Imperial College London

Professor William Cookson

Faculty of MedicineNational Heart & Lung Institute

Professor of Genomic Medicine
 
 
 
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Contact

 

+44 (0)20 7594 2943w.cookson

 
 
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Location

 

400Guy Scadding BuildingRoyal Brompton Campus

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Summary

 

Publications

Publication Type
Year
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396 results found

Cuthbertson L, Löber U, Ish-Horowicz JS, McBrien CN, Churchward C, Parker JC, Olanipekun MT, Burke C, McGowan A, Davies GA, Lewis KE, Hopkin JM, Chung KF, O'Carroll O, Faul J, Creaser-Thomas J, Andrews M, Ghosal R, Piatek S, Willis-Owen SAG, Bartolomaeus TUP, Birkner T, Dwyer S, Kumar N, Turek EM, William Musk A, Hui J, Hunter M, James A, Dumas M-E, Filippi S, Cox MJ, Lawley TD, Forslund SK, Moffatt MF, Cookson WOCet al., 2024, Genomic attributes of airway commensal bacteria and mucosa, Communications Biology, Vol: 7, ISSN: 2399-3642

Microbial communities at the airway mucosal barrier are conserved and highly ordered, in likelihood reflecting co-evolution with human host factors. Freed of selection to digest nutrients, the airway microbiome underpins cognate management of mucosal immunity and pathogen resistance. We show here the initial results of systematic culture and whole-genome sequencing of the thoracic airway bacteria, identifying 52 novel species amongst 126 organisms that constitute 75% of commensals typically present in heathy individuals. Clinically relevant genes encode antimicrobial synthesis, adhesion and biofilm formation, immune modulation, iron utilisation, nitrous oxide (NO) metabolism and sphingolipid signalling. Using whole-genome content we identify dysbiotic features that may influence asthma and chronic obstructive pulmonary disease. We match isolate gene content to transcripts and metabolites expressed late in airway epithelial differentiation, identifying pathways to sustain host interactions with microbiota. Our results provide a systematic basis for decrypting interactions between commensals, pathogens, and mucosa in lung diseases of global significance.

Journal article

Chrisochoidou Y, Roy R, Farahmand P, Gonzalez G, Doig J, Krasny L, Rimmer EF, Willis AE, MacFarlane M, Huang PH, Carragher NO, Munro AF, Murphy DJ, Veselkov K, Seckl MJ, Moffatt MF, Cookson WOC, Pardo OEet al., 2023, Crosstalk with lung fibroblasts shapes the growth and therapeutic response of mesothelioma cells., Cell Death Dis, Vol: 14

Mesothelioma is an aggressive cancer of the mesothelial layer associated with an extensive fibrotic response. The latter is in large part mediated by cancer-associated fibroblasts which mediate tumour progression and poor prognosis. However, understanding of the crosstalk between cancer cells and fibroblasts in this disease is mostly lacking. Here, using co-cultures of patient-derived mesothelioma cell lines and lung fibroblasts, we demonstrate that fibroblast activation is a self-propagated process producing a fibrotic extracellular matrix (ECM) and triggering drug resistance in mesothelioma cells. Following characterisation of mesothelioma cells/fibroblasts signalling crosstalk, we identify several FDA-approved targeted therapies as far more potent than standard-of-care Cisplatin/Pemetrexed in ECM-embedded co-culture spheroid models. In particular, the SRC family kinase inhibitor, Saracatinib, extends overall survival well beyond standard-of-care in a mesothelioma genetically-engineered mouse model. In short, we lay the foundation for the rational design of novel therapeutic strategies targeting mesothelioma/fibroblast communication for the treatment of mesothelioma patients.

Journal article

Eastwood M, Marc ST, Gao X, Sailem H, Offman J, Karteris E, Fernandez AM, Jonigkh D, Cookson W, Moffatt M, Popat S, Minhas F, Robertus JLet al., 2023, Malignant Mesothelioma subtyping via sampling driven multiple instance prediction on tissue image and cell morphology data, ARTIFICIAL INTELLIGENCE IN MEDICINE, Vol: 143, ISSN: 0933-3657

Journal article

Cardenas PA, Cox MJ, Willis-Owen SA, Moffatt MF, Cookson WO, Cooper PJet al., 2023, Delayed acquisition of airway commensals in antibiotic naïve children and its relationship with wheezing in rural Ecuador, FRONTIERS IN ALLERGY, Vol: 4

Journal article

Tonder AJV, Ellis HC, Churchward CP, Kumar K, Ramadan N, Benson S, Parkhill J, Moffatt MF, Loebinger MR, Cookson WOCet al., 2023, <i>Mycobacterium</i><i> avium</i> complex genomics and transmission in a London hospital, EUROPEAN RESPIRATORY JOURNAL, Vol: 61, ISSN: 0903-1936

Journal article

Davies J, Hughes D, Rosenthal M, Cuthbertson L, ramadan N, Felton I, Simmonds N, Loebinger M, price H, Armstrong-James D, elborn S, Cookson W, Moffatt Met al., 2023, An invisible threat? Aspergillus positive cultures and co-infecting bacteria in airway sample, Journal of Cystic Fibrosis, Vol: 22, Pages: 320-326, ISSN: 1569-1993

BackgroundAspergillus fumigatus (Af) infection is associated with poor lung health in chronic suppurative lung diseases but often goes undetected. We hypothesised that inhibition of Af growth by Pseudomonas aeruginosa (Pa) increases the frequency of false-negative Af culture in co-infected people. Using a substantial group of cystic fibrosis (CF) airway samples, we assessed the relationship between Af and bacterial pathogens, additionally comparing fungal culture with next-generation sequencing.MethodsFrequency of co-culture was assessed for 44,554 sputum/BAL cultures, from 1,367 CF patients between the years 2010–2020. In a subgroup, Internal Transcribed Spacer-2 (ITS2) fungal sequencing was used to determine sequencing-positive, culture-negative (S+/C-) rates.ResultsPa+ samples were nearly 40% less likely (P<0.0001) than Pa- samples to culture Af, an effect that was also seen with some other Gram-negative isolates. This impact varied with Pa density and appeared to be moderated by Staphylococcus aureus co-infection. Sequencing identified Af-S+/C- for 40.1% of tested sputa. Samples with Pa had higher rates of Af-S+/C- (49.3%) than those without (35.7%; RR 1.38 [1.02–1.93], P<0.05). Af-S+/C- rate was not changed by other common bacterial infections. Pa did not affect the S+/C- rates of Candida, Exophiala or Scedosporium.ConclusionsPa/ Af co-positive cultures are less common than expected in CF. Our findings suggest an Af-positive culture is less likely in the presence of Pa. Interpretation of negative cultures should be cautious, particularly in Pa-positive samples, and a companion molecular diagnostic could be useful. Further work investigating mechanisms, alternative detection techniques and other chronic suppurative lung diseases is needed.

Journal article

Zhang YZ, Nicholson AG, Ly F, Rice A, Robertus JL, Lim E, Begum S, Buderi S, Anikin V, Finch J, Asadi N, Popat S, McDonald F, De Sousa P, Molyneaux PL, Moffatt MF, Cookson WO, Kemp S, Shah PL, Ridge CA, Desai S, Padley S, Devaraj A, Jordan S, Beddow E, Brambilla Cet al., 2022, Prediction of Clinically Significant Pathological Upstaging in Resected Lung Cancer: Insight from COVID-19 Pandemic (1st wave), Publisher: ELSEVIER SCIENCE INC, Pages: S112-S114, ISSN: 1556-0864

Conference paper

Zhang YZ, Sherlock S, Brambilla C, MacMahon S, Thompson L, Rice A, Robertus JL, Lim E, Begum S, Buderi S, Jordan S, Anikin V, Finch J, Asadi N, Beddow E, McDonald F, Antoniou G, Moffatt MF, Cookson WO, Shah PL, Devaraj A, Popat S, Nicholson AGet al., 2022, Adenocarcinoma Grade Correlates with PD-L1 and TP53, but not EGFR/KRAS Status and Diagnostic Yield: Analysis of 346 Cases, Publisher: ELSEVIER SCIENCE INC, Pages: S516-S517, ISSN: 1556-0864

Conference paper

Shah A, Hull J, Moffatt M, Cookson W, Kelleher W, Cuthbertson Let al., 2022, Evidence of immunometabolic dysregulation and airway dysbiosis in athletes susceptible to respiratory illness, EBioMedicine, Vol: 79, Pages: 1-16, ISSN: 2352-3964

BackgroundRespiratory tract infection (RTI) is a leading cause of training and in-competition time-loss in athlete health. The immune factors associated with RTI susceptibility remain unclear. In this study, we prospectively characterise host immune factors in elite athletes exhibiting RTI susceptibility.MethodsPeripheral blood lymphocyte flow cytometry phenotyping and 16S rRNA microbial sequencing of oropharyngeal swabs was performed in a prospective elite athlete cohort study (n = 121). Mass cytometry, peripheral blood mononuclear cell (PBMC) stimulation and plasma metabolic profiling was performed in age-matched highly-susceptible (HS) athletes (≥4RTI in last 18 months) (n = 22) compared to non-susceptible (NS) (≤1RTI in last 18 months) (n = 23) athletes. Findings were compared to non-athletic healthy controls (HC) (n = 19).FindingsAthletes (n = 121) had a reduced peripheral blood memory T regulatory cell compartment compared to HC (p = 0.02 (95%CI:0.1,1.0)) and reduced upper airway bacterial biomass compared to HC (p = 0.032, effect size r = 0.19). HS athletes (n = 22) had lower circulating memory T regulatory cells compared to NS (n = 23) athletes (p = 0.005 (95%CI:-1.5,-0.15)) and HC (p = 0.002 (95%CI:-1.9,-0.3) with PBMC microbial stimulation assays revealing a T-helper 2 skewed immune response compared to HC. Plasma metabolomic profiling showed differences in sphingolipid pathway metabolites (a class of lipids important in infection and inflammation regulation) in HS compared to NS athletes and HC, with sphingomyelin predictive of RTI infection susceptibility (p = 0.005).InterpretationAthletes susceptible to RTI have reduced circulating memory T regulatory cells, metabolic dysregulation of the sphingolipid pathway and evidence of upper airway bacterial dysbiosis.FundingThis study was funded by the English Institute of Sport (UK).

Journal article

Nastase A, Mandal A, Lu SK, Anbunathan H, Morris-Rosendahl D, Zhang YZ, Sun X-M, Gennatas S, Rintoul RC, Edwards M, Bowman A, Chernova T, Benepal T, Lim E, Taylor AN, Nicholson AG, Popat S, Willis AE, MacFarlane M, Lathrop M, Bowcock AM, Moffatt MF, Cookson WOCMet al., 2022, Integrated genomics point to immune vulnerabilities in pleural mesothelioma (vol 11, 19138, 2021), SCIENTIFIC REPORTS, Vol: 12, ISSN: 2045-2322

Journal article

Singanayagam A, Footitt J, Marczynski M, Radicioni G, Cross MT, Finney LJ, Trujillo-Torralbo M-B, Calderazzo MA, Zhu J, Aniscenko J, Clarke TB, Molyneaux PL, Bartlett NW, Moffatt MF, Cookson WO, Wedzicha JA, Evans CM, Boucher RC, Kesimer M, Lieleg O, Mallia P, Johnston SLet al., 2022, Airway mucins promote immunopathology in virus-exacerbated chronic obstructive pulmonary disease., Journal of Clinical Investigation, Vol: 132, Pages: 1-16, ISSN: 0021-9738

The respiratory tract surface is protected from inhaled pathogens by a secreted layer of mucus rich in mucin glycoproteins. Abnormal mucus accumulation is a cardinal feature of chronic respiratory diseases but the relationship between mucus and pathogens during exacerbations is poorly understood. We identified elevations in airway MUC5AC and MUC5B concentrations during spontaneous and experimentally-induced chronic obstructive pulmonary disease (COPD) exacerbations. MUC5AC was more sensitive to changes in expression during exacerbation and was therefore more predictably associated with virus load, inflammation, symptom severity, decrements in lung function, and secondary bacterial infections. MUC5AC was functionally related to inflammation as Muc5ac-deficient (Muc5ac-/-) mice had attenuated rhinovirus (RV)-induced airway inflammation and exogenous MUC5AC glycoprotein administration augmented inflammatory responses and increased release of extracellular adenosine triphosphate (ATP) in mice and human airway epithelial cell cultures. Hydrolysis of ATP suppressed MUC5AC augmentation of rhinovirus-induced inflammation in mice. Therapeutic suppression of mucin production using an epidermal growth factor receptor (EGFR) antagonist ameliorated immunopathology in a mouse COPD exacerbation model. The coordinated virus induction of MUC5AC and MUC5B suggests that non-Th2 mechanisms trigger mucin hypersecretion during exacerbations. Our data identifies a pro-inflammatory role for MUC5AC during viral infection and suggest that MUC5AC inhibition may ameliorate COPD exacerbations.

Journal article

Cookson W, Moffatt M, Rapeport G, Quint Jet al., 2022, A pandemic lesson for global lung diseases: exacerbations are preventable., American Journal of Respiratory and Critical Care Medicine, Vol: 205, Pages: 1271-1280, ISSN: 1073-449X

A dramatic global reduction in the incidence of common seasonal respiratory viral infections has resulted from measures to limit the transmission of SARS2-Cov-19 during the pandemic . This has been accompanied by falls reaching 50% internationally in the incidence of acute exacerbations of pre-existing chronic respiratory diseases that include asthma, Chronic Obstructive Pulmonary Disease (COPD) and Cystic Fibrosis (CF). At the same time, the incidence of acute bacterial pneumonia and sepsis has fallen steeply world-wide. Such findings demonstrate the profound impact of common respiratory viruses on the course of these global illnesses. Reduced transmission of common respiratory bacterial pathogens and their interactions with viruses appear also as central factors. This review summarises pandemic changes in exacerbation rates of asthma, COPD, Cystic Fibrosis (CF) and pneumonia. We draw attention to the substantial body of knowledge about respiratory virus infections in these conditions, and that it has not yet translated into clinical practice. Now the large-scale of benefits that could be gained by managing these pathogens is unmistakable, we suggest the field merits substantial academic and industrial investment. We consider how pandemic-inspired measures for prevention and treatment of common infections should become a cornerstone for managing respiratory diseases. This article is open access and distributed under the terms of the Creative Commons Attribution Non-Commercial No Derivatives License 4.0 (http://creativecommons.org/licenses/by-nc-nd/4.0/).

Journal article

White AD, Sibley L, Sarfas C, Morrison AL, Bewley K, Churchward C, Fotheringham S, Gkolfinos K, Gooch K, Handley A, Humphries HE, Hunter L, Kennard C, Longet S, Mabbutt A, Moffatt M, Rayner E, Tipton T, Watson R, Hall Y, Bodman-Smith M, Gleeson F, Dennis M, Salguero FJ, Carroll M, McShane H, Cookson W, Hopkin J, Sharpe Set al., 2022, Influence of Aerosol Delivered BCG Vaccination on Immunological and Disease Parameters Following SARS-CoV-2 Challenge in Rhesus Macaques, FRONTIERS IN IMMUNOLOGY, Vol: 12, ISSN: 1664-3224

Journal article

van Tonder AJ, Ellis HC, Churchward CP, Kumar K, Ramadan N, Benson S, Parkhill J, Moffatt MF, Loebinger MR, Cookson WOCet al., 2022, <i>Mycobacterium avium</i> complex (MAC) genomics and transmission in a London hospital

<jats:title>Abstract</jats:title><jats:p>Non-tuberculous mycobacteria (NTM) are ubiquitous environmental microorganisms and opportunistic pathogens in individuals with pre-existing lung conditions such as cystic fibrosis (CF) and non-CF bronchiectasis (BX). Whilst recent studies of <jats:italic>Mycobacterium abscessus</jats:italic> have identified transmission within single CF centres as well as nationally and globally, transmission of other NTM species is less well studied. We sequenced 996 Mycobacterium avium complex (MAC) isolates from CF and non-CF patients at the Royal Brompton Hospital (RBH), London. Genomic analysis was used to analyse local transmission. Epidemiological links were identified from patient records. These and previously published genomes were used to characterise global population structures. Analysis of the three predominant MAC species identified putative transmission clusters that contained patients with CF, BX and other lung conditions, although few epidemiological links could be identified. For <jats:italic>M. avium</jats:italic>, lineages were largely limited to single countries, whilst for <jats:italic>M. chimaera</jats:italic>, global transmission clusters previously associated with heater cooler units (HCUs) were found. However, the immediate ancestor of the lineage causing the major HCU-associated outbreak was a lineage already circulating in patients with pre-existing lung conditions. CF and non-CF patients shared transmission chains even in the presence of CF patient-focussed hospital control measures, although the lack of epidemiological links suggested that most transmission is indirect and may involve environmental intermediates or else asymptomatic carriage in the wider population. The major HCU-associated <jats:italic>M. chimaera</jats:italic> lineage being derived from an already circulating lineage, suggests that HCUs, while being responsible for a major global

Journal article

Cuthbertson L, James P, Habibi MS, Thwaites RS, Paras A, Chiu C, Openshaw PJM, Cookson WOC, Moffatt MFet al., 2022, Resilience of the respiratory microbiome in controlled adult RSV challenge study, European Respiratory Journal, Vol: 59, ISSN: 0903-1936

Journal article

Eastwood M, Marc ST, Gao X, Sailem H, Offman J, Karteris E, Fernandez AM, Jonigk D, Cookson W, Moffatt M, Popat S, Minhas F, Robertus JLet al., 2022, Malignant Mesothelioma Subtyping of Tissue Images via Sampling Driven Multiple Instance Prediction, 20th International Conference on Artificial Intelligence in Medicine (AIME), Publisher: SPRINGER INTERNATIONAL PUBLISHING AG, Pages: 263-272, ISSN: 0302-9743

Conference paper

Ahmed B, Cox MJ, Cuthbertson L, James P, Gardner L, Cookson W, Davies J, Moffatt M, Bush Aet al., 2021, Comparison of the airway microbiota in children with chronic suppurative lung disease, BMJ Open Respiratory Research, Vol: 8, Pages: 1-10, ISSN: 2052-4439

Rationale:The airway microbiota is important in chronic suppurative lung diseases (CSLD), such as primary ciliary dyskinesia (PCD) and cystic fibrosis (CF). This comparison has not previously been described but is important because difference between the two diseases may relate to the differing prognoses and lead to pathological insights and potentially, new treatments. Objectives:To compare the longitudinal development of the airway microbiota in children with PCD to that of CF and relate this to age and clinical status. Methods:Sixty-two age-matched children (age range 0.5–17 years) with PCD or CF (n=31 in each group) were recruited prospectively and followed for 1.1 years. Throat swabs or sputum as well as clinical information were collected at routine clinical appointments. 16S rRNA gene sequencing was performed. Measurements and Main Results:The microbiota was highly individual and more diverse in PCD and differed in community composition when compared with CF. Whilst Streptococcus was the most abundant genus in both conditions, Pseudomonas was more abundant in CF with Haemophilus more abundant in PCD (Padj=0.0005). In PCD only, an inverse relationship was seen in the relative abundance of Streptococcus and Haemophilus with age. Conclusions:Bacterial community composition differs between children with PCD and those with CF. Pseudomonas is more prevalent in CF and Haemophilus in PCD, at least until infection with Pseudomonas supervenes. Interactions between organisms, particularly members of Haemophilus, Streptococcus, and Pseudomonas genera appear important. Study of the interactions between these organisms may lead to new therapies or risk stratification.

Journal article

Cuthbertson L, Turner SEG, Jackson A, Ranson C, Loosemore M, Kelleher P, Cookson WOC, Moffatt MF, Hull JH, Shah Aet al., 2021, ELITE ATHLETES SUSCEPTIBLE TO RESPIRATORY TRACT INFECTION ARE CHARACTERISED BY REDUCED CIRCULATING MEMORY T REGULATORY CELLS, UPPER AIRWAY MICROBIAL DYSBIOSIS AND DYSREGULATION OF SPHINGOLIPID METABOLISM, Publisher: BMJ PUBLISHING GROUP, Pages: A61-A62, ISSN: 0040-6376

Conference paper

Zhu Z, Li J, Si J, Ma B, Shi H, Lv J, Cao W, Guo Y, Millwood IY, Walters RG, Lin K, Yang L, Chen Y, Du H, Yu B, Hasegawa K, Camargo CA, Moffatt MF, Cookson WOC, Chen J, Chen Z, Li L, Yu C, Liang Let al., 2021, A large-scale genome-wide association analysis of lung function in the Chinese population identifies novel loci and highlights shared genetic aetiology with obesity, European Respiratory Journal, Vol: 58, Pages: 1-16, ISSN: 0903-1936

Background Lung function is a heritable complex phenotype with obesity being one of its important risk factors. However, knowledge of their shared genetic basis is limited. Most genome-wide association studies (GWASs) for lung function have been based on European populations, limiting the generalisability across populations. Large-scale lung function GWASs in other populations are lacking.Methods We included 100 285 subjects from the China Kadoorie Biobank (CKB). To identify novel loci for lung function, single-trait GWAS analyses were performed on forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC) and FEV1/FVC in the CKB. We then performed genome-wide cross-trait analysis between lung function and obesity traits (body mass index (BMI), BMI-adjusted waist-to-hip ratio and BMI-adjusted waist circumference) to investigate the shared genetic effects in the CKB. Finally, polygenic risk scores (PRSs) of lung function were developed in the CKB and their interaction with BMI's association on lung function were examined. We also conducted cross-trait analysis in parallel with the CKB using up to 457 756 subjects from the UK Biobank (UKB) for replication and investigation of ancestry-specific effects.Results We identified nine genome-wide significant novel loci for FEV1, six for FVC and three for FEV1/FVC in the CKB. FEV1 and FVC showed significant negative genetic correlation with obesity traits in both the CKB and UKB. Genetic loci shared between lung function and obesity traits highlighted important biological pathways, including cell proliferation, embryo, skeletal and tissue development, and regulation of gene expression. Mendelian randomisation analysis suggested significant negative causal effects of BMI on FEV1 and on FVC in both the CKB and UKB. Lung function PRSs significantly modified the effect of change in BMI on change in lung function during an average follow-up of 8 years.Conclusion This large-scale GWAS of lung function identified novel loci

Journal article

Nastase A, Mandal A, Lu SK, Abunathan H, Morris-Rosendahl D, Zhand YZ, Sun X-M, Gennatas S, Rintoul R, Edwards M, Bowman A, Chernova T, Benepal T, Lim E, Newman Taylor A, Nicholson A, Popat S, Willis A, MacFarlane M, Lathrop M, Bowcock A, Moffatt M, Cookson Wet al., 2021, Integrated genomics point to immune vulnerabilities in pleural mesothelioma, Scientific Reports, Vol: 11, ISSN: 2045-2322

Pleural mesothelioma is an aggressive malignancy with limited effective therapies. In order to identify therapeutic targets, we integrated SNP genotyping, sequencing and transcriptomics from tumours and low-passage patient-derived cells. Previously unrecognised deletions of SUFU locus (10q24.32), observed in 21% of 118 tumours, resulted in disordered expression of transcripts from Hedgehog pathways and the T-cell synapse including VISTA. Co-deletion of Interferon Type I genes and CDKN2A was present in half of tumours and was a predictor of poor survival. We also found previously unrecognised deletions in RB1 in 26% of cases and show sub-micromolar responses to downstream PLK1, CHEK1 and Aurora Kinase inhibitors in primary mesothelioma cells. Defects in Hippo pathways that included RASSF7 amplification and NF2 or LATS1/2 mutations were present in 50% of tumours and were accompanied by micromolar responses to the YAP1 inhibitor Verteporfin. Our results suggest new therapeutic avenues in mesothelioma and indicate targets and biomarkers for immunotherapy.

Journal article

Cookson W, Turek E, Moffatt M, Cox M, Hunter M, Hui J, James P, Willis-Owen S, Cuthbertson L, James A, Musk Aet al., 2021, Airway microbial communities, smoking and asthma in a general population sample, EBioMedicine, Vol: 71, Pages: 1-9, ISSN: 2352-3964

BackgroundNormal airway microbial communities play a central role in respiratory health but arepoorly characterized. Cigarette smoking is the dominant global environmental influenceon lung function, and asthma has become the most prevalent chronic respiratorydisease worldwide. Both conditions have major microbial components that areincompletely defined.MethodsWe investigated airway bacterial communities in a general population sample of 529Australian adults. Posterior oropharyngeal swabs were analyzed by sequencing of the16S rRNA gene. The microbiota were characterized according to their prevalence,abundance and network memberships.FindingsThe microbiota were similar across the general population, and were stronglyorganized into co-abundance networks. Smoking associated with diversity loss,negative effects on abundant taxa, profound alterations to network structure andexpansion of Streptococcus spp. By contrast, the asthmatic microbiota wereselectively affected by an increase in Neisseria spp. and by reduced numbers of lowabundance but prevalent organisms.InterpretationOur study shows that the healthy airway microbiota in this population were containedwithin a highly structured ecosystem, suggesting balanced relationships between themicrobiome and human host factors. The marked abnormalities in smokers maycontribute to chronic obstructive pulmonary disease (COPD) and lung cancer. Thenarrow spectrum of abnormalities in asthmatics encourages investigation of damagingand protective effects of specific bacteria.

Journal article

Domingo-Sabugo C, Willis-Owen SAG, Mandal A, Nastase A, Dwyer S, Brambilla C, Gálvez JH, Zhuang Q, Popat S, Eveleigh R, Munter M, Lim E, Nicholson AG, Lathrop M, Cookson WOC, Moffatt MFet al., 2021, Distinct pancreatic and neuronal Lung Carcinoid molecular subtypes revealed by integrative omic analysis

<jats:title>Summary</jats:title><jats:p>Lung Carcinoids (L-CDs) are uncommon low-grade neuroendocrine tumours that are only recently becoming characterised at the molecular level. Notably data on the molecular events that precipitate altered gene expression programmes are very limited. Here we have identified two discrete L-CD subtypes from transcriptomic and whole-genome DNA methylation data, and comprehensively defined their molecular profiles using Whole-Exome Sequencing (WES) and Single Nucleotide Polymorphism (SNP) genotyping. Subtype (Group) 1 features upregulation of neuronal markers (L-CD-NeU) and is characterised by focal spindle cell morphology, peripheral location (71%), high mutational load (<jats:italic>P</jats:italic>=3.4×10<jats:sup>−4</jats:sup>), recurrent copy number alterations and is enriched for Atypical Lung Carcinoids. Group 2 (L-CD-PanC) are centrally located and feature upregulation of pancreatic and metabolic pathway genes concordant with promoter hypomethylation of beta cell and genes related to insulin secretion (<jats:italic>P</jats:italic>&lt;1×10<jats:sup>−6</jats:sup>). L-CD-NeU tumours harbour mutations in chromatin remodelling and in SWI/SNF complex members, while L-CD-PanC tumours show aflatoxin mutational signatures and significant DNA methylation loss genome-wide, particularly enriched in repetitive elements (<jats:italic>P</jats:italic>&lt;2.2 × 10<jats:sup>−16</jats:sup>). Our findings provide novel insights into the distinct mechanisms of epigenetic dysregulation in these lung malignancies, potentially opening new avenues for biomarker selection and treatment in L-CD patients.</jats:p>

Journal article

Willis-Owen S, Domingo Sabugo C, Starren E, Liang L, Freidin M, Arseneault M, Zhang Y, Kiong Lu S, Popat S, Lim E, Nicholson A, Riazalhosseini Y, Lathrop M, Cookson W, Moffatt Met al., 2021, Y disruption, autosomal hypomethylation and poor male lung cancer survival, Scientific Reports, Vol: 11, ISSN: 2045-2322

Lung cancer is the most frequent cause of cancer death worldwide. It affects more men than women, and men generally have worse survival outcomes. We compared gene co-expression networks in affected and unaffected lung tissue from 126 consecutive patients with Stage IA–IV lung cancer undergoing surgery with curative intent. We observed marked degradation of a sex-associated transcription network in tumour tissue. This disturbance, detected in 27.7% of male tumours in the discovery dataset and 27.3% of male tumours in a further 123-sample replication dataset, was coincident with partial losses of the Y chromosome and extensive autosomal DNA hypomethylation. Central to this network was the epigenetic modifier and regulator of sexually dimorphic gene expression, KDM5D. After accounting for prognostic and epidemiological covariates including stage and histology, male patients with tumour KDM5D deficiency showed a significantly increased risk of death (Hazard Ratio [HR] 3.80, 95% CI 1.40–10.3, P = 0.009). KDM5D deficiency was confirmed as a negative prognostic indicator in a further 1100 male lung tumours (HR 1.67, 95% CI 1.4–2.0, P = 1.2 × 10–10). Our findings identify tumour deficiency of KDM5D as a prognostic marker and credible mechanism underlying sex disparity in lung cancer.

Journal article

Laura G, Liu Y, Fernandes K, Willis-Owen SAG, Ito K, Cookson WO, Moffatt MF, Zhang Yet al., 2021, ORMDL3 regulates poly I:C induced inflammatory responses in airway epithelial cells, BMC Pulmonary Medicine, Vol: 21, ISSN: 1471-2466

Background:Oroscomucoid 3 (ORMDL3) has been linked to susceptibility of childhood asthma and respiratory viral infection. Polyinosinic-polycytidylic acid (poly I:C) is a synthetic analog of viral double-stranded RNA, a toll-like receptor 3 (TLR3) ligand and mimic of viral infection.Methods:To investigate the functional role of ORMDL3 in the poly I:C-induced inflammatory response in airway epithelial cells, ORMDL3 knockdown and over-expression models were established in human A549 epithelial cells and primary normal human bronchial epithelial (NHBE) cells. The cells were stimulated with poly I:C or the Th17 cytokine IL-17A. IL-6 and IL-8 levels in supernatants, mRNA levels of genes in the TLR3 pathway and inflammatory response from cell pellets were measured. ORMDL3 knockdown models in A549 and BEAS-2B epithelial cells were then infected with live human rhinovirus (HRV16) followed by IL-6 and IL-8 measurement.Results:ORMDL3 knockdown and over-expression had little influence on the transcript levels of TLR3 in airway epithelial cells. Time course studies showed that ORMDL3-deficient A549 and NHBE cells had an attenuated IL-6 and IL-8 response to poly I:C stimulation. A549 and NHBE cells over-expressing ORMDL3 released relatively more IL-6 and IL-8 following poly I:C stimulation. IL-17A exhibited a similar inflammatory response in ORMDL3 knockdown and over-expressing cells, but co-stimulation of poly I:C and IL-17A did not significantly enhance the IL-6 and IL-8 response. Transcript abundance of IFNB following poly I:C stimulation was not significantly altered by ORMDL3 knockdown or over-expression. Dampening of the IL-6 response by ORMDL3 knockdown was confirmed in HRV16 infected BEAS-2B and A549 cells.Conclusions:ORMDL3 regulates the viral inflammatory response in airway epithelial cells via mechanisms independent of the TLR3 pathway.

Journal article

Cuthbertson L, Felton I, James P, Cox MJ, Bilton D, Schelenz S, Loebinger MR, Cookson WOC, Simmonds NJ, Moffatt MFet al., 2021, The fungal airway microbiome in cystic fibrosis and non-cystic fibrosis bronchiectasis, Journal of Cystic Fibrosis, Vol: 20, Pages: 295-302, ISSN: 1569-1993

BackgroundThe prevalence of fungal disease in cystic fibrosis (CF) and non-CF bronchiectasis is increasing and the clinical spectrum is widening. Poor sensitivity and a lack of standard diagnostic criteria renders interpretation of culture results challenging. In order to develop effective management strategies, a more accurate and comprehensive understanding of the airways fungal microbiome is required. The study aimed to use DNA sequences from sputum to assess the load and diversity of fungi in adults with CF and non-CF bronchiectasis.MethodsNext generation sequencing of the ITS2 region was used to examine fungal community composition (n = 176) by disease and underlying clinical subgroups including allergic bronchopulmonary aspergillosis, chronic necrotizing pulmonary aspergillosis, non-tuberculous mycobacteria, and fungal bronchitis. Patients with no known active fungal disease were included as disease controls.ResultsITS2 sequencing greatly increased the detection of fungi from sputum. In patients with CF fungal diversity was lower, while burden was higher than those with non-CF bronchiectasis. The most common operational taxonomic unit (OTU) in patients with CF was Candida parapsilosis (20.4%), whereas in non-CF bronchiectasis sputum Candida albicans (21.8%) was most common. CF patients with overt fungal bronchitis were dominated by Aspergillus spp., Exophiala spp., Candida parapsilosis or Scedosporium spp.ConclusionThis study provides a framework to more accurately characterize the extended spectrum of fungal airways diseases in adult suppurative lung diseases.

Journal article

Hughes DA, Cuthbertson L, Price H, Felton I, Coates M, Simmonds NJ, Loebinger MR, Armstrong-James D, Elborn JS, Cookson WO, Moffatt MF, Davies JCet al., 2021, PSEUDOMONAS AERUGINOSA IMPAIRS GROWTH OF ASPERGILLUS FROM CF AIRWAY SAMPLES, Publisher: BMJ PUBLISHING GROUP, Pages: A159-A159, ISSN: 0040-6376

Conference paper

Feng Y-CA, Guo Y, Pain L, Lathrop GM, Laprise C, Moffatt MF, Cookson WOCM, Liang Let al., 2021, Estimating cell-type-specific DNA methylation effects in heterogeneous cellular populations, EPIGENOMICS, Vol: 13, Pages: 87-97, ISSN: 1750-1911

Journal article

Broderick DTJ, Waite DW, Marsh RL, Camargo CA, Cardenas P, Chang AB, Cookson WOC, Cuthbertson L, Dai W, Everard ML, Gervaix A, Harris JK, Hasegawa K, Hoffman LR, Hong S-J, Josset L, Kelly MS, Kim B-S, Kong Y, Li SC, Mansbach JM, Mejias A, O'Toole GA, Paalanen L, Pérez-Losada M, Pettigrew MM, Pichon M, Ramilo O, Ruokolainen L, Sakwinska O, Seed PC, van der Gast CJ, Wagner BD, Yi H, Zemanick ET, Zheng Y, Pillarisetti N, Taylor MWet al., 2021, Bacterial Signatures of Paediatric Respiratory Disease: An Individual Participant Data Meta-Analysis., Front Microbiol, Vol: 12, ISSN: 1664-302X

Introduction: The airway microbiota has been linked to specific paediatric respiratory diseases, but studies are often small. It remains unclear whether particular bacteria are associated with a given disease, or if a more general, non-specific microbiota association with disease exists, as suggested for the gut. We investigated overarching patterns of bacterial association with acute and chronic paediatric respiratory disease in an individual participant data (IPD) meta-analysis of 16S rRNA gene sequences from published respiratory microbiota studies. Methods: We obtained raw microbiota data from public repositories or via communication with corresponding authors. Cross-sectional analyses of the paediatric (<18 years) microbiota in acute and chronic respiratory conditions, with >10 case subjects were included. Sequence data were processed using a uniform bioinformatics pipeline, removing a potentially substantial source of variation. Microbiota differences across diagnoses were assessed using alpha- and beta-diversity approaches, machine learning, and biomarker analyses. Results: We ultimately included 20 studies containing individual data from 2624 children. Disease was associated with lower bacterial diversity in nasal and lower airway samples and higher relative abundances of specific nasal taxa including Streptococcus and Haemophilus. Machine learning success in assigning samples to diagnostic groupings varied with anatomical site, with positive predictive value and sensitivity ranging from 43 to 100 and 8 to 99%, respectively. Conclusion: IPD meta-analysis of the respiratory microbiota across multiple diseases allowed identification of a non-specific disease association which cannot be recognised by studying a single disease. Whilst imperfect, machine learning offers promise as a potential additional tool to aid clinical diagnosis.

Journal article

Nakanishi T, Forgetta V, Handa T, Hirai T, Mooser V, Lathrop GM, Cookson WOCM, Richards JBet al., 2020, The undiagnosed disease burden associated with alpha-1 antitrypsin deficiency genotypes, European Respiratory Journal, Vol: 56, Pages: 1-11, ISSN: 0903-1936

Alpha-1 antitrypsin deficiency (AATD), mainly due to the PI*ZZ genotype in SERPINA1, is one of the most common inherited diseases. Since it is associated with a high disease burden and partially prevented by smoking cessation, identification of PI*ZZ individuals through genotyping could improve health outcomes.We examined the frequency of the PI*ZZ genotype in individuals with and without diagnosed AATD from UK Biobank, and assessed the associations of the genotypes with clinical outcomes and mortality. A phenome-wide association study (PheWAS) was conducted to reveal disease associations with genotypes. A polygenic risk score (PRS) for forced expiratory volume in 1 s (FEV1)/forced vital capacity (FVC) ratio was used to evaluate variable penetrance of PI*ZZ.Among 458 164 European-ancestry participants in UK Biobank, 140 had the PI*ZZ genotype and only nine (6.4%, 95% CI 3.4–11.7%) of them were diagnosed with AATD. Those with PI*ZZ had a substantially higher odds of COPD (OR 8.8, 95% CI 5.8–13.3), asthma (OR 2.0, 95% CI 1.4–3.0), bronchiectasis (OR 7.3, 95%CI 3.2–16.8), pneumonia (OR 2.7, 95% CI 1.5–4.9) and cirrhosis (OR 7.8, 95% CI 2.5–24.6) diagnoses and a higher hazard of mortality (2.4, 95% CI 1.2–4.6), compared to PI*MM (wildtype) (n=398 424). These associations were stronger among smokers. PheWAS demonstrated associations with increased odds of empyema, pneumothorax, cachexia, polycythaemia, aneurysm and pancreatitis. Polygenic risk score and PI*ZZ were independently associated with FEV1/FVC <0.7 (OR 1.4 per 1-sd change, 95% CI 1.4–1.5 and OR 4.5, 95% CI 3.0–6.9, respectively).The important underdiagnosis of AATD, whose outcomes are partially preventable through smoking cession, could be improved through genotype-guided diagnosis.

Journal article

Zhang YZ, Brambilla C, Molyneaux PL, Rice A, Robertus JL, Jordan S, Lim E, Lang-Lazdunski L, Begum S, Dusmet M, Anikin V, Popat S, Cookson WO, Moffatt MF, Nicholson AGet al., 2020, Atypical mesothelial proliferation (amp) of the pleura: multidisciplinary approach, prognostic stratification and proposal of minimally invasive malignant pleural mesothelioma, Publisher: SPRINGER, Pages: S24-S25, ISSN: 0945-6317

Conference paper

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