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Golovina E, Fadason T, Jaros RK, Kumar H, John J, Burrowes K, Tawhai M, O'Sullivan JM. De novo discovery of traits co-occurring with chronic obstructive pulmonary disease. Life Sci Alliance 2023; 6:6/3/e202201609. [PMID: 36574990 PMCID: PMC9795035 DOI: 10.26508/lsa.202201609] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 12/28/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a heterogeneous group of chronic lung conditions. Genome-wide association studies have identified single-nucleotide polymorphisms (SNPs) associated with COPD and the co-occurring conditions, suggesting common biological mechanisms underlying COPD and these co-occurring conditions. To identify them, we have integrated information across different biological levels (i.e., genetic variants, lung-specific 3D genome structure, gene expression and protein-protein interactions) to build lung-specific gene regulatory and protein-protein interaction networks. We have queried these networks using disease-associated SNPs for COPD, unipolar depression and coronary artery disease. COPD-associated SNPs can control genes involved in the regulation of lung or pulmonary function, asthma, brain region volumes, cortical surface area, depressed affect, neuroticism, Parkinson's disease, white matter microstructure and smoking behaviour. We describe the regulatory connections, genes and biochemical pathways that underlay these co-occurring trait-SNP-gene associations. Collectively, our findings provide new avenues for the investigation of the underlying biology and diverse clinical presentations of COPD. In so doing, we identify a collection of genetic variants and genes that may aid COPD patient stratification and treatment.
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Affiliation(s)
| | - Tayaza Fadason
- Liggins Institute, University of Auckland, Auckland, New Zealand.,Maurice Wilkins Centre, University of Auckland, Auckland, New Zealand
| | - Rachel K Jaros
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Haribalan Kumar
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Joyce John
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Kelly Burrowes
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Merryn Tawhai
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Justin M O'Sullivan
- Liggins Institute, University of Auckland, Auckland, New Zealand .,Maurice Wilkins Centre, University of Auckland, Auckland, New Zealand.,MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK.,Garvan Institute of Medical Research, Sydney, Australia.,Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
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2
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Hong SW, Park J, Jeong H, Kim M. Evaluation of the microbiome composition in particulate matter inside and outside of pig houses. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2021; 63:640-650. [PMID: 34189511 PMCID: PMC8203996 DOI: 10.5187/jast.2021.e52] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 02/24/2021] [Accepted: 02/28/2021] [Indexed: 12/12/2022]
Abstract
Particulate matter (PM) produced in pig houses may contain microbes which can
spread by airborne transmission, and PM and microbes in PM adversely affect
human and animal health. To investigate the microbiome in PM from pig houses,
nine PM samples were collected in summer 2020 inside and outside of pig houses
located in Jangseong-gun, Jeollanam-do Province, Korea, comprising three PM
samples from within a nursery pig house (I-NPH), three samples from within a
finishing pig house (I-FPH), and three samples from outside of the pig houses
(O-PH). Microbiomes were analyzed using 16S rRNA gene amplicon sequencing.
Firmicutes was the most dominant phylum and accounted for 64.8%–97.5% of
total sequences in all the samples, followed by Proteobacteria
(1.4%–21.8%) and Bacteroidetes (0.3%–13.7%). In total, 31 genera
were represented by > 0.3% of all sequences, and only
Lactobacillus, Turicibacter, and
Aerococcus differed significantly among the three PM sample
types. All three genera were more abundant in the I-FPH samples than in the O-PH
samples. Alpha diversity indices did not differ significantly among the three PM
types, and a principal coordinate analysis suggested that overall microbial
communities were similar across PM types. The concentration of PM did not
significantly differ among the three PM types, and no significant correlation of
PM concentration with the abundance of any potential pathogen was observed. The
present study demonstrates that microbial composition in PM inside and outside
of pig houses is similar, indicating that most microbe-containing PM inside pig
houses leaks to the outside from where it, along with microbe-containing PM on
the outside, may re-enter the pig houses. Our results may provide useful
insights regarding strategies to mitigate potential risk associated with pig
farming PM and pathogens in PM.
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Affiliation(s)
- Se-Woon Hong
- Department of Rural and Biosystems Engineering, Chonnam National University, Gwangju 61186, Korea.,Education and Research Unit for Climate-Smart Reclaimed-Tideland Agriculture, Chonnam National University, Gwangju 61186, Korea.,AgriBio Institute of Climate Change Management, Chonnam National University, Gwangju 61186, Korea
| | - Jinseon Park
- AgriBio Institute of Climate Change Management, Chonnam National University, Gwangju 61186, Korea
| | - Hanna Jeong
- Department of Rural and Biosystems Engineering, Chonnam National University, Gwangju 61186, Korea.,Education and Research Unit for Climate-Smart Reclaimed-Tideland Agriculture, Chonnam National University, Gwangju 61186, Korea
| | - Minseok Kim
- AgriBio Institute of Climate Change Management, Chonnam National University, Gwangju 61186, Korea.,Department of Animal Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea
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Lassmann-Klee PG, Sundblad BM, Malmberg LP, Sovijärvi ARA, Piirilä P. Measurement of bronchial hyperreactivity: comparison of three Nordic dosimetric methods. Scandinavian Journal of Clinical and Laboratory Investigation 2020; 80:222-229. [PMID: 32031428 DOI: 10.1080/00365513.2020.1719541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Clinical testing of bronchial hyperreactivity (BHR) provides valuable information in asthma diagnostics. Nevertheless, the test results depend to a great extent on the testing procedure: test substance, apparatus and protocol. In Nordic countries, three protocols predominate in the testing field: Per Malmberg, Nieminen and Sovijärvi methods. However, knowledge of their equivalence is limited. We aimed to find equivalent provocative doses (PD) to obtain similar bronchoconstrictive responses for the three protocols. We recruited 31 patients with suspected asthma and health care workers and performed BHR testing with methacholine according to Malmberg and Nieminen methods, and with histamine according to Sovijärvi. We obtained the individual response-dose slopes for each method and predicted equivalent PD values. Applying a mixed-model, we found significant differences in the mean (standard error of mean) response-dose (forced expiratory volume in one second (FEV1)%/mg): Sovijärvi 7.2 (1.5), Nieminen 13.8 (4.2) and Malmberg 26 (7.3). We found that the earlier reported cut-point values for moderate BHR and marked BHR between the Sovijärvi (PD15) and Nieminen (PD20) methods were similar, but with the Malmberg method a significant bronchoconstrictive reaction was measured with lower PD20 values. We obtained a relationship between slope values and PD (mg) between different methods, useful in epidemiological research and clinical practice.
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Affiliation(s)
- Paul G Lassmann-Klee
- Unit of Clinical Physiology, Helsinki University Central Hospital, University of Helsinki, Helsinki, Finland
| | - Britt-Marie Sundblad
- The National Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Leo P Malmberg
- Laboratory of Clinical Physiology, Skin and Allergy Hospital, Helsinki, Finland
| | - Anssi R A Sovijärvi
- Unit of Clinical Physiology, Helsinki University Central Hospital, University of Helsinki, Helsinki, Finland
| | - Päivi Piirilä
- Unit of Clinical Physiology, Helsinki University Central Hospital, University of Helsinki, Helsinki, Finland
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Chen J, Li X, Huang C, Lin Y, Dai Q. Change of Serum Inflammatory Cytokines Levels in Patients With Chronic Obstructive Pulmonary Disease, Pneumonia and Lung Cancer. Technol Cancer Res Treat 2020; 19:1533033820951807. [PMID: 33111646 PMCID: PMC7607805 DOI: 10.1177/1533033820951807] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 07/19/2020] [Accepted: 07/28/2020] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVE This study aimed to investigate the serum inflammatory cytokines levels in patients with COPD, pneumonia and lung cancer, and assess the correlation between the levels of inflammatory cytokines levels and development of these diseases. METHODS Two hundred thirty-two patients including 114 patients with pneumonia, 76 patients with chronic obstructive pulmonary disease (COPD) and 42 patients with lung cancer, and 62 age-matched healthy volunteers as controls were enrolled. The pro-inflammatory cytokine IL-6, IL-2, IFN-γ, TNF-α, anti-inflammatory cytokines IL-4 and IL-10 in serum were analyzed by flow cytometry microsphere array (CBA). RESULTS We found that the levels of TNF-α and IL-10 in patients with lung cancer, COPD and pneumonia were significantly higher than control group. The IL-6 in the lung cancer group were significantly increased compared with the controls and COPD group, pneumonia group. IFN-γ and IL-2 levels were lower in lung cancer compared with controls and COPD group, pneumonia group. TNF-α, IL-4 and IL-10 levels were increased in patients with COPD and pneumonia compared with controls. In addition, the concentrations of IFN-γ and IL-6 were increased in acute exacerbation COPD (AECOPD) group compared with stable COPD group. CONCLUSION In conclusion, elevated TNF-α and IL-10 levels in serum may be related with lung diseases including lung cancer, COPD and pneumonia. Additionally, IFN-γ and IL-6 might be potential biomarkers for the further deterioration of lung disease patients. The increased concentrations of IFN-γ and IL-6 might be used to predict the exacerbation of COPD.
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Affiliation(s)
- Jian Chen
- Central Laboratory, Longyan First Hospital Affiliated to Fujian Medical University, Longyan, Fujian, China
| | - Xincai Li
- Central Laboratory, Longyan First Hospital Affiliated to Fujian Medical University, Longyan, Fujian, China
| | - ChaoLin Huang
- Central Laboratory, Longyan First Hospital Affiliated to Fujian Medical University, Longyan, Fujian, China
| | - Ying Lin
- Longyan Maternal and Child Health Hospital, Longyan, Fujian, China
| | - Qingfu Dai
- Central Laboratory, Longyan First Hospital Affiliated to Fujian Medical University, Longyan, Fujian, China
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Jiang S, Mohammadtursun N, Qiu J, Li Q, Sun J, Dong J. Recent advances on animal models related to chronic obstructive pulmonary disease. TRADITIONAL MEDICINE AND MODERN MEDICINE 2019. [DOI: 10.1142/s2575900019300017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) has become an important public health problem in the world. According to reports, COPD ranks fourth in the global cause of death, causing a serious economic burden on society. The pathogenesis of COPD is complex, making it difficult to simulate the pathological changes and clinical features of COPD. Moreover, the COPD animal model has an irreplaceable role in the study of etiology, pathology and treatment. It is worth noting that the risk factors for chronic obstructive pulmonary disease persist, and the economic burden of global chronic obstructive pulmonary disease is expected to continue to increase in the coming decades. Establishing a standardized, a clinically realistic COPD animal model has always been a research direction that scholars are keen on. Therefore, it is essential to establish an economical animal model. The establishment of a suitable animal model can accurately simulate the pathological features of human chronic obstructive pulmonary disease and help to develop effective interventions and treatments in a short period of time. This review integrates the experimental animal species selected in the animal models used in COPD studies. Subsequently, different methods and mechanisms for establishing animal models were summarized according to different modeling factors. Finally, the criteria for evaluating existing animal models are discussed. It is hoped that the summary of this paper will guide the establishment of relevant animal models for future COPD research.
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Affiliation(s)
- Shan Jiang
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, P. R. China
- Institutes of Integrative Medicine, Fudan University, Shanghai, P. R. China
| | - Nabjian Mohammadtursun
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, P. R. China
- Institutes of Integrative Medicine, Fudan University, Shanghai, P. R. China
- College of Xinjiang Uyghur Medicine, Hotan, Xinjiang, P. R. China
| | - Jian Qiu
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, P. R. China
- Institutes of Integrative Medicine, Fudan University, Shanghai, P. R. China
| | - Qiuping Li
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, P. R. China
- Institutes of Integrative Medicine, Fudan University, Shanghai, P. R. China
| | - Jing Sun
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, P. R. China
- Institutes of Integrative Medicine, Fudan University, Shanghai, P. R. China
| | - Jingcheng Dong
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, P. R. China
- Institutes of Integrative Medicine, Fudan University, Shanghai, P. R. China
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