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Melani AS, Croce S, Fabbri G, Messina M, Bargagli E. Inhaled Corticosteroids in Subjects with Chronic Obstructive Pulmonary Disease: An Old, Unfinished History. Biomolecules 2024; 14:195. [PMID: 38397432 PMCID: PMC10887366 DOI: 10.3390/biom14020195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/17/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is one of the major causes of disability and death. Maintenance use of inhaled bronchodilator(s) is the cornerstone of COPD pharmacological therapy, but inhaled corticosteroids (ICSs) are also commonly used. This narrative paper reviews the role of ICSs as maintenance treatment in combination with bronchodilators, usually in a single inhaler, in stable COPD subjects. The guidelines strongly recommend the addition of an ICS in COPD subjects with a history of concomitant asthma or as a step-up on the top of dual bronchodilators in the presence of hospitalization for exacerbation or at least two moderate exacerbations per year plus high blood eosinophil counts (≥300/mcl). This indication would only involve some COPD subjects. In contrast, in real life, triple inhaled therapy is largely used in COPD, independently of symptoms and in the presence of exacerbations. We will discuss the results of recent randomized controlled trials that found reduced all-cause mortality with triple inhaled therapy compared with dual inhaled long-acting bronchodilator therapy. ICS use is frequently associated with common local adverse events, such as dysphonia, oral candidiasis, and increased risk of pneumonia. Other side effects, such as systemic toxicity and unfavorable changes in the lung microbiome, are suspected mainly at higher doses of ICS in elderly COPD subjects with comorbidities, even if not fully demonstrated. We conclude that, contrary to real life, the use of ICS should be carefully evaluated in stable COPD patients.
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Affiliation(s)
- Andrea S. Melani
- Respiratory Diseases Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; (S.C.); (G.F.); (M.M.); (E.B.)
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Choi Y, Cha J, Choi S. Evaluation of penalized and machine learning methods for asthma disease prediction in the Korean Genome and Epidemiology Study (KoGES). BMC Bioinformatics 2024; 25:56. [PMID: 38308205 PMCID: PMC10837879 DOI: 10.1186/s12859-024-05677-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 01/26/2024] [Indexed: 02/04/2024] Open
Abstract
BACKGROUND Genome-wide association studies have successfully identified genetic variants associated with human disease. Various statistical approaches based on penalized and machine learning methods have recently been proposed for disease prediction. In this study, we evaluated the performance of several such methods for predicting asthma using the Korean Chip (KORV1.1) from the Korean Genome and Epidemiology Study (KoGES). RESULTS First, single-nucleotide polymorphisms were selected via single-variant tests using logistic regression with the adjustment of several epidemiological factors. Next, we evaluated the following methods for disease prediction: ridge, least absolute shrinkage and selection operator, elastic net, smoothly clipped absolute deviation, support vector machine, random forest, boosting, bagging, naïve Bayes, and k-nearest neighbor. Finally, we compared their predictive performance based on the area under the curve of the receiver operating characteristic curves, precision, recall, F1-score, Cohen's Kappa, balanced accuracy, error rate, Matthews correlation coefficient, and area under the precision-recall curve. Additionally, three oversampling algorithms are used to deal with imbalance problems. CONCLUSIONS Our results show that penalized methods exhibit better predictive performance for asthma than that achieved via machine learning methods. On the other hand, in the oversampling study, randomforest and boosting methods overall showed better prediction performance than penalized methods.
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Affiliation(s)
- Yongjun Choi
- Department of Applied Artificial Intelligence, College of Computing, Hanyang University, 55 Hanyang-daehak-ro, Sangnok-gu, Ansan, 15588, South Korea
| | - Junho Cha
- Department of Applied Artificial Intelligence, College of Computing, Hanyang University, 55 Hanyang-daehak-ro, Sangnok-gu, Ansan, 15588, South Korea
| | - Sungkyoung Choi
- Department of Applied Artificial Intelligence, College of Computing, Hanyang University, 55 Hanyang-daehak-ro, Sangnok-gu, Ansan, 15588, South Korea.
- Department of Mathematical Data Science, College of Science and Convergence Technology, Hanyang University, 55 Hanyang-daehak-ro, Sangnok-gu, Ansan, 15588, South Korea.
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3
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Partanen JJ, Häppölä P, Zhou W, Lehisto AA, Ainola M, Sutinen E, Allen RJ, Stockwell AD, Leavy OC, Oldham JM, Guillen-Guio B, Cox NJ, Hirbo JB, Schwartz DA, Fingerlin TE, Flores C, Noth I, Yaspan BL, Jenkins RG, Wain LV, Ripatti S, Pirinen M, Laitinen T, Kaarteenaho R, Myllärniemi M, Daly MJ, Koskela JT. Leveraging global multi-ancestry meta-analysis in the study of idiopathic pulmonary fibrosis genetics. CELL GENOMICS 2022; 2:100181. [PMID: 36777997 PMCID: PMC9903787 DOI: 10.1016/j.xgen.2022.100181] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/24/2022] [Accepted: 09/07/2022] [Indexed: 04/12/2023]
Abstract
The research of rare and devastating orphan diseases, such as idiopathic pulmonary fibrosis (IPF) has been limited by the rarity of the disease itself. The prognosis is poor-the prevalence of IPF is only approximately four times the incidence, limiting the recruitment of patients to trials and studies of the underlying biology. Global biobanking efforts can dramatically alter the future of IPF research. We describe a large-scale meta-analysis of IPF, with 8,492 patients and 1,355,819 population controls from 13 biobanks around the globe. Finally, we combine this meta-analysis with the largest available meta-analysis of IPF, reaching 11,160 patients and 1,364,410 population controls. We identify seven novel genome-wide significant loci, only one of which would have been identified if the analysis had been limited to European ancestry individuals. We observe notable pleiotropy across IPF susceptibility and severe COVID-19 infection and note an unexplained sex-heterogeneity effect at the strongest IPF locus MUC5B.
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Affiliation(s)
- Juulia J. Partanen
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Paavo Häppölä
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Wei Zhou
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Arto A. Lehisto
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Mari Ainola
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Pulmonary Medicine, Heart and Lung Center, Helsinki University Hospital, Helsinki, Finland
| | - Eva Sutinen
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Pulmonary Medicine, Heart and Lung Center, Helsinki University Hospital, Helsinki, Finland
| | - Richard J. Allen
- Department of Health Sciences, University of Leicester, Leicester, UK
| | | | - Olivia C. Leavy
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Justin M. Oldham
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of California, Davis, Sacramento, CA, USA
| | | | - Nancy J. Cox
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetic Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jibril B. Hirbo
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetic Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Tasha E. Fingerlin
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Carlos Flores
- Research Unit, Hospital Universitario Ntra. Sra. de Candelaria, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Faculty of Health Sciences, University of Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Imre Noth
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | | | - R. Gisli Jenkins
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Louise V. Wain
- Department of Health Sciences, University of Leicester, Leicester, UK
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Samuli Ripatti
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Matti Pirinen
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - International IPF Genetics Consortium
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Pulmonary Medicine, Heart and Lung Center, Helsinki University Hospital, Helsinki, Finland
- Department of Health Sciences, University of Leicester, Leicester, UK
- Human Genetics, Genentech, South San Francisco, CA, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of California, Davis, Sacramento, CA, USA
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetic Institute, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine, University of Colorado, Aurora, CO, USA
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
- Research Unit, Hospital Universitario Ntra. Sra. de Candelaria, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Faculty of Health Sciences, University of Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Virginia, Charlottesville, VA, USA
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
- Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Administration Center, Tampere University Hospital and University of Tampere, Tampere, Finland
- Research Unit of Internal Medicine, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
| | - Global Biobank Meta-Analysis Initiative (GBMI)
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Pulmonary Medicine, Heart and Lung Center, Helsinki University Hospital, Helsinki, Finland
- Department of Health Sciences, University of Leicester, Leicester, UK
- Human Genetics, Genentech, South San Francisco, CA, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of California, Davis, Sacramento, CA, USA
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetic Institute, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine, University of Colorado, Aurora, CO, USA
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
- Research Unit, Hospital Universitario Ntra. Sra. de Candelaria, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Faculty of Health Sciences, University of Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Virginia, Charlottesville, VA, USA
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
- Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Administration Center, Tampere University Hospital and University of Tampere, Tampere, Finland
- Research Unit of Internal Medicine, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
| | - Tarja Laitinen
- Administration Center, Tampere University Hospital and University of Tampere, Tampere, Finland
| | - Riitta Kaarteenaho
- Research Unit of Internal Medicine, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
| | - Marjukka Myllärniemi
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Pulmonary Medicine, Heart and Lung Center, Helsinki University Hospital, Helsinki, Finland
| | - Mark J. Daly
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jukka T. Koskela
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
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Hasegawa RB, Small DS. Estimating Malaria Vaccine Efficacy in the Absence of a Gold Standard Case Definition: Mendelian Factorial Design. J Am Stat Assoc 2022. [DOI: 10.1080/01621459.2020.1863222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Raiden B. Hasegawa
- Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, PA
| | - Dylan S. Small
- Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, PA
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5
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Flatby HM, Rasheed H, Ravi A, Thomas LF, Liyanarachi KV, Afset JE, DeWan AT, Brumpton BM, Hveem K, Åsvold BO, Simonsen GS, Furberg AS, Damås JK, Solligård E, Rogne T. Risk of lower respiratory tract infections: a genome-wide association study with Mendelian randomization analysis in three independent European populations. Clin Microbiol Infect 2022; 28:732.e1-732.e7. [PMID: 34763054 DOI: 10.1016/j.cmi.2021.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 10/20/2021] [Accepted: 11/01/2021] [Indexed: 12/28/2022]
Abstract
OBJECTIVE Lower respiratory tract infections (LRTIs) are a leading cause of morbidity and mortality worldwide. Few studies have previously investigated genetic susceptibility and potential risk factors for LRTI. METHODS We used data from the UK Biobank, Trøndelag Health Study (HUNT), and FinnGen to conduct a genome-wide association study (GWAS). Cases were subjects hospitalized with LRTI, and controls were subjects with no such hospitalization. We conducted stratification and interaction analyses to evaluate whether the genetic effect of LRTI differed by sex or smoking. Mendelian randomization (MR) analyses were conducted to identify the unconfounded relationship between cardiometabolic risk factors and LRTI. RESULTS A total of 25 320 cases and 575 294 controls were included. The 15q25.1 locus reached genome-wide significance in the meta-analysis (rs10519203: OR 0.94, p 3.87e-11). The protective effect of effect allele of rs10519203 was present among smokers (OR 0.90, 95%CI 0.87-0.92, p 1.38e-15) but not among never-smokers (OR 1.01, 95%CI 0.97-1.06, p 5.20e-01). In MR analyses, we found that increasing body mass index (OR 1.31, 95%CI 1.24-1.40, p 3.78e-18), lifetime smoking (OR 2.83, 95%CI 2.34-3.42, p 6.56e-27), and systolic blood pressure robustly increased the risk of LRTIs (OR 1.11, 95%CI 1.02-1.22, p 1.48e-02). CONCLUSION A region in 15q25.1 was strongly associated with LRTI susceptibility. Reduction in the prevalence of smoking, overweight, obesity, and hypertension may reduce the disease burden of LRTIs.
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Affiliation(s)
- Helene M Flatby
- Gemini Centre for Sepsis Research, Department of Circulation and Medical Imaging, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Clinic of Anaesthesia and Intensive Care, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway.
| | - Humaira Rasheed
- K.G. Jebsen Centre for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Clinic of Medicine, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Anuradha Ravi
- Gemini Centre for Sepsis Research, Department of Circulation and Medical Imaging, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Clinic of Anaesthesia and Intensive Care, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Laurent F Thomas
- K.G. Jebsen Centre for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway; BioCore-Bioinformatics Core Facility, Norwegian University of Science and Technology, Trondheim, Norway; Clinic of Laboratory Medicine, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Kristin V Liyanarachi
- Gemini Centre for Sepsis Research, Department of Circulation and Medical Imaging, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Department of Infectious Diseases, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Jan E Afset
- Gemini Centre for Sepsis Research, Department of Circulation and Medical Imaging, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway; Clinic of Laboratory Medicine, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway; Department of Medical Microbiology, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Andrew T DeWan
- Department of Chronic Disease Epidemiology and Center for Perinatal, Pediatric and Environmental Epidemiology, Yale School of Public Health, New Haven, CT, USA; Gemini Centre for Sepsis Research, Department of Circulation and Medical Imaging, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ben M Brumpton
- K.G. Jebsen Centre for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Clinic of Medicine, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway; HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway
| | - Kristian Hveem
- K.G. Jebsen Centre for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Department of Research, Innovation, and Education, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Bjørn O Åsvold
- Department of Endocrinology, Clinic of Medicine, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway; HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway; K.G. Jebsen Centre for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Gunnar S Simonsen
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway; Research Group for Host-Microbe Interaction, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Anne-Sofie Furberg
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway; Faculty of Health and Social Sciences, Molde University College, Molde, Norway
| | - Jan K Damås
- Gemini Centre for Sepsis Research, Department of Circulation and Medical Imaging, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Department of Infectious Diseases, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Erik Solligård
- Gemini Centre for Sepsis Research, Department of Circulation and Medical Imaging, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Clinic of Anaesthesia and Intensive Care, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Tormod Rogne
- Gemini Centre for Sepsis Research, Department of Circulation and Medical Imaging, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Department of Chronic Disease Epidemiology and Center for Perinatal, Pediatric and Environmental Epidemiology, Yale School of Public Health, New Haven, CT, USA; Clinic of Anaesthesia and Intensive Care, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
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Wnt/β-catenin signalling: function, biological mechanisms, and therapeutic opportunities. Signal Transduct Target Ther 2022; 7:3. [PMID: 34980884 PMCID: PMC8724284 DOI: 10.1038/s41392-021-00762-6] [Citation(s) in RCA: 517] [Impact Index Per Article: 258.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 06/28/2021] [Accepted: 07/07/2021] [Indexed: 02/06/2023] Open
Abstract
The Wnt/β-catenin pathway comprises a family of proteins that play critical roles in embryonic development and adult tissue homeostasis. The deregulation of Wnt/β-catenin signalling often leads to various serious diseases, including cancer and non-cancer diseases. Although many articles have reviewed Wnt/β-catenin from various aspects, a systematic review encompassing the origin, composition, function, and clinical trials of the Wnt/β-catenin signalling pathway in tumour and diseases is lacking. In this article, we comprehensively review the Wnt/β-catenin pathway from the above five aspects in combination with the latest research. Finally, we propose challenges and opportunities for the development of small-molecular compounds targeting the Wnt signalling pathway in disease treatment.
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7
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Suzuki M, Cole JJ, Konno S, Makita H, Kimura H, Nishimura M, Maciewicz RA. Large-scale plasma proteomics can reveal distinct endotypes in chronic obstructive pulmonary disease and severe asthma. Clin Transl Allergy 2021; 11:e12091. [PMID: 34962717 PMCID: PMC8686766 DOI: 10.1002/clt2.12091] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 11/09/2021] [Accepted: 12/07/2021] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Chronic airway diseases including chronic obstructive pulmonary disease (COPD) and asthma are heterogenous in nature and endotypes within are underpinned by complex biology. This study aimed to investigate the utility of proteomic profiling of plasma combined with bioinformatic mining, and to define molecular endotypes and expand our knowledge of the underlying biology in chronic respiratory diseases. METHODS The plasma proteome was evaluated using an aptamer-based affinity proteomics platform (SOMAscan®), representing 1238 proteins in 34 subjects with stable COPD and 51 subjects with stable but severe asthma. For each disease, we evaluated a range of clinical/demographic characteristics including bronchodilator reversibility, blood eosinophilia levels, and smoking history. We applied modified bioinformatic approaches used in the evaluation of RNA transcriptomics. RESULTS Subjects with COPD and severe asthma were distinguished from each other by 365 different protein abundancies, with differential pathway networks and upstream modulators. Furthermore, molecular endotypes within each disease could be defined. The protein groups that defined these endotypes had both known and novel biology including groups significantly enriched in exosomal markers derived from immune/inflammatory cells. Finally, we observed associations to clinical characteristics that previously have been under-explored. CONCLUSION This investigational study evaluating the plasma proteome in clinically-phenotyped subjects with chronic airway diseases provides support that such a method can be used to define molecular endotypes and pathobiological mechanisms that underpins these endotypes. It provided new concepts about the complexity of molecular pathways that define these diseases. In the longer term, such information will help to refine treatment options for defined groups.
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Affiliation(s)
- Masaru Suzuki
- Department of Respiratory Medicine, Faculty of Medicine and Graduate School of MedicineHokkaido UniversitySapporoJapan
| | - John J. Cole
- GLAZgo Discovery CentreUniversity of GlasgowGlasgowUK
| | - Satoshi Konno
- Department of Respiratory Medicine, Faculty of Medicine and Graduate School of MedicineHokkaido UniversitySapporoJapan
| | - Hironi Makita
- Department of Respiratory Medicine, Faculty of Medicine and Graduate School of MedicineHokkaido UniversitySapporoJapan
- Hokkaido Medical Research Institute for Respiratory DiseasesSapporoJapan
| | - Hiroki Kimura
- Department of Respiratory Medicine, Faculty of Medicine and Graduate School of MedicineHokkaido UniversitySapporoJapan
| | - Masaharu Nishimura
- Department of Respiratory Medicine, Faculty of Medicine and Graduate School of MedicineHokkaido UniversitySapporoJapan
- Hokkaido Medical Research Institute for Respiratory DiseasesSapporoJapan
| | - Rose A. Maciewicz
- GLAZgo Discovery CentreUniversity of GlasgowGlasgowUK
- Respiratory, Inflammation and Autoimmunity, Innovative Medicines and Early Development Biotech UnitAstraZenecaGothenburgSweden
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8
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Bertrams W, Jung AL, Maxheim M, Schmeck B. [Role of genetic factors in pneumonia and COVID-19]. PNEUMOLOGE 2021; 18:212-217. [PMID: 33716601 PMCID: PMC7934978 DOI: 10.1007/s10405-021-00385-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 02/03/2021] [Indexed: 11/25/2022]
Abstract
Die Pneumonie ist die Infektionskrankheit mit der weltweit höchsten Mortalität. Die häufigsten Erreger sind Bakterien, es gibt jedoch auch epidemisch oder pandemisch auftretende virale Lungenentzündungen durch Influenza- oder Coronaviren, wie die aktuelle Pandemie durch das SARS Coronavirus 3766 Fälle (SARS-CoV-2). Wichtige Herausforderungen liegen neben dem Auftreten von Antibiotikaresistenzen und Immunpathologien etwa in der Sepsis in der Betrachtung der Suszeptibilität individueller Patienten: Hier werden vor allen Dingen das Lebensalter, Medikamente und Komorbiditäten betrachtet. Es gibt jedoch auch klare Hinweise für genetische Einflüsse auf das individuelle Risiko, an einer Pneumonie zu erkranken oder einen schweren Verlauf der Erkrankung zu entwickeln. In diesem Beitrag wollen wir die genetischen Einflüsse auf die Pneumonie und ihre klinische Bedeutung darstellen.
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Affiliation(s)
- Wilhelm Bertrams
- Institut für Lungenforschung, Universities of Gießen and Marburg Lung Center (UGMLC), Philipps-Universität Marburg, Hans-Meerwein-Str. 2, 35043 Marburg, Deutschland
| | - Anna Lena Jung
- Institut für Lungenforschung, Universities of Gießen and Marburg Lung Center (UGMLC), Philipps-Universität Marburg, Hans-Meerwein-Str. 2, 35043 Marburg, Deutschland
| | - Michael Maxheim
- Klinik für Innere Medizin mit Schwerpunkt Pneumologie, Universitätsklinikum Marburg, Philipps-Universität Marburg, Marburg, Deutschland
| | - Bernd Schmeck
- Institut für Lungenforschung, Universities of Gießen and Marburg Lung Center (UGMLC), Philipps-Universität Marburg, Hans-Meerwein-Str. 2, 35043 Marburg, Deutschland
- Klinik für Innere Medizin mit Schwerpunkt Pneumologie, Universitätsklinikum Marburg, Philipps-Universität Marburg, Marburg, Deutschland
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9
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Chen HH, Shaw DM, Petty LE, Graff M, Bohlender RJ, Polikowsky HG, Zhong X, Kim D, Buchanan VL, Preuss MH, Shuey MM, Loos RJF, Huff CD, Cox NJ, Bastarache JA, Bastarache L, North KE, Below JE. Host genetic effects in pneumonia. Am J Hum Genet 2021; 108:194-201. [PMID: 33357513 PMCID: PMC7820802 DOI: 10.1016/j.ajhg.2020.12.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 12/02/2020] [Indexed: 01/05/2023] Open
Abstract
Given the coronavirus disease 2019 (COVID-19) pandemic, investigations into host susceptibility to infectious diseases and downstream sequelae have never been more relevant. Pneumonia is a lung disease that can cause respiratory failure and hypoxia and is a common complication of infectious diseases, including COVID-19. Few genome-wide association studies (GWASs) of host susceptibility and severity of pneumonia have been conducted. We performed GWASs of pneumonia susceptibility and severity in the Vanderbilt University biobank (BioVU) with linked electronic health records (EHRs), including Illumina Expanded Multi-Ethnic Global Array (MEGAEX)-genotyped European ancestry (EA, n= 69,819) and African ancestry (AA, n = 15,603) individuals. Two regions of large effect were identified: the CFTR locus in EA (rs113827944; OR = 1.84, p value = 1.2 × 10-36) and HBB in AA (rs334 [p.Glu7Val]; OR = 1.63, p value = 3.5 × 10-13). Mutations in these genes cause cystic fibrosis (CF) and sickle cell disease (SCD), respectively. After removing individuals diagnosed with CF and SCD, we assessed heterozygosity effects at our lead variants. Further GWASs after removing individuals with CF uncovered an additional association in R3HCC1L (rs10786398; OR = 1.22, p value = 3.5 × 10-8), which was replicated in two independent datasets: UK Biobank (n = 459,741) and 7,985 non-overlapping BioVU subjects, who are genotyped on arrays other than MEGAEX. This variant was also validated in GWASs of COVID-19 hospitalization and lung function. Our results highlight the importance of the host genome in infectious disease susceptibility and severity and offer crucial insight into genetic effects that could potentially influence severity of COVID-19 sequelae.
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Affiliation(s)
- Hung-Hsin Chen
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Douglas M Shaw
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Lauren E Petty
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Misa Graff
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Ryan J Bohlender
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77230, USA
| | - Hannah G Polikowsky
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Xue Zhong
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Daeeun Kim
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Victoria L Buchanan
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Michael H Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Megan M Shuey
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chad D Huff
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77230, USA
| | - Nancy J Cox
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Julie A Bastarache
- Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kari E North
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Jennifer E Below
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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10
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Ragland MF, Benway CJ, Lutz SM, Bowler RP, Hecker J, Hokanson JE, Crapo JD, Castaldi PJ, DeMeo DL, Hersh CP, Hobbs BD, Lange C, Beaty TH, Cho MH, Silverman EK. Genetic Advances in Chronic Obstructive Pulmonary Disease. Insights from COPDGene. Am J Respir Crit Care Med 2020; 200:677-690. [PMID: 30908940 DOI: 10.1164/rccm.201808-1455so] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a common and progressive disease that is influenced by both genetic and environmental factors. For many years, knowledge of the genetic basis of COPD was limited to Mendelian syndromes, such as alpha-1 antitrypsin deficiency and cutis laxa, caused by rare genetic variants. Over the past decade, the proliferation of genome-wide association studies, the accessibility of whole-genome sequencing, and the development of novel methods for analyzing genetic variation data have led to a substantial increase in the understanding of genetic variants that play a role in COPD susceptibility and COPD-related phenotypes. COPDGene (Genetic Epidemiology of COPD), a multicenter, longitudinal study of over 10,000 current and former cigarette smokers, has been pivotal to these breakthroughs in understanding the genetic basis of COPD. To date, over 20 genetic loci have been convincingly associated with COPD affection status, with additional loci demonstrating association with COPD-related phenotypes such as emphysema, chronic bronchitis, and hypoxemia. In this review, we discuss the contributions of the COPDGene study to the discovery of these genetic associations as well as the ongoing genetic investigations of COPD subtypes, protein biomarkers, and post-genome-wide association study analysis.
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Affiliation(s)
- Margaret F Ragland
- Division of Pulmonary Sciences and Critical Care Medicine, School of Medicine, and
| | | | | | | | - Julian Hecker
- Harvard T. H. Chan School of Public Health, Boston, Massachusetts; and
| | - John E Hokanson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, Colorado
| | | | | | - Dawn L DeMeo
- Channing Division of Network Medicine and.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Craig P Hersh
- Channing Division of Network Medicine and.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Brian D Hobbs
- Channing Division of Network Medicine and.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Christoph Lange
- Harvard T. H. Chan School of Public Health, Boston, Massachusetts; and
| | - Terri H Beaty
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
| | - Michael H Cho
- Channing Division of Network Medicine and.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Edwin K Silverman
- Channing Division of Network Medicine and.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
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11
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Halu A, Liu S, Baek SH, Hobbs BD, Hunninghake GM, Cho MH, Silverman EK, Sharma A. Exploring the cross-phenotype network region of disease modules reveals concordant and discordant pathways between chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis. Hum Mol Genet 2020; 28:2352-2364. [PMID: 30997486 DOI: 10.1093/hmg/ddz069] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 03/12/2019] [Accepted: 03/23/2019] [Indexed: 12/16/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF) are two pathologically distinct chronic lung diseases that are associated with cigarette smoking. Genetic studies have identified shared loci for COPD and IPF, including several loci with opposite directions of effect. The existence of additional shared genetic loci, as well as potential shared pathobiological mechanisms between the two diseases at the molecular level, remains to be explored. Taking a network-based approach, we built disease modules for COPD and IPF using genome-wide association studies-implicated genes. The two disease modules displayed strong disease signals in an independent gene expression data set of COPD and IPF lung tissue and showed statistically significant overlap and network proximity, sharing 19 genes, including ARHGAP12 and BCHE. To uncover pathways at the intersection of COPD and IPF, we developed a metric, NetPathScore, which prioritizes the pathways of a disease by their network overlap with another disease. Applying NetPathScore to the COPD and IPF disease modules enabled the determination of concordant and discordant pathways between these diseases. Concordant pathways between COPD and IPF included extracellular matrix remodeling, Mitogen-activated protein kinase (MAPK) signaling and ALK pathways, whereas discordant pathways included advanced glycosylation end product receptor signaling and telomere maintenance and extension pathways. Overall, our findings reveal shared molecular interaction regions between COPD and IPF and shed light on the congruent and incongruent biological processes lying at the intersection of these two complex diseases.
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Affiliation(s)
- Arda Halu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shikang Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, USA
| | - Seung Han Baek
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Brian D Hobbs
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Gary M Hunninghake
- Division of Pulmonary and Critical Care, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Amitabh Sharma
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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12
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Baschal EE, Larson ED, Bootpetch Roberts TC, Pathak S, Frank G, Handley E, Dinwiddie J, Moloney M, Yoon PJ, Gubbels SP, Scholes MA, Cass SP, Jenkins HA, Frank DN, Yang IV, Schwartz DA, Ramakrishnan VR, Santos-Cortez RLP. Identification of Novel Genes and Biological Pathways That Overlap in Infectious and Nonallergic Diseases of the Upper and Lower Airways Using Network Analyses. Front Genet 2020; 10:1352. [PMID: 32010199 PMCID: PMC6979043 DOI: 10.3389/fgene.2019.01352] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/10/2019] [Indexed: 12/16/2022] Open
Abstract
Previous genetic studies on susceptibility to otitis media and airway infections have focused on immune pathways acting within the local mucosal epithelium, and outside of allergic rhinitis and asthma, limited studies exist on the overlaps at the gene, pathway or network level between the upper and lower airways. In this report, we compared [1] pathways identified from network analysis using genes derived from published genome-wide family-based and association studies for otitis media, sinusitis, and lung phenotypes, to [2] pathways identified using differentially expressed genes from RNA-sequence data from lower airway, sinus, and middle ear tissues, in particular cholesteatoma tissue compared to middle ear mucosa. For otitis media, a large number of genes (n = 1,806) were identified as differentially expressed between cholesteatoma and middle ear mucosa, which in turn led to the identification of 68 pathways that are enriched in cholesteatoma. Two differentially expressed genes CR1 and SAA1 overlap in middle ear, sinus, and lower airway samples and are potentially novel genes for otitis media susceptibility. In addition, 56 genes were differentially expressed in both tissues from the middle ear and either sinus or lower airways. Pathways that are common in upper and lower airway diseases, whether from published DNA studies or from our RNA-sequencing analyses, include chromatin organization/remodeling, endocytosis, immune system process, protein folding, and viral process. Taken together, our findings from genetic susceptibility and differential tissue expression studies support the hypothesis that the unified airway theory wherein the upper and lower respiratory tracts act as an integrated unit also applies to infectious and nonallergic airway epithelial disease. Our results may be used as reference for identification of genes or pathways that are relevant to upper and lower airways, whether common across sites, or unique to each disease.
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Affiliation(s)
- Erin E Baschal
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Eric D Larson
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Tori C Bootpetch Roberts
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Shivani Pathak
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Gretchen Frank
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Elyse Handley
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, CO, United States
| | - Jordyn Dinwiddie
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, CO, United States
| | - Molly Moloney
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Patricia J Yoon
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, CO, United States
| | - Samuel P Gubbels
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Melissa A Scholes
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, CO, United States
| | - Stephen P Cass
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Herman A Jenkins
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Daniel N Frank
- Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Ivana V Yang
- Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - David A Schwartz
- Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Vijay R Ramakrishnan
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Regie Lyn P Santos-Cortez
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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13
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Khadzhieva MB, Kuzovlev AN, Salnikova LE. Pneumonia: host susceptibility and shared genetics with pulmonary function and other traits. Clin Exp Immunol 2019; 198:367-380. [PMID: 31487037 DOI: 10.1111/cei.13367] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2019] [Indexed: 12/16/2022] Open
Abstract
Pneumonia is a common and severe infectious lung disease. Host genetics, together with underlying medical and lifestyle conditions, determine pneumonia susceptibility. We performed a secondary analysis of the results of two genome-wide studies for pneumonia in 23andMe participants (40 600 cases/90 039 controls) (Tian et al., 2017) and UK Biobank (BB) participants (12 614 cases/324 585 controls) (via the Global Biobank Engine) and used the GTEx database to correlate the results with expression quantitative trait loci (eQTLs) data in lung and whole blood. In the 23andMe pneumonia single nucleotide polymorphism (SNP) set, 177 genotyped SNPs in the human leukocyte antigen (HLA) region satisfied the genome-wide significance level, P ≤ 5·0E-08. Several target genes (e.g. C4A, VARS2, SFTA2, HLA-C, HLA-DQA2) were unidirectionally regulated by many HLA eSNPs associated with a higher risk of pneumonia. In lung, C4A transcript was up-regulated by 291 pneumonia risk alleles spanning the half the HLA region. Among SNPs correlated with the expression levels of SFTA2 and VARS2, approximately 75% overlapped: all risk alleles were associated with VARS2 up-regulation and SFTA2 down-regulation. To find shared gene loci between pneumonia and pulmonary function (PF), we used data from the Global Biobank Engine and literature on genome-wide association studies (GWAS) of PF in general populations. Numerous gene loci overlapped between pneumonia and PF: 28·8% in the BB data set and 49·2% in the 23andMe data set. Enrichment analysis within the database of Genotypes and Phenotypes (dbGaP) and National Human Genome Research Institute-European Bioinformatics Institute (NHGRI-EBI) Catalog of pneumonia and pneumonia/PF gene sets identified significant overlap between these gene sets and genes related to inflammatory, developmental, neuropsychiatric and cardiovascular and obesity-related traits.
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Affiliation(s)
- M B Khadzhieva
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia.,N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.,Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - A N Kuzovlev
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
| | - L E Salnikova
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia.,N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.,Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
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14
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Dela Cruz CS, Wunderink RG, Christiani DC, Cormier SA, Crothers K, Doerschuk CM, Evans SE, Goldstein DR, Khatri P, Kobzik L, Kolls JK, Levy BD, Metersky ML, Niederman MS, Nusrat R, Orihuela CJ, Peyrani P, Prince AS, Ramírez JA, Ridge KM, Sethi S, Suratt BT, Sznajder JI, Tsalik EL, Walkey AJ, Yende S, Aggarwal NR, Caler EV, Mizgerd JP. Future Research Directions in Pneumonia. NHLBI Working Group Report. Am J Respir Crit Care Med 2019; 198:256-263. [PMID: 29546996 DOI: 10.1164/rccm.201801-0139ws] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Pneumonia is a complex pulmonary disease in need of new clinical approaches. Although triggered by a pathogen, pneumonia often results from dysregulations of host defense that likely precede infection. The coordinated activities of immune resistance and tissue resilience then dictate whether and how pneumonia progresses or resolves. Inadequate or inappropriate host responses lead to more severe outcomes such as acute respiratory distress syndrome and to organ dysfunction beyond the lungs and over extended time frames after pathogen clearance, some of which increase the risk for subsequent pneumonia. Improved understanding of such host responses will guide the development of novel approaches for preventing and curing pneumonia and for mitigating the subsequent pulmonary and extrapulmonary complications of pneumonia. The NHLBI assembled a working group of extramural investigators to prioritize avenues of host-directed pneumonia research that should yield novel approaches for interrupting the cycle of unhealthy decline caused by pneumonia. This report summarizes the working group's specific recommendations in the areas of pneumonia susceptibility, host response, and consequences. Overarching goals include the development of more host-focused clinical approaches for preventing and treating pneumonia, the generation of predictive tools (for pneumonia occurrence, severity, and outcome), and the elucidation of mechanisms mediating immune resistance and tissue resilience in the lung. Specific areas of research are highlighted as especially promising for making advances against pneumonia.
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Affiliation(s)
- Charles S Dela Cruz
- 1 Pulmonary, Critical Care and Sleep Medicine, Center for Pulmonary Infection Research and Treatment, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Richard G Wunderink
- 2 Pulmonary and Critical Care, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - David C Christiani
- 3 Department of Environmental Health, Harvard T. H. Chan School of Public Health, and.,4 Pulmonary and Critical Care Division, Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts
| | - Stephania A Cormier
- 5 Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana
| | - Kristina Crothers
- 6 Department of Medicine, University of Washington, Seattle, Washington
| | - Claire M Doerschuk
- 7 Marsico Lung Institute and.,8 Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Scott E Evans
- 9 Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Daniel R Goldstein
- 10 Department of Internal Medicine.,11 Department of Microbiology and Immunology, and.,12 Institute of Gerontology, University of Michigan, Ann Arbor, Michigan
| | - Purvesh Khatri
- 13 Center for Biomedical Information Research, Stanford University, Stanford, California
| | - Lester Kobzik
- 3 Department of Environmental Health, Harvard T. H. Chan School of Public Health, and
| | - Jay K Kolls
- 14 Center for Translational Research in Infection and Inflammation, Tulane School of Medicine, New Orleans, Louisiana
| | - Bruce D Levy
- 15 Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Mark L Metersky
- 16 Division of Pulmonary, Critical Care and Sleep Medicine, University of Connecticut School of Medicine, Farmington, Connecticut
| | - Michael S Niederman
- 17 Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Roomi Nusrat
- 18 Department of Medicine, Rutgers Robert Wood Johnson School of Medicine, New Brunswick, New Jersey
| | - Carlos J Orihuela
- 19 Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Paula Peyrani
- 20 Division of Infectious Diseases, Department of Medicine, University of Louisville, Louisville, Kentucky
| | - Alice S Prince
- 21 Department of Pediatrics, Columbia University, New York, New York
| | - Julio A Ramírez
- 20 Division of Infectious Diseases, Department of Medicine, University of Louisville, Louisville, Kentucky
| | - Karen M Ridge
- 2 Pulmonary and Critical Care, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Sanjay Sethi
- 22 Pulmonary, Critical Care and Sleep Medicine, Jacobs School of Medicine, University at Buffalo, State University of New York, Buffalo, New York
| | - Benjamin T Suratt
- 23 Pulmonary and Critical Care Medicine, University of Vermont College of Medicine, Burlington, Vermont
| | - Jacob I Sznajder
- 2 Pulmonary and Critical Care, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Ephraim L Tsalik
- 24 Emergency Medicine Service, Durham Veterans Affairs Health Care System, Durham, North Carolina.,25 Department of Medicine, Duke University School of Medicine, Durham, North Carolina
| | - Allan J Walkey
- 26 Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts
| | - Sachin Yende
- 27 Department of Critical Care Medicine, Clinical Research, Investigation, and Systems Modeling of Acute Illness Center, University of Pittsburgh, Pittsburgh, Pennsylvania.,28 Center for Health Equity Research and Promotion, VA Pittsburgh Healthcare System, Pittsburgh, Pennsylvania; and
| | - Neil R Aggarwal
- 29 Division of Lung Diseases, NHLBI, NIH, Bethesda, Maryland
| | | | - Joseph P Mizgerd
- 26 Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts
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15
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Bell D, Bell AH, Kupferman ME, Prieto VG, Weber RS, Hanna EY. Comparative transcriptome analysis of sinonasal inverted papilloma and associated squamous cell carcinoma: Out-HOXing developmental genes. Head Neck 2019; 41:3090-3104. [PMID: 31041828 DOI: 10.1002/hed.25795] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/26/2019] [Accepted: 04/23/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Sinonasal papilloma has a tendency toward local destruction, recurrence, and malignant transformation. This study aimed to unravel mechanisms in the malignant transformation of sinonasal papillomas using RNA-seq. METHODS The cohort consisted of 37 consecutive patients; tumor histology included a continuum spectrum (sinonasal papillomas/dysplastic/carcinomas-in-situ/invasive squamous cell carcinomas). These were microdissected and RNA was subjected to whole-transcriptome shotgun sequencing. RESULTS RNA-seq and pathway analysis showed that the highest expressed genes/potential drivers were development- and differentiation-related genes. The protein expression of six highly upregulated genes (HOXA9, EN1, DUX4, CA9, CD1a, and CK5/6) validated the RNA-seq results. HOXA9 and CA9 were found to be expressed in most of the carcinoma samples but were largely negative in papillomas; all of the CA9-negative carcinomas were recurrent. CONCLUSIONS We conclude that sinonasal carcinomas arising from papillomas are mainly defined by overexpressed developmental/homeobox genes, which provide the potential for transformation/plasticity, along with differentiation and proliferation behavior of neoplastic cells. Our results support HOXA9 and CA9 as biomarkers for carcinomas, with CA9 emerging as a predictive marker of recurrence.
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Affiliation(s)
- Diana Bell
- Department of Pathology Research, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Achim H Bell
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael E Kupferman
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Victor G Prieto
- Department of Pathology Research, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Randal S Weber
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ehab Y Hanna
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
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16
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Abstract
INTRODUCTION Chronic obstructive pulmonary disease (COPD) is a heterogeneous condition, which presents the opportunity for precision therapy based on genetics or other biomarkers. Areas covered: Alpha-1 antitrypsin deficiency, a genetic form of emphysema, provides an example of this precision approach to diagnosis and therapy. To date, research in COPD pharmacogenomics has been limited by small sample sizes, lack of accessible target tissue, failure to consider COPD subtypes, and different outcomes relevant for various medications. There have been several published genome-wide association studies and other omics studies in COPD pharmacogenomics; however, clinical implementation remains far away. There is a growing evidence base for precision prescription of inhaled corticosteroids in COPD, based on clinical phenotypes and blood biomarkers, but not yet based on pharmacogenomics. Expert opinion: At this time, there is insufficient evidence for clinical implementation of COPD pharmacogenomics. Additional genome-wide studies will be required to discover predictors of drug response and to identify genomic biomarkers of COPD subtypes, which could be targeted with subtype-directed therapies.
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Affiliation(s)
- Craig P Hersh
- a Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine , Brigham and Women's Hospital, Harvard Medical School , Boston , MA , USA
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17
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Abstract
Research and application of genomic medicine in lung disease during the past century has clarified our understanding and focus on specific phenotypes, helping clinicians tailor treatment for individual patients. Cystic fibrosis and lung cancer have been researched extensively; specific genotypes have been instrumental in precision medicine to treat these lung diseases. Asthma and chronic obstructive pulmonary disease are more complex and heterogeneous in their pathogenesis, genotypic profile, and phenotypic expression, making treatment more difficult with increasing disease severity. This article focuses on the evolving state of the science of precision medicine in lung cancer, chronic obstructive pulmonary disease, asthma, and cystic fibrosis. The body of knowledge in lung disease is growing related to pharmacogenomics, clinical guidelines, genome editing, and approaches to genomic health that will guide clinical treatment options, reduce risk, and promote health.
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Hayden LP, Hardin ME, Qiu W, Lynch DA, Strand MJ, van Beek EJ, Crapo JD, Silverman EK, Hersh CP. Asthma Is a Risk Factor for Respiratory Exacerbations Without Increased Rate of Lung Function Decline: Five-Year Follow-up in Adult Smokers From the COPDGene Study. Chest 2017; 153:368-377. [PMID: 29248621 DOI: 10.1016/j.chest.2017.11.038] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 09/19/2017] [Accepted: 11/06/2017] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Previous investigations in adult smokers from the COPDGene Study have shown that early-life respiratory disease is associated with reduced lung function, COPD, and airway thickening. Using 5-year follow-up data, we assessed disease progression in subjects who had experienced early-life respiratory disease. We hypothesized that there are alternative pathways to reaching reduced FEV1 and that subjects who had childhood pneumonia, childhood asthma, or asthma-COPD overlap (ACO) would have less lung function decline than subjects without these conditions. METHODS Subjects returning for 5-year follow-up were assessed. Childhood pneumonia was defined by self-reported pneumonia at < 16 years. Childhood asthma was defined as self-reported asthma diagnosed by a health professional at < 16 years. ACO was defined as subjects with COPD who self-reported asthma diagnosed by a health-professional at ≤ 40 years. Smokers with and those without these early-life respiratory diseases were compared on measures of disease progression. RESULTS Follow-up data from 4,915 subjects were examined, including 407 subjects who had childhood pneumonia, 323 subjects who had childhood asthma, and 242 subjects with ACO. History of childhood asthma or ACO was associated with an increased exacerbation frequency (childhood asthma, P < .001; ACO, P = .006) and odds of severe exacerbations (childhood asthma, OR, 1.41; ACO, OR, 1.42). History of childhood pneumonia was associated with increased exacerbations in subjects with COPD (absolute difference [β], 0.17; P = .04). None of these early-life respiratory diseases were associated with an increased rate of lung function decline or progression on CT scans. CONCLUSIONS Subjects who had early-life asthma are at increased risk of developing COPD and of having more active disease with more frequent and severe respiratory exacerbations without an increased rate of lung function decline over a 5-year period. TRIAL REGISTRY ClinicalTrials.gov; No. NCT00608764; https://clinicaltrials.gov.
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Affiliation(s)
- Lystra P Hayden
- Division of Respiratory Diseases, Boston Children's Hospital, Boston, MA; Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA.
| | - Megan E Hardin
- Clinical Discovery Unit, Early Clinical Discovery, AstraZeneca, Waltham, MA
| | - Weiliang Qiu
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA
| | - David A Lynch
- Department of Radiology, National Jewish Health, Denver, CO
| | - Matthew J Strand
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, CO
| | - Edwin J van Beek
- Department of Radiology, University of Edinburgh, Edinburgh, Scotland
| | - James D Crapo
- Division of Pulmonary, Critical Care, and Sleep Medicine, National Jewish Health, Denver, CO
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA
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Aherrahrou R, Aherrahrou Z, Schunkert H, Erdmann J. Coronary artery disease associated gene Phactr1 modulates severity of vascular calcification in vitro. Biochem Biophys Res Commun 2017; 491:396-402. [DOI: 10.1016/j.bbrc.2017.07.090] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 07/14/2017] [Indexed: 12/20/2022]
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Hayden LP, Cho MH, McDonald MLN, Crapo JD, Beaty TH, Silverman EK, Hersh CP. Susceptibility to Childhood Pneumonia: A Genome-Wide Analysis. Am J Respir Cell Mol Biol 2017; 56:20-28. [PMID: 27508494 DOI: 10.1165/rcmb.2016-0101oc] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Previous studies have indicated that in adult smokers, a history of childhood pneumonia is associated with reduced lung function and chronic obstructive pulmonary disease. There have been few previous investigations using genome-wide association studies to investigate genetic predisposition to pneumonia. This study aims to identify the genetic variants associated with the development of pneumonia during childhood and over the course of the lifetime. Study subjects included current and former smokers with and without chronic obstructive pulmonary disease participating in the COPDGene Study. Pneumonia was defined by subject self-report, with childhood pneumonia categorized as having the first episode at <16 years. Genome-wide association studies for childhood pneumonia (843 cases, 9,091 control subjects) and lifetime pneumonia (3,766 cases, 5,659 control subjects) were performed separately in non-Hispanic whites and African Americans. Non-Hispanic white and African American populations were combined in the meta-analysis. Top genetic variants from childhood pneumonia were assessed in network analysis. No single-nucleotide polymorphisms reached genome-wide significance, although we identified potential regions of interest. In the childhood pneumonia analysis, this included variants in NGR1 (P = 6.3 × 10-8), PAK6 (P = 3.3 × 10-7), and near MATN1 (P = 2.8 × 10-7). In the lifetime pneumonia analysis, this included variants in LOC339862 (P = 8.7 × 10-7), RAPGEF2 (P = 8.4 × 10-7), PHACTR1 (P = 6.1 × 10-7), near PRR27 (P = 4.3 × 10-7), and near MCPH1 (P = 2.7 × 10-7). Network analysis of the genes associated with childhood pneumonia included top networks related to development, blood vessel morphogenesis, muscle contraction, WNT signaling, DNA damage, apoptosis, inflammation, and immune response (P ≤ 0.05). We have identified genes potentially associated with the risk of pneumonia. Further research will be required to confirm these associations and to determine biological mechanisms. CLINICAL TRIAL REGISTRATION NCT00608764.
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Affiliation(s)
- Lystra P Hayden
- 1 Division of Respiratory Diseases, Boston Children's Hospital, Boston, Massachusetts.,2 Channing Division of Network Medicine and
| | - Michael H Cho
- 2 Channing Division of Network Medicine and.,3 Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | | | - Terri H Beaty
- 5 Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland
| | - Edwin K Silverman
- 2 Channing Division of Network Medicine and.,3 Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Craig P Hersh
- 2 Channing Division of Network Medicine and.,3 Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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