes malignant progression. CONCLUSIONS These findings demonstrate progressive 3q amplification in the evolution of preinvasive SQC and implicate SOX2 as a key target of this dynamic process.
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Affiliation(s)
- Frank McCaughan
- Centre for Respiratory Research, Royal Free and University College Medical School, London, United Kingdom.
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Abstract
The term 'single-molecule genomics' (SMG) describes a group of molecular methods in which single molecules are detected or sequenced. The focus on the analysis of individual molecules distinguishes these techniques from more traditional methods, in which template DNA is cloned or PCR-amplified prior to analysis. Although technically challenging, the analysis of single molecules has the potential to play a major role in the delivery of truly personalized medicine. The two main subgroups of SMG methods are single-molecule digital PCR and single-molecule sequencing. Single-molecule PCR has a number of advantages over competing technologies, including improved detection of rare genetic variants and more precise analysis of copy-number variation, and is more easily adapted to the often small amount of material that is available in clinical samples. Single-molecule sequencing refers to a number of different methods that are mainly still in development but have the potential to make a huge impact on personalized medicine in the future.
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Affiliation(s)
- Frank McCaughan
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.
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McCaughan F, Darai-Ramqvist E, Bankier AT, Konfortov BA, Foster N, George PJ, Rabbitts TH, Kost-Alimova M, Rabbitts PH, Dear PH. Microdissection molecular copy-number counting (microMCC)--unlocking cancer archives with digital PCR. J Pathol 2008; 216:307-16. [PMID: 18773450 DOI: 10.1002/path.2413] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Most cancer genomes are characterized by the gain or loss of copies of some sequences through deletion, amplification or unbalanced translocations. Delineating and quantifying these changes is important in understanding the initiation and progression of cancer, in identifying novel therapeutic targets, and in the diagnosis and prognosis of individual patients. Conventional methods for measuring copy-number are limited in their ability to analyse large numbers of loci, in their dynamic range and accuracy, or in their ability to analyse small or degraded samples. This latter limitation makes it difficult to access the wealth of fixed, archived material present in clinical collections, and also impairs our ability to analyse small numbers of selected cells from biopsies. Molecular copy-number counting (MCC), a digital PCR technique, has been used to delineate a non-reciprocal translocation using good quality DNA from a renal carcinoma cell line. We now demonstrate microMCC, an adaptation of MCC which allows the precise assessment of copy number variation over a significant dynamic range, in template DNA extracted from formalin-fixed paraffin-embedded clinical biopsies. Further, microMCC can accurately measure copy number variation at multiple loci, even when applied to picogram quantities of grossly degraded DNA extracted after laser capture microdissection of fixed specimens. Finally, we demonstrate the power of microMCC to precisely interrogate cancer genomes, in a way not currently feasible with other methodologies, by defining the position of a junction between an amplified and non-amplified genomic segment in a bronchial carcinoma. This has tremendous potential for the exploitation of archived resources for high-resolution targeted cancer genomics and in the future for interrogating multiple loci in cancer diagnostics or prognostics.
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Affiliation(s)
- F McCaughan
- Centre for Respiratory Research, Department of Medicine, Royal Free and University College Medical School, The Rayne Institute, London WC1E 6JJ, UK
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McCaughan F, Holmes A, Lynn WA, Friedland JS. Mycobacterium tuberculosis infection complicated by Eales disease with peripheral neuropathy. Clin Infect Dis 2002; 35:e89-91. [PMID: 12355398 DOI: 10.1086/342888] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2002] [Revised: 05/15/2002] [Indexed: 11/03/2022] Open
Abstract
Eales disease, which is reported mainly in patients from the Indian subcontinent, is characterized by ophthalmic abnormalities that are sometimes followed by neurologic sequelae, and it is associated with previous Mycobacterium tuberculosis infection. We describe the first patient, to our knowledge, to receive a diagnosis of active tuberculosis and concurrent, severe neurological Eales disease, including peripheral neuropathy. The patient recovered completely after receiving steroid therapy.
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Affiliation(s)
- Frank McCaughan
- Department of Infectious Diseases, Imperial College, Hammersmith Hospital, London, W12 0NN, United Kingdom
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