1
|
Anim M, Sogkas G, Camacho-Ordonez N, Schmidt G, Elsayed A, Proietti M, Witte T, Grimbacher B, Atschekzei F. Novel hypermorphic variants in IRF2BP2 identified in patients with common variable immunodeficiency and autoimmunity. Clin Immunol 2024; 266:110326. [PMID: 39059757 DOI: 10.1016/j.clim.2024.110326] [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: 06/03/2024] [Revised: 07/12/2024] [Accepted: 07/21/2024] [Indexed: 07/28/2024]
Abstract
The interferon regulatory factor 2 binding protein 2 (IRF2BP2) is a transcriptional regulator, functioning a transcriptional corepressor by interacting with the interferon regulatory factor-2. The ubiquitous expression of IRF2BP2 by diverse cell types and tissues suggests its potential involvement in different cell signalling pathways. Variants inIRF2BP2have been recently identified to cause familial common variable immunodeficiency (CVID) characterized by immune dysregulation. This study investigated three rare novel variants inIRF2BP2, identified in patients with primary antibody deficiency and autoimmunity by whole exome-sequencing (WES). Following transient overexpression of EGFP-fused mutants in HEK293 cells and transfection in Jurkat cell lines, we used fluorescence microscopy, real-time PCR and Western blotting to analyze their effects on IRF2BP2 expression, subcellular localization, nuclear translocation of IRF2, and the transcriptional activation of NFκB1(p50). We found altered IRF2BP2 mRNA and protein expression levels in the mutants compared to the wild type after IRF2BP2 overexpression. In confocal fluorescence microscopy, variants in the C-terminal RING finger domain showed an irregular aggregate formation and distribution instead of the expected nuclear localization compared to the variants in the N-terminal zinc finger domain and their wildtype counterpart. Immunoblotting revealed an impaired IRF2 and NFκB1 (p50) nuclear localization in the mutants compared to the IRF2BP2 wildtype counterpart. LPS stimulation reduced IRF2BP2 mRNA expression in the variants compared to the wild type. Our findings significantly contribute to understanding the clinical significance of IRF2BP2 mutations in the pathogenesis of immunodeficiency and immune dysregulation. We observed impairment of the nuclear translocation of IRF2 and NFκB1 (p50) due to the upregulation of IRF2BP2, potentially affecting specific gene expressions involved in immune regulation.
Collapse
Affiliation(s)
- Manfred Anim
- Department of Rheumatology and Immunology, Hannover Medical School, Hannover, Germany; Hannover Biomedical Research School (HBRS), Hannover Medical School, Hanover, Germany
| | - Georgios Sogkas
- Department of Rheumatology and Immunology, Hannover Medical School, Hannover, Germany; RESIST - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Hanover, Germany
| | - Nadezhda Camacho-Ordonez
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany; Clinic of Rheumatology and Clinical Immunology, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany
| | - Gunnar Schmidt
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Abdulwahab Elsayed
- Department of Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
| | - Michele Proietti
- Department of Rheumatology and Immunology, Hannover Medical School, Hannover, Germany; RESIST - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Hanover, Germany.; Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Torsten Witte
- Department of Rheumatology and Immunology, Hannover Medical School, Hannover, Germany; RESIST - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Hanover, Germany
| | - Bodo Grimbacher
- RESIST - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Hanover, Germany.; Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Clinic of Rheumatology and Clinical Immunology, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany; DZIF - German Center for Infection Research, Satellite Center Freiburg, Germany
| | - Faranaz Atschekzei
- Department of Rheumatology and Immunology, Hannover Medical School, Hannover, Germany; RESIST - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Hanover, Germany..
| |
Collapse
|
2
|
Perea L, Faner R, Chalmers JD, Sibila O. Pathophysiology and genomics of bronchiectasis. Eur Respir Rev 2024; 33:240055. [PMID: 38960613 PMCID: PMC11220622 DOI: 10.1183/16000617.0055-2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 05/02/2024] [Indexed: 07/05/2024] Open
Abstract
Bronchiectasis is a complex and heterogeneous inflammatory chronic respiratory disease with an unknown cause in around 30-40% of patients. The presence of airway infection together with chronic inflammation, airway mucociliary dysfunction and lung damage are key components of the vicious vortex model that better describes its pathophysiology. Although bronchiectasis research has significantly increased over the past years and different endotypes have been identified, there are still major gaps in the understanding of the pathophysiology. Genomic approaches may help to identify new endotypes, as has been shown in other chronic airway diseases, such as COPD.Different studies have started to work in this direction, and significant contributions to the understanding of the microbiome and proteome diversity have been made in bronchiectasis in recent years. However, the systematic application of omics approaches to identify new molecular insights into the pathophysiology of bronchiectasis (endotypes) is still limited compared with other respiratory diseases.Given the complexity and diversity of these technologies, this review describes the key components of the pathophysiology of bronchiectasis and how genomics can be applied to increase our knowledge, including the study of new techniques such as proteomics, metabolomics and epigenomics. Furthermore, we propose that the novel concept of trained innate immunity, which is driven by microbiome exposures leading to epigenetic modifications, can complement our current understanding of the vicious vortex. Finally, we discuss the challenges, opportunities and implications of genomics application in clinical practice for better patient stratification into new therapies.
Collapse
Affiliation(s)
- Lidia Perea
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Rosa Faner
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias M.P. (CIBERES), Barcelona, Spain
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Oriol Sibila
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias M.P. (CIBERES), Barcelona, Spain
- Respiratory Department, Hospital Clínic, University of Barcelona, Barcelona, Spain
| |
Collapse
|
3
|
LaFon DC, Dransfield MT. Bronchiectasis-Chronic Obstructive Pulmonary Disease Overlap: A ROSE by Any Other Name? Am J Respir Crit Care Med 2024; 210:20-21. [PMID: 38452226 PMCID: PMC11197067 DOI: 10.1164/rccm.202402-0314ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 03/06/2024] [Indexed: 03/09/2024] Open
Affiliation(s)
- David C LaFon
- Division of Pulmonary, Allergy, and Critical Care Medicine Heersink School of Medicine University of Alabama at Birmingham Birmingham, Alabama
| | - Mark T Dransfield
- Division of Pulmonary, Allergy, and Critical Care Medicine Heersink School of Medicine University of Alabama at Birmingham Birmingham, Alabama
- Birmingham VA Medical Center Birmingham, Alabama
| |
Collapse
|
4
|
Chen J, Xu Z, Sun L, Yu K, Hersh CP, Boueiz A, Hokanson JE, Sciurba FC, Silverman EK, Castaldi PJ, Batmanghelich K. Deep Learning Integration of Chest Computed Tomography Imaging and Gene Expression Identifies Novel Aspects of COPD. CHRONIC OBSTRUCTIVE PULMONARY DISEASES (MIAMI, FLA.) 2023; 10:355-368. [PMID: 37413999 DOI: 10.15326/jcopdf.2023.0399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Rationale Chronic obstructive pulmonary disease (COPD) is characterized by pathologic changes in the airways, lung parenchyma, and persistent inflammation, but the links between lung structural changes and blood transcriptome patterns have not been fully described. Objections The objective of this study was to identify novel relationships between lung structural changes measured by chest computed tomography (CT) and blood transcriptome patterns measured by blood RNA sequencing (RNA-seq). Methods CT scan images and blood RNA-seq gene expression from 1223 participants in the COPD Genetic Epidemiology (COPDGene®) study were jointly analyzed using deep learning to identify shared aspects of inflammation and lung structural changes that we labeled image-expression axes (IEAs). We related IEAs to COPD-related measurements and prospective health outcomes through regression and Cox proportional hazards models and tested them for biological pathway enrichment. Results We identified 2 distinct IEAs: IEAemph which captures an emphysema-predominant process with a strong positive correlation to CT emphysema and a negative correlation to forced expiratory volume in 1 second and body mass index (BMI); and IEAairway which captures an airway-predominant process with a positive correlation to BMI and airway wall thickness and a negative correlation to emphysema. Pathway enrichment analysis identified 29 and 13 pathways significantly associated with IEAemph and IEAairway, respectively (adjusted p<0.001). Conclusions Integration of CT scans and blood RNA-seq data identified 2 IEAs that capture distinct inflammatory processes associated with emphysema and airway-predominant COPD.
Collapse
Affiliation(s)
- Junxiang Chen
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Zhonghui Xu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - Li Sun
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Ke Yu
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Craig P Hersh
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - Adel Boueiz
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - John E Hokanson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - Frank C Sciurba
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - Peter J Castaldi
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
- Division of General Internal Medicine and Primary Care, Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - Kayhan Batmanghelich
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| |
Collapse
|
5
|
Yang C, Yang L, Yang L, Li S, Ye L, Ye J, Chen C, Zeng Y, Zhu M, Lin X, Peng Q, Wang Y, Jin M. Plasma Proteomics Study Between the Frequent Exacerbation and Infrequent Exacerbation Phenotypes of Chronic Obstructive Pulmonary Disease. Int J Chron Obstruct Pulmon Dis 2023; 18:1713-1728. [PMID: 37581107 PMCID: PMC10423573 DOI: 10.2147/copd.s408361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 07/09/2023] [Indexed: 08/16/2023] Open
Abstract
Background Frequent exacerbation (FE) and infrequent exacerbation (IE) are two phenotypes of chronic obstructive pulmonary disease (COPD), of which FE is associated with a higher incidence of exacerbation and a serious threat to human health. Because the pathogenesis mechanisms of FE are unclear, this study aims to identify FE-related proteins in the plasma via proteomics for use as predictive, diagnostic, and therapeutic biomarkers of COPD. Methods A cross-sectional study was conducted in which plasma protein profiles were analyzed in COPD patients at stable stage, and differentially expressed proteins (DEPs) were screened out between the FE and IE patients. FE-related DEPs were identified using data-independent acquisition-based proteomics and bioinformatics analyses. In addition, FE-related candidates were verified by enzyme-linked immunosorbent assay. Results In this study, 47 DEPs were screened out between the FE and IE groups, including 20 upregulated and 27 downregulated proteins. Key biological functions (eg, neutrophil degranulation, extracellular exosome, protein homodimerization activity) and signaling pathways (eg, arginine and proline metabolism) were enriched in association with the FE phenotype. Receiver operating characteristic (ROC) analysis of the 11 combined DEPs revealed an area under the curve of 0.985 (p <0.05) for discriminating FE from IE. Moreover, correlation and ROC curve analyses indicated that creatine kinase, M-type (CKM) and fat storage-inducing transmembrane protein 1 (FITM1) might be clinically significant in patients with the FE phenotype. In addition, plasma expression levels of CKM and FITM1 were validated to be significantly decreased in the FE group compared with the IE group (CKM: p <0.01; FITM1: p <0.05). Conclusion In this study, novel insights into COPD pathogenesis were provided by investigating and comparing plasma protein profiles between the FE and IE patients. CKM, FITM1, and a combinative biomarker panel may serve as useful tools for assisting in the precision diagnosis and effective treatment of the FE phenotype of COPD.
Collapse
Affiliation(s)
- Chengyu Yang
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, People’s Republic of China
- Department of Pulmonary and Critical Care Medicine, Huadong Hospital, Fudan University, Shanghai, 200040, People’s Republic of China
| | - Li Yang
- Department of Pulmonary and Critical Care Medicine, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, People’s Republic of China
- Key Laboratory of Interventional Pulmonology of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, People’s Republic of China
| | - Lei Yang
- Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen, Guangdong, 518055, People’s Republic of China
| | - Shuiming Li
- Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen, Guangdong, 518055, People’s Republic of China
| | - Ling Ye
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, People’s Republic of China
- Department of Allergy, Zhongshan Hospital, Fudan University, Shanghai, 200032, People’s Republic of China
| | - Jinfeng Ye
- Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen, Guangdong, 518055, People’s Republic of China
| | - Chengshui Chen
- Department of Pulmonary and Critical Care Medicine, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, People’s Republic of China
- Key Laboratory of Interventional Pulmonology of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, People’s Republic of China
- Department of Pulmonary and Critical Care Medicine, the Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People’s Hospital, Zhejiang, 324000, People’s Republic of China
| | - Yiming Zeng
- Department of Pulmonary and Critical Care Medicine, the Second Affiliated Hospital of Fujian Medical University, Respiratory Medicine Center of Fujian Province, Quanzhou, Fujian, 362000, People’s Republic of China
| | - Mengchan Zhu
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, People’s Republic of China
| | - Xiaoping Lin
- Department of Pulmonary and Critical Care Medicine, the Second Affiliated Hospital of Fujian Medical University, Respiratory Medicine Center of Fujian Province, Quanzhou, Fujian, 362000, People’s Republic of China
| | - Qing Peng
- Department of Pulmonary and Critical Care Medicine, Minhang Hospital, Fudan University, Shanghai, 201199, People’s Republic of China
| | - Yun Wang
- Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen, Guangdong, 518055, People’s Republic of China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, Guangdong, 515041, People’s Republic of China
| | - Meiling Jin
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, People’s Republic of China
- Department of Allergy, Zhongshan Hospital, Fudan University, Shanghai, 200032, People’s Republic of China
| |
Collapse
|
6
|
Ryu MH, Yun JH, Morrow JD, Saferali A, Castaldi P, Chase R, Stav M, Xu Z, Barjaktarevic I, Han M, Labaki W, Huang YJ, Christenson S, O’Neal W, Bowler R, Sin DD, Freeman CM, Curtis JL, Hersh CP. Blood Gene Expression and Immune Cell Subtypes Associated with Chronic Obstructive Pulmonary Disease Exacerbations. Am J Respir Crit Care Med 2023; 208:247-255. [PMID: 37286295 PMCID: PMC10395718 DOI: 10.1164/rccm.202301-0085oc] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 06/06/2023] [Indexed: 06/09/2023] Open
Abstract
Rationale: Acute exacerbations of chronic obstructive pulmonary disease (AE-COPDs) are associated with a significant disease burden. Blood immune phenotyping may improve our understanding of a COPD endotype at increased risk of exacerbations. Objective: To determine the relationship between the transcriptome of circulating leukocytes and COPD exacerbations. Methods: Blood RNA sequencing data (n = 3,618) from the COPDGene (Genetic Epidemiology of COPD) study were analyzed. Blood microarray data (n = 646) from the ECLIPSE (Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints) study were used for validation. We tested the association between blood gene expression and AE-COPDs. We imputed the abundance of leukocyte subtypes and tested their association with prospective AE-COPDs. Flow cytometry was performed on blood in SPIROMICS (Subpopulations and Intermediate Outcomes in COPD Study) (n = 127), and activation markers for T cells were tested for association with prospective AE-COPDs. Measurements and Main Results: Exacerbations were reported 4,030 and 2,368 times during follow-up in COPDGene (5.3 ± 1.7 yr) and ECLIPSE (3 yr), respectively. We identified 890, 675, and 3,217 genes associated with a history of AE-COPDs, persistent exacerbations (at least one exacerbation per year), and prospective exacerbation rate, respectively. In COPDGene, the number of prospective exacerbations in patients with COPD (Global Initiative for Chronic Obstructive Lung Disease stage ⩾2) was negatively associated with circulating CD8+ T cells, CD4+ T cells, and resting natural killer cells. The negative association with naive CD4+ T cells was replicated in ECLIPSE. In the flow-cytometry study, an increase in CTLA4 on CD4+ T cells was positively associated with AE-COPDs. Conclusions: Individuals with COPD with lower circulating lymphocyte counts, particularly decreased CD4+ T cells, are more susceptible to AE-COPDs, including persistent exacerbations.
Collapse
Affiliation(s)
- Min Hyung Ryu
- Channing Division of Network Medicine and
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Jeong H. Yun
- Channing Division of Network Medicine and
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Jarrett D. Morrow
- Channing Division of Network Medicine and
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Aabida Saferali
- Channing Division of Network Medicine and
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Peter Castaldi
- Channing Division of Network Medicine and
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | | | - Meryl Stav
- Channing Division of Network Medicine and
| | | | - Igor Barjaktarevic
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California
| | - MeiLan Han
- Division of Pulmonary and Critical Care Medicine and
| | - Wassim Labaki
- Division of Pulmonary and Critical Care Medicine and
| | - Yvonne J. Huang
- Division of Pulmonary and Critical Care Medicine and
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan
| | - Stephanie Christenson
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, California
| | - Wanda O’Neal
- Marsico Lung Institute, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Russell Bowler
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, National Jewish Health, Denver, Colorado
| | - Don D. Sin
- Centre for Heart and Lung Innovation, St. Paul’s Hospital, Vancouver, British Columbia, Canada
- Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; and
| | | | - Jeffrey L. Curtis
- Division of Pulmonary and Critical Care Medicine and
- Medical Service, VA Ann Arbor Healthcare System, Ann Arbor, Michigan
| | - Craig P. Hersh
- Channing Division of Network Medicine and
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| |
Collapse
|
7
|
Polverino F, Kalhan R. Leveraging Omics to Predict Chronic Obstructive Pulmonary Disease Exacerbations: The "Immunome". Am J Respir Crit Care Med 2023; 208:220-222. [PMID: 37352489 PMCID: PMC10395726 DOI: 10.1164/rccm.202306-0978ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 06/23/2023] [Indexed: 06/25/2023] Open
Affiliation(s)
- Francesca Polverino
- Section of Pulmonary and Critical Care Medicine Baylor College of Medicine Houston, Texas
| | - Ravi Kalhan
- Feinberg School of Medicine Northwestern University Chicago, Illinois
| |
Collapse
|
8
|
LaFon DC, Woo H, Fedarko N, Azar A, Hill H, Tebo AE, Martins TB, Han MK, Krishnan JA, Ortega VE, Barjaktarevic I, Kaner RJ, Hastie A, O'Neal WK, Couper D, Woodruff PG, Curtis JL, Hansel NN, Nahm MH, Dransfield MT, Putcha N. Reduced quantity and function of pneumococcal antibodies are associated with exacerbations of COPD in SPIROMICS. Clin Immunol 2023; 250:109324. [PMID: 37030524 PMCID: PMC10171244 DOI: 10.1016/j.clim.2023.109324] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/24/2023] [Accepted: 04/04/2023] [Indexed: 04/10/2023]
Abstract
While hypogammaglobulinemia is associated with COPD exacerbations, it is unknown whether frequent exacerbators have specific defects in antibody production/function. We hypothesized that reduced quantity/function of serum pneumococcal antibodies correlate with exacerbation risk in the SPIROMICS cohort. We measured total pneumococcal IgG in n = 764 previously vaccinated participants with COPD. In a propensity-matched subset of n = 200 with vaccination within five years (n = 50 without exacerbations in the previous year; n = 75 with one, n = 75 with ≥2), we measured pneumococcal IgG for 23 individual serotypes, and pneumococcal antibody function for 4 serotypes. Higher total pneumococcal IgG, serotype-specific IgG (17/23 serotypes), and antibody function (3/4 serotypes) were independently associated with fewer prior exacerbations. Higher pneumococcal IgG (5/23 serotypes) predicted lower exacerbation risk in the following year. Pneumococcal antibodies are inversely associated with exacerbations, supporting the presence of immune defects in frequent exacerbators. With further study, pneumococcal antibodies may be useful biomarkers for immune dysfunction in COPD.
Collapse
Affiliation(s)
- David C LaFon
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, United States; UAB Lung Health Center, Birmingham, AL, United States.
| | - Han Woo
- Johns Hopkins University, Baltimore, MD, United States
| | - Neal Fedarko
- Johns Hopkins University, Baltimore, MD, United States
| | - Antoine Azar
- Johns Hopkins University, Baltimore, MD, United States
| | - Harry Hill
- Department of Pathology, University of Utah Health and ARUP Laboratories, Salt Lake City, UT, United States
| | - Anne E Tebo
- Department of Pathology, University of Utah Health and ARUP Laboratories, Salt Lake City, UT, United States; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Thomas B Martins
- Department of Pathology, University of Utah Health and ARUP Laboratories, Salt Lake City, UT, United States
| | - MeiLan K Han
- Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI, United States
| | | | | | - Igor Barjaktarevic
- Pulmonary and Critical Care, University of California Los Angeles, Los Angeles, CA, United States
| | | | - Annette Hastie
- Wake Forest University School of Medicine, Winston-Salem, NC, United States
| | - Wanda K O'Neal
- Marisco Lung Institute, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - David Couper
- University of North Carolina Department of Biostatistics, Chapel Hill, NC, United States
| | | | - Jeffrey L Curtis
- Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI, United States; VA Ann Arbor Healthcare System, Ann Arbor, MI, United States
| | | | - Moon H Nahm
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, United States; Department of Microbiology, University of Alabama at Birmingham, United States
| | - Mark T Dransfield
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, United States; UAB Lung Health Center, Birmingham, AL, United States; Birmingham VA Medical Center, Birmingham, AL, United States
| | | |
Collapse
|
9
|
Banaganapalli B, Mallah B, Alghamdi KS, Albaqami WF, Alshaer DS, Alrayes N, Elango R, Shaik NA. Integrative weighted molecular network construction from transcriptomics and genome wide association data to identify shared genetic biomarkers for COPD and lung cancer. PLoS One 2022; 17:e0274629. [PMID: 36194576 PMCID: PMC9531836 DOI: 10.1371/journal.pone.0274629] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 09/01/2022] [Indexed: 11/05/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a multifactorial progressive airflow obstruction in the lungs, accounting for high morbidity and mortality across the world. This study aims to identify potential COPD blood-based biomarkers by analyzing the dysregulated gene expression patterns in blood and lung tissues with the help of robust computational approaches. The microarray gene expression datasets from blood (136 COPD and 6 controls) and lung tissues (16 COPD and 19 controls) were analyzed to detect shared differentially expressed genes (DEGs). Then these DEGs were used to construct COPD protein network-clusters and functionally enrich them against gene ontology annotation terms. The hub genes in the COPD network clusters were then queried in GWAS catalog and in several cancer expression databases to explore their pathogenic roles in lung cancers. The comparison of blood and lung tissue datasets revealed 63 shared DEGs. Of these DEGs, 12 COPD hub gene-network clusters (SREK1, TMEM67, IRAK2, MECOM, ASB4, C1QTNF2, CDC42BPA, DPF3, DET1, CCDC74B, KHK, and DDX3Y) connected to dysregulations of protein degradation, inflammatory cytokine production, airway remodeling, and immune cell activity were prioritized with the help of protein interactome and functional enrichment analysis. Interestingly, IRAK2 and MECOM hub genes from these COPD network clusters are known for their involvement in different pulmonary diseases. Additional COPD hub genes like SREK1, TMEM67, CDC42BPA, DPF3, and ASB4 were identified as prognostic markers in lung cancer, which is reported in 1% of COPD patients. This study identified 12 gene network- clusters as potential blood based genetic biomarkers for COPD diagnosis and prognosis.
Collapse
Affiliation(s)
- Babajan Banaganapalli
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
- * E-mail: (BB); (NAS)
| | - Bayan Mallah
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Kawthar Saad Alghamdi
- Department of Biology, Faculty of Science, University of Hafr Al Batin, Hafr Al Batin, Saudi Arabia
| | - Walaa F. Albaqami
- Department of Science, Prince Sultan Military College of Health Sciences, Dhahran, Saudi Arabia
| | - Dalal Sameer Alshaer
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nuha Alrayes
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ramu Elango
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Noor A. Shaik
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
- * E-mail: (BB); (NAS)
| |
Collapse
|
10
|
Barta I, Paska C, Antus B. Sputum Cytokine Profiling in COPD: Comparison Between Stable Disease and Exacerbation. Int J Chron Obstruct Pulmon Dis 2022; 17:1897-1908. [PMID: 36017119 PMCID: PMC9397440 DOI: 10.2147/copd.s364982] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 07/21/2022] [Indexed: 12/03/2022] Open
Abstract
Purpose Cytokines are extracellular signaling proteins that have been widely implicated in the pathogenesis of chronic obstructive pulmonary disease (COPD). Here, we investigated cytokine expression both at the mRNA and protein level in the sputum of healthy individuals, stable COPD patients, and those experiencing a severe acute exacerbation (AECOPD) requiring hospitalization. Patients and Methods Sputum was collected in 19 healthy controls, 25 clinically stable COPD patients, and 31 patients with AECOPD. In AECOPD patients sample collection was performed both at the time of hospital admission and at discharge following treatment. Sputum supernatant was analyzed by an antibody microarray detecting 120 cytokines simultaneously, while the mRNA expression of 14 selected cytokines in sputum cells was investigated by real-time PCR (qPCR). Results Proteomic analysis identified interleukin (IL)-6 and growth-regulated oncogene (GRO)α as the only sputum cytokines that were differentially expressed between stable COPD patients and healthy controls. At the onset of AECOPD, several cytokines exhibited altered sputum expression compared to stable COPD. Recovery from AECOPD induced significant changes in the sputum cytokine protein profile; however, the length of hospitalization was insufficient for most cytokines to return to stable levels. With regard to gene expression analysis by qPCR, we found that bone morphogenetic protein (BMP)-4 was up-regulated, while IL-1α, monokine-induced by interferon-γ (MIG), and BMP-6 were down-regulated at the mRNA level in patients with AECOPD compared to stable disease. Conclusion The sputum cytokine signature of AECOPD differs from that of stable COPD. Protein level changes are asynchronous with changes in gene expression at the mRNA level in AECOPD. The observation that the levels of most cytokines do not stabilize with acute treatment of AECOPD suggests a prolonged effect of exacerbation on the status of COPD patients.
Collapse
Affiliation(s)
- Imre Barta
- Department of Pathophysiology, National Koranyi Institute of Pulmonology, Budapest, Hungary
| | - Csilla Paska
- Department of Pathophysiology, National Koranyi Institute of Pulmonology, Budapest, Hungary
| | - Balazs Antus
- Department of Pathophysiology, National Koranyi Institute of Pulmonology, Budapest, Hungary.,Department of Pulmonology, National Koranyi Institute of Pulmonology, Budapest, Hungary
| |
Collapse
|
11
|
Mostafaei S, Borna H, Emamvirdizadeh A, Arabfard M, Ahmadi A, Salimian J, Salesi M, Azimzadeh Jamalkandi S. Causal Path of COPD Progression-Associated Genes in Different Biological Samples. COPD 2022; 19:290-299. [PMID: 35696265 DOI: 10.1080/15412555.2022.2081541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is a progressive inflammatory disease with pulmonary and extra-pulmonary complications. Due to the disease's systemic nature, many investigations investigated the genetic alterations in various biological samples. We aimed to infer causal genes in COPD's pathogenesis in different biological samples using elastic-net logistic regression and the Structural Equation Model. Samples of small airway epithelial cells, bronchoalveolar lavage macrophages, lung tissue biopsy, sputum, and blood samples were selected (135, 70, 235, 143, and 226 samples, respectively). Elastic-net Logistic Regression analysis was implemented to identify the most important genes involved in COPD progression. Thirty-three candidate genes were identified as essential factors in the pathogenesis of COPD and regulation of lung function. Recognized candidate genes in small airway epithelial (SAE) cells have the highest area under the ROC curve (AUC = 97%, SD = 3.9%). Our analysis indicates that macrophages and epithelial cells are more influential in COPD progression at the transcriptome level.
Collapse
Affiliation(s)
- Shayan Mostafaei
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.,Department of Biostatistics, Faculty of Health, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Hojat Borna
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.,Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Alireza Emamvirdizadeh
- Department of Molecular Genetics, Faculty of Bio Sciences, Tehran North Branch, Islamic Azad University, Tehran, Iran
| | - Masoud Arabfard
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Ahmadi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Jafar Salimian
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mahmood Salesi
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Sadegh Azimzadeh Jamalkandi
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| |
Collapse
|
12
|
Kim JS, Axelsson GT, Moll M, Anderson MR, Bernstein EJ, Putman RK, Hida T, Hatabu H, Hoffman EA, Raghu G, Kawut SM, Doyle MF, Tracy R, Launer LJ, Manichaikul A, Rich SS, Lederer DJ, Gudnason V, Hobbs BD, Cho MH, Hunninghake GM, Garcia CK, Gudmundsson G, Barr RG, Podolanczuk AJ. Associations of Monocyte Count and Other Immune Cell Types with Interstitial Lung Abnormalities. Am J Respir Crit Care Med 2022; 205:795-805. [PMID: 34929108 PMCID: PMC10394677 DOI: 10.1164/rccm.202108-1967oc] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Rationale: Higher blood monocyte counts are associated with worse survival in adults with clinically diagnosed pulmonary fibrosis. Their association with the development and progression of interstitial lung abnormalities (ILA) in humans is unknown. Objectives: We evaluated the associations of blood monocyte count, and other immune cell types, with ILA, high-attenuation areas, and FVC in four independent cohorts. Methods: We included participants with measured monocyte counts and computed tomographic (CT) imaging enrolled in MESA (Multi-Ethnic Study of Atherosclerosis, n = 484), AGES-Reykjavik (Age/Gene Environment Susceptibility Study, n = 3,547), COPDGene (Genetic Epidemiology of COPD, n = 2,719), and the ECLIPSE (Evaluation of COPD Longitudinally to Identify Predictive Surrogate End-points, n = 646). Measurements and Main Results: After adjustment for covariates, a 1-SD increment in blood monocyte count was associated with ILA in MESA (odds ratio [OR], 1.3; 95% confidence interval [CI], 1.0-1.8), AGES-Reykjavik (OR, 1.2; 95% CI, 1.1-1.3), COPDGene (OR, 1.3; 95% CI, 1.2-1.4), and ECLIPSE (OR, 1.2; 95% CI, 1.0-1.4). A higher monocyte count was associated with ILA progression over 5 years in AGES-Reykjavik (OR, 1.2; 95% CI, 1.0-1.3). Compared with participants without ILA, there was a higher percentage of activated monocytes among those with ILA in MESA. Higher monocyte count was associated with greater high-attenuation areas in MESA and lower FVC in MESA and COPDGene. Associations of other immune cell types were less consistent. Conclusions: Higher blood monocyte counts were associated with the presence and progression of interstitial lung abnormalities and lower FVC.
Collapse
Affiliation(s)
- John S Kim
- Department of Medicine, and.,Department of Medicine, Columbia University, New York, New York
| | - Gísli Thor Axelsson
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland.,Icelandic Heart Association, Kopavogur, Iceland
| | - Matthew Moll
- Division of Pulmonary and Critical Care and.,Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | | | | | - Tomoyuki Hida
- Department of Radiology, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroto Hatabu
- Department of Radiology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Eric A Hoffman
- Department of Radiology.,Department of Medicine, and.,Department of Biomedical Engineering, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Ganesh Raghu
- Department of Medicine, University of Washington, Seattle, Washington
| | - Steven M Kawut
- Department of Medicine and.,Department of Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Margaret F Doyle
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Colchester, Vermont
| | - Russell Tracy
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Colchester, Vermont
| | - Lenore J Launer
- Laboratory of Epidemiology and Population Sciences, Intramural Research Program, National Institute of on Aging, National Institutes of Health, Bethesda, Maryland
| | - Ani Manichaikul
- Center for Public Health Genomics and Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Stephen S Rich
- Center for Public Health Genomics and Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, Virginia
| | | | - Vilmundur Gudnason
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland.,Icelandic Heart Association, Kopavogur, Iceland
| | - Brian D Hobbs
- Division of Pulmonary and Critical Care and.,Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Michael H Cho
- Division of Pulmonary and Critical Care and.,Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | | | - Gunnar Gudmundsson
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland.,Department of Respiratory Medicine and Sleep, Landspitali University Hospital, Reykjavik, Iceland
| | - R Graham Barr
- Department of Medicine, Columbia University, New York, New York.,Department of Epidemiology, Mailman School of Public Health, New York, New York; and
| | - Anna J Podolanczuk
- Department of Medicine, Columbia University, New York, New York.,Division of Pulmonary and Critical Care Medicine, Weill Cornell Medical Center, New York, New York
| |
Collapse
|
13
|
Moll M, Boueiz A, Ghosh AJ, Saferali A, Lee S, Xu Z, Yun JH, Hobbs BD, Hersh CP, Sin DD, Tal-Singer R, Silverman EK, Cho MH, Castaldi PJ. Development of a Blood-based Transcriptional Risk Score for Chronic Obstructive Pulmonary Disease. Am J Respir Crit Care Med 2022; 205:161-170. [PMID: 34739356 PMCID: PMC8787248 DOI: 10.1164/rccm.202107-1584oc] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/03/2021] [Indexed: 01/17/2023] Open
Abstract
Rationale: The ability of peripheral blood biomarkers to assess chronic obstructive pulmonary disease (COPD) risk and progression is unknown. Genetics and gene expression may capture important aspects of COPD-related biology that predict disease activity. Objectives: Develop a transcriptional risk score (TRS) for COPD and assess the contribution of the TRS and a polygenic risk score (PRS) for disease susceptibility and progression. Methods: We randomly split 2,569 COPDGene (Genetic Epidemiology of COPD) participants with whole-blood RNA sequencing into training (n = 1,945) and testing (n = 624) samples and used 468 ECLIPSE (Evaluation of COPD Longitudinally to Identify Predictive Surrogate End-points) COPD cases with microarray data for replication. We developed a TRS using penalized regression (least absolute shrinkage and selection operator) to model FEV1/FVC and studied the predictive value of TRS for COPD (Global Initiative for Chronic Obstructive Lung Disease 2-4), prospective FEV1 change (ml/yr), and additional COPD-related traits. We adjusted for potential confounders, including age and smoking. We evaluated the predictive performance of the TRS in the context of a previously derived PRS and clinical factors. Measurements and Main Results: The TRS included 147 transcripts and was associated with COPD (odds ratio, 3.3; 95% confidence interval [CI], 2.4-4.5; P < 0.001), FEV1 change (β, -17 ml/yr; 95% CI, -28 to -6.6; P = 0.002), and other COPD-related traits. In ECLIPSE cases, we replicated the association with FEV1 change (β, -8.2; 95% CI, -15 to -1; P = 0.025) and the majority of other COPD-related traits. Models including PRS, TRS, and clinical factors were more predictive of COPD (area under the receiver operator characteristic curve, 0.84) and annualized FEV1 change compared with models with one risk score or clinical factors alone. Conclusions: Blood transcriptomics can improve prediction of COPD and lung function decline when added to a PRS and clinical risk factors.
Collapse
Affiliation(s)
- Matthew Moll
- Channing Division of Network Medicine
- Division of Pulmonary and Critical Care Medicine, and
| | - Adel Boueiz
- Channing Division of Network Medicine
- Division of Pulmonary and Critical Care Medicine, and
| | - Auyon J. Ghosh
- Channing Division of Network Medicine
- Division of Pulmonary and Critical Care Medicine, and
| | | | - Sool Lee
- Channing Division of Network Medicine
- Department of Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, North Carolina
| | | | - Jeong H. Yun
- Channing Division of Network Medicine
- Division of Pulmonary and Critical Care Medicine, and
| | - Brian D. Hobbs
- Channing Division of Network Medicine
- Division of Pulmonary and Critical Care Medicine, and
| | - Craig P. Hersh
- Channing Division of Network Medicine
- Division of Pulmonary and Critical Care Medicine, and
| | - Don D. Sin
- Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, British Columbia, Canada
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; and
| | | | - Edwin K. Silverman
- Channing Division of Network Medicine
- Division of Pulmonary and Critical Care Medicine, and
| | - Michael H. Cho
- Channing Division of Network Medicine
- Division of Pulmonary and Critical Care Medicine, and
| | - Peter J. Castaldi
- Channing Division of Network Medicine
- Division of General Internal Medicine and Primary Care, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| |
Collapse
|
14
|
Noël A, Perveen Z, Xiao R, Hammond H, Le Donne V, Legendre K, Gartia MR, Sahu S, Paulsen DB, Penn AL. Mmp12 Is Upregulated by in utero Second-Hand Smoke Exposures and Is a Key Factor Contributing to Aggravated Lung Responses in Adult Emphysema, Asthma, and Lung Cancer Mouse Models. Front Physiol 2021; 12:704401. [PMID: 34912233 PMCID: PMC8667558 DOI: 10.3389/fphys.2021.704401] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 10/19/2021] [Indexed: 12/18/2022] Open
Abstract
Matrix metalloproteinase-12 (Mmp12) is upregulated by cigarette smoke (CS) and plays a critical role in extracellular matrix remodeling, a key mechanism involved in physiological repair processes, and in the pathogenesis of emphysema, asthma, and lung cancer. While cigarette smoking is associated with the development of chronic obstructive pulmonary diseases (COPD) and lung cancer, in utero exposures to CS and second-hand smoke (SHS) are associated with asthma development in the offspring. SHS is an indoor air pollutant that causes known adverse health effects; however, the mechanisms by which in utero SHS exposures predispose to adult lung diseases, including COPD, asthma, and lung cancer, are poorly understood. In this study, we tested the hypothesis that in utero SHS exposure aggravates adult-induced emphysema, asthma, and lung cancer. Methods: Pregnant BALB/c mice were exposed from gestational days 6–19 to either 3 or 10mg/m3 of SHS or filtered air. At 10, 11, 16, or 17weeks of age, female offspring were treated with either saline for controls, elastase to induce emphysema, house-dust mite (HDM) to initiate asthma, or urethane to promote lung cancer. At sacrifice, specific disease-related lung responses including lung function, inflammation, gene, and protein expression were assessed. Results: In the elastase-induced emphysema model, in utero SHS-exposed mice had significantly enlarged airspaces and up-regulated expression of Mmp12 (10.3-fold compared to air-elastase controls). In the HDM-induced asthma model, in utero exposures to SHS produced eosinophilic lung inflammation and potentiated Mmp12 gene expression (5.7-fold compared to air-HDM controls). In the lung cancer model, in utero exposures to SHS significantly increased the number of intrapulmonary metastases at 58weeks of age and up-regulated Mmp12 (9.3-fold compared to air-urethane controls). In all lung disease models, Mmp12 upregulation was supported at the protein level. Conclusion: Our findings revealed that in utero SHS exposures exacerbate lung responses to adult-induced emphysema, asthma, and lung cancer. Our data show that MMP12 is up-regulated at the gene and protein levels in three distinct adult lung disease models following in utero SHS exposures, suggesting that MMP12 is central to in utero SHS-aggravated lung responses.
Collapse
Affiliation(s)
- Alexandra Noël
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, United States
| | - Zakia Perveen
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, United States
| | - Rui Xiao
- Department of Anesthesiology, Columbia University Medical Center, New York, NY, United States
| | - Harriet Hammond
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, United States
| | | | - Kelsey Legendre
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, United States
| | - Manas Ranjan Gartia
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, LA, United States
| | - Sushant Sahu
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, LA, United States
| | - Daniel B Paulsen
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, United States
| | - Arthur L Penn
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, United States
| |
Collapse
|
15
|
Hu Y, Cheng X, Qiu Z, Chen X. Identification of Metabolism-Associated Molecular Subtypes of Chronic Obstructive Pulmonary Disease. Int J Chron Obstruct Pulmon Dis 2021; 16:2351-2362. [PMID: 34429593 PMCID: PMC8374844 DOI: 10.2147/copd.s316304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/02/2021] [Indexed: 02/05/2023] Open
Abstract
Purpose This study aimed to identify the COPD molecular subtypes reflecting pulmonary function damage on the basis of metabolism-related gene expression, which provided the opportunity to study the metabolic heterogeneity and the association of metabolic pathways with pulmonary function damage. Methods Univariate linear regression and the Boruta algorithm were used to select metabolism-related genes associated with forced expiratory volume in the first second (FEV1) and FEV1/forced vital capacity (FVC) in the Evaluation of COPD to Longitudinally Identify Predictive Surrogate Endpoints (ECLIPSE) cohort. COPD subtypes were further identified by consensus clustering with best-fit. Then, we analyzed the differences in the clinical characteristics, metabolic pathways, immune cell characteristics, and transcription features among the subtypes. Results This study identified two subtypes (C1 and C2). C1 exhibited higher levels of lower pulmonary function and innate immunity than C2. Ten metabolic pathways were confirmed as key metabolic pathways. The pathways related to N-glycan, hexosamine, purine, alanine, aspartate and glutamate tended to be positively associated with the abundance of adaptive immune cells and negatively associated with the abundance of innate immune cells. In addition, other pathways had opposite trends. All results were verified in Genetic Epidemiology of COPD (COPDGene) datasets. Conclusion The two subtypes reflect the pulmonary function damage and help to further understand the metabolic mechanism of pulmonary function in COPD. Further studies are needed to prove the prognostic and therapeutic value of the subtypes.
Collapse
Affiliation(s)
- Yuanlong Hu
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, People's Republic of China
| | - Xiaomeng Cheng
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, People's Republic of China
| | - Zhanjun Qiu
- The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong, People's Republic of China
| | - Xianhai Chen
- The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong, People's Republic of China
| |
Collapse
|
16
|
Hosking L, Yeo A, Hoffman J, Chiano M, Fraser D, Ghosh S, Lipson DA, Martin N, Condreay LD, Cox C, St Jean P. Genetics plays a limited role in predicting chronic obstructive pulmonary disease treatment response and exacerbation. Respir Med 2021; 187:106573. [PMID: 34428673 DOI: 10.1016/j.rmed.2021.106573] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 07/27/2021] [Accepted: 08/08/2021] [Indexed: 12/27/2022]
Abstract
BACKGROUND Combination treatments, targeting multiple disease processes, benefit subjects with acute exacerbation of chronic obstructive pulmonary disease (AECOPD). However, predicting treatment response and exacerbation risk remain challenging. OBJECTIVE To identify genetic associations with AECOPD risk and response to combination therapy (fluticasone furoate, umeclidinium bromide and vilanterol). METHODS The genetic basis of AECOPD disease was investigated in 19,841 subjects from 23 clinical studies and 2 disease cohorts to identify exacerbation disease targets. AECOPD pharmacogenetic effects were examined in 8439 moderate to severe COPD patients with exacerbation rate, lung function and quality of life endpoints; results were followed up in an additional 2201 subjects. RESULTS We did not identify significant associations in the AECOPD disease analysis. In the AECOPD pharmacogenetics analysis, rs56195836 (MAPK8) was significantly associated with moderate to severe exacerbation rate in subjects on fluticasone furoate with baseline blood eosinophils ≥150 cells/μl (P = 1.8 × 10-8). Post-hoc, one variant was associated with on-treatment moderate to severe exacerbation rate stratifying by exacerbation history. AZU1 rs1962343 was significantly associated in subjects with frequent moderate exacerbation history when treated with fluticasone furoate/vilanterol (P = 1.1 × 10-8). Neither of these signals was supported in independent follow-up. CONCLUSION Common genetic variants do not play major roles in AECOPD disease nor predict response to triple therapy or its components in moderate to very severe COPD.
Collapse
Affiliation(s)
| | | | | | | | | | | | - David A Lipson
- GSK, Collegeville, PA, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Neil Martin
- GSK, Brentford, Middlesex, UK; University of Leicester, Leicester, Leicestershire, UK.
| | | | | | | |
Collapse
|
17
|
Zhao Y, Li M, Yang Y, Wu T, Huang Q, Wu Q, Ren C. Identification of Macrophage Polarization-Related Genes as Biomarkers of Chronic Obstructive Pulmonary Disease Based on Bioinformatics Analyses. BIOMED RESEARCH INTERNATIONAL 2021; 2021:9921012. [PMID: 34250093 PMCID: PMC8238569 DOI: 10.1155/2021/9921012] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/04/2021] [Indexed: 12/15/2022]
Abstract
OBJECTIVES Chronic obstructive pulmonary disease (COPD) is characterized by lung inflammation and remodeling. Macrophage polarization is associated with inflammation and tissue remodeling, as well as immunity. Therefore, this study attempts to investigate the diagnostic value and regulatory mechanism of macrophage polarization-related genes for COPD by bioinformatics analysis and to provide a new theoretical basis for experimental research. METHODS The raw gene expression profile dataset (GSE124180) was collected from the Gene Expression Omnibus (GEO) database. Next, a weighted gene coexpression network analysis (WGCNA) was conducted to screen macrophage polarization-related genes. The differentially expressed genes (DEGs) between the COPD and normal samples were generated using DESeq2 v3.11 and overlapped with the macrophage polarization-related genes. Moreover, functional annotations of overlapped genes were conducted by Database for Annotation, Visualization and Integrated Discovery (DAVID) Bioinformatics Resource. The immune-related genes were selected, and their correlation with the differential immune cells was analyzed by Pearson. Finally, receiver operating characteristic (ROC) curves were used to verify the diagnostic value of genes. RESULTS A total of 4922 coexpressed genes related to macrophage polarization were overlapped with the 203 DEGs between the COPD and normal samples, obtaining 25 genes related to COPD and macrophage polarization. GEM, S100B, and GZMA of them participated in the immune response, which were considered the candidate biomarkers. GEM and S100B were significantly correlated with marker genes of B cells which had a significant difference between the COPD and normal samples. Moreover, GEM was highly associated with the genes in the PI3K/Akt/GSK3β signaling pathway, regulation of actin cytoskeleton, and calcium signaling pathway based on a Pearson correlation analysis of the candidate genes and the genes in the B cell receptor signaling pathway. PPI network analysis also indicated that GEM might participate in the regulation of the PI3K/Akt/GSK3β signaling pathway. The ROC curve showed that GEM possessed an excellent accuracy in distinguishing COPD from normal samples. CONCLUSIONS The data provide a transcriptome-based evidence that GEM is related to COPD and macrophage polarization likely contributes to COPD diagnosis. At the same time, it is hoped that in-depth functional mining can provide new ideas for exploring the COPD pathogenesis.
Collapse
Affiliation(s)
- Yalin Zhao
- Respiratory and Critical Care Medicine, Kunming First People's Hospital, Kunming, Yunnan Province, China
| | - Meihua Li
- Respiratory and Critical Care Medicine, Kunming First People's Hospital, Kunming, Yunnan Province, China
| | - Yanxia Yang
- Respiratory and Critical Care Medicine, Kunming First People's Hospital, Kunming, Yunnan Province, China
| | - Tao Wu
- Respiratory and Critical Care Medicine, Kunming First People's Hospital, Kunming, Yunnan Province, China
| | - Qingyuan Huang
- Respiratory and Critical Care Medicine, Kunming First People's Hospital, Kunming, Yunnan Province, China
| | - Qinghua Wu
- Respiratory and Critical Care Medicine, Kunming First People's Hospital, Kunming, Yunnan Province, China
| | - Chaofeng Ren
- Respiratory and Critical Care Medicine, Kunming First People's Hospital, Kunming, Yunnan Province, China
| |
Collapse
|
18
|
Begg M, Hamblin JN, Jarvis E, Bradley G, Mark S, Michalovich D, Lennon M, Wajdner HE, Amour A, Wilson R, Saunders K, Tanaka R, Arai S, Tang T, Van Holsbeke C, De Backer J, Vos W, Titlestad IL, FitzGerald JM, Killian K, Bourbeau J, Poirier C, Maltais F, Cahn A, Hessel EM. Exploring PI3Kδ Molecular Pathways in Stable COPD and Following an Acute Exacerbation, Two Randomized Controlled Trials. Int J Chron Obstruct Pulmon Dis 2021; 16:1621-1636. [PMID: 34113094 PMCID: PMC8184158 DOI: 10.2147/copd.s309303] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/04/2021] [Indexed: 11/23/2022] Open
Abstract
Background Inhibition of phosphoinositide 3-kinase δ (PI3Kδ) exerts corrective effects on the dysregulated migration characteristics of neutrophils isolated from patients with chronic obstructive pulmonary disease (COPD). Objective To develop novel, induced sputum endpoints to demonstrate changes in neutrophil phenotype in the lung by administering nemiralisib, a potent and selective inhaled PI3Kδ inhibitor, to patients with stable COPD or patients with acute exacerbation (AE) of COPD. Methods In two randomized, double-blind, placebo-controlled clinical trials patients with A) stable COPD (N=28, randomized 3:1) or B) AECOPD (N=44, randomized 1:1) received treatment with inhaled nemiralisib (1mg). Endpoints included induced sputum at various time points before and during treatment for the measurement of transcriptomics (primary endpoint), inflammatory mediators, functional respiratory imaging (FRI), and spirometry. Results In stable COPD patients, the use of nemiralisib was associated with alterations in sputum neutrophil transcriptomics suggestive of an improvement in migration phenotype; however, the same nemiralisib-evoked effects were not observed in AECOPD. Inhibition of sputum inflammatory mediators was also observed in stable but not AECOPD patients. In contrast, a placebo-corrected improvement in forced expiratory volume in 1 sec of 136 mL (95% Credible Intervals -46, 315mL) with a probability that the true treatment ratio was >0% (Pr(θ>0)) of 93% was observed in AECOPD. However, FRI endpoints remained unchanged. Conclusion We provide evidence for nemiralisib-evoked changes in neutrophil migration phenotype in stable COPD but not AECOPD, despite improving lung function in the latter group. We conclude that induced sputum can be used for measuring evidence of alteration of neutrophil phenotype in stable patients, and our study provides a data set of the sputum transcriptomic changes during recovery from AECOPD.
Collapse
Affiliation(s)
- Malcolm Begg
- Refractory Respiratory Inflammation Discovery Performance Unit, GlaxoSmithKline, Stevenage, UK
| | - J Nicole Hamblin
- Refractory Respiratory Inflammation Discovery Performance Unit, GlaxoSmithKline, Stevenage, UK
| | - Emily Jarvis
- Biostatistics, GlaxoSmithKline R&D, Stevenage, UK
| | - Glyn Bradley
- Computational Biology, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, UK
| | - Stephen Mark
- Study Management, Clinical Development, GlaxoSmithKline, Mississauga, ON, Canada
| | | | - Mark Lennon
- Nonclinical and Translational Statistics, GlaxoSmithKline, Stevenage, UK
| | | | - Augustin Amour
- Adaptive Immunity Research Unit, GlaxoSmithKline, Stevenage, UK
| | - Robert Wilson
- Refractory Respiratory Inflammation Discovery Performance Unit, GlaxoSmithKline, Stevenage, UK
| | - Ken Saunders
- Adaptive Immunity Research Unit, GlaxoSmithKline, Stevenage, UK
| | - Rikako Tanaka
- Data Management & Strategy, Clinical Development, GlaxoSmithKline, Tokyo, Japan
| | - Saki Arai
- Data Management & Strategy, Clinical Development, GlaxoSmithKline, Tokyo, Japan
| | - Teresa Tang
- Pharma Safety, Clinical Development, GlaxoSmithKline, Brentford, Middlesex, UK
| | | | | | - Wim Vos
- FLUIDDA nv, Kontich, 2550, Belgium
| | - Ingrid L Titlestad
- Department of Respiratory Medicine, Odense University Hospital and University of Southern Denmark, Odense, Denmark
| | - J Mark FitzGerald
- Centre for Heart and Lung Health, University of British Columbia, Vancouver, BC, Canada
| | - Kieran Killian
- Cardiorespiratory Research Laboratory, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
| | - Jean Bourbeau
- Department of Medicine, Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Claude Poirier
- Department of Medicine, Respiratory Medicine Division, University of Montreal, Montreal, QC, Canada
| | - François Maltais
- Institut Universitaire de Cardiologie et de Pneumologie de Québe, Université Laval, Quebec City, QC, Canada
| | - Anthony Cahn
- Refractory Respiratory Inflammation Discovery Performance Unit, GlaxoSmithKline, Stevenage, UK
| | - Edith M Hessel
- Refractory Respiratory Inflammation Discovery Performance Unit, GlaxoSmithKline, Stevenage, UK
| |
Collapse
|
19
|
Gupta A, Singh N, Kumar A, Verma UP, Verma AK, Shyam H, Lal N, Kant S, Kumari A. Differential expression of inflammatory responsive genes between chronic periodontitis and periodontally affected bronchiectasis patients. MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS 2020; 9:169-172. [PMID: 33344663 PMCID: PMC7731971 DOI: 10.22099/mbrc.2020.37397.1508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The study aimed to investigate differential expression of targeted inflammatory-immune responsive genes [LTA, LTB, TNFSF4, TNFSF11/RANKL, TNFSF13, TNFSF13B, TNFRSF11B/ Osteoprotegerin; OPG and GFPT1/GFA ] in gingival tissues of bronchiectasis patients having chronic periodontitis in North central Indian population. Gingival tissues were collected from 30 systemically healthy chronic periodontitis patients (CP), 30 bronchiectasis patients with chronic periodontitis (B+CP), 3 systemically healthy with healthy gingiva (healthy control; HC) and 3 bronchiectasis with healthy gingiva (bronchiectasis control; BC). Statistical analysis revealed 7 genes to be significantly upregulated on comparing CP with B+CP i.e LTA (P<0.0001) in B+CP while LTB (P<0.0001), TNFSF4 (P=0.0003), TNFSF11 (P<0.0001), TNFSF13 (P=0.0003), TNFSF13B (P<0.0001) and TNFRSF11B (P=0.0004) in CP group. LTA (Lymphotoxin A) gene could be a potential genetic marker in bronchiectasis patients with chronic periodontitis.
Collapse
Affiliation(s)
- Abhaya Gupta
- Department of Periodontology, Faculty of Dental Sciences, King George's Medical University, Uttar Pradesh, Lucknow, India
| | - Neetu Singh
- Department of Molecular Biology, Center for Advanced Research, King George's Medical University, Uttar Pradesh, Lucknow, India
| | - Anil Kumar
- Department of Molecular Biology, Center for Advanced Research, King George's Medical University, Uttar Pradesh, Lucknow, India
| | - Umesh Pratap Verma
- Department of Periodontology, Faculty of Dental Sciences, King George's Medical University, Uttar Pradesh, Lucknow, India
| | - Ajay Kumar Verma
- Department of Respiratory Medicine, King George's Medical University, Uttar Pradesh, Lucknow, India
| | - Hari Shyam
- Department of Molecular Biology, Center for Advanced Research, King George's Medical University, Uttar Pradesh, Lucknow, India
| | - Nand Lal
- Department of Periodontology, Faculty of Dental Sciences, King George's Medical University, Uttar Pradesh, Lucknow, India
| | - Surya Kant
- Department of Respiratory Medicine, King George's Medical University, Uttar Pradesh, Lucknow, India
| | - Ankur Kumari
- Department of Periodontology, Faculty of Dental Sciences, King George's Medical University, Uttar Pradesh, Lucknow, India
| |
Collapse
|
20
|
Zhang J, Zhu C, Gao H, Liang X, Fan X, Zheng Y, Chen S, Wan Y. Identification of biomarkers associated with clinical severity of chronic obstructive pulmonary disease. PeerJ 2020; 8:e10513. [PMID: 33354437 PMCID: PMC7733647 DOI: 10.7717/peerj.10513] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 11/17/2020] [Indexed: 11/20/2022] Open
Abstract
We sought to identify the biomarkers related to the clinical severity of stage I to stage IV chronic obstructive pulmonary disease (COPD). Gene expression profiles from the blood samples of COPD patients at each of the four stages were acquired from the Gene Expression Omnibus Database (GEO, accession number: GSE54837). Genes showing expression changes among the different stages were sorted by soft clustering. We performed functional enrichment, protein-protein interaction (PPI), and miRNA regulatory network analyses for the differentially expressed genes. The biomarkers associated with the clinical classification of COPD were selected from logistic regression models and the relationships between TLR2 and inflammatory factors were verified in clinical blood samples by qPCR and ELISA. Gene clusters demonstrating continuously rising or falling changes in expression (clusters 1, 2, and 7 and clusters 5, 6, and 8, respectively) from stage I to IV were defined as upregulated and downregulated genes, respectively, and further analyzed. The upregulated genes were enriched in functions associated with defense, inflammatory, or immune responses. The downregulated genes were associated with lymphocyte activation and cell activation. TLR2, HMOX1, and CD79A were hub proteins in the integrated network of PPI and miRNA regulatory networks. TLR2 and CD79A were significantly correlated with clinical classifications. TLR2 was closely associated with inflammatory responses during COPD progression. Functions associated with inflammatory and immune responses as well as lymphocyte activation may play important roles in the progression of COPD from stage I to IV. TLR2 and CD79A may serve as potential biomarkers for the clinical severity of COPD. TLR2 and CD79A may also serve as independent biomarkers in the clinical classification in COPD. TLR2 may play an important role in the inflammatory responses of COPD.
Collapse
Affiliation(s)
- Jie Zhang
- Department of Respiratory Diseases, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, Jiangsu, China
| | - Changli Zhu
- Department of Respiratory Diseases, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, Jiangsu, China
| | - Hong Gao
- Department of Respiratory Diseases, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, Jiangsu, China
| | - Xun Liang
- College of Nursing and Midwifery, Jiangsu College of Nursing, Huai'an, Jiangsu, China
| | - Xiaoqian Fan
- Department of Emergency Medicine, Suqian First Hospital, Suqian, Jiangsu, China
| | - Yulong Zheng
- Department of Respiratory Diseases, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, Jiangsu, China
| | - Song Chen
- Institute of Medicinal Biotechnology, Jiangsu College of Nursing, Huai'an, Jiangsu, China
| | - Yufeng Wan
- Department of Respiratory Diseases, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, Jiangsu, China
| |
Collapse
|
21
|
Jolliffe DA, Stefanidis C, Wang Z, Kermani NZ, Dimitrov V, White JH, McDonough JE, Janssens W, Pfeffer P, Griffiths CJ, Bush A, Guo Y, Christenson S, Adcock IM, Chung KF, Thummel KE, Martineau AR. Vitamin D Metabolism Is Dysregulated in Asthma and Chronic Obstructive Pulmonary Disease. Am J Respir Crit Care Med 2020; 202:371-382. [PMID: 32186892 DOI: 10.1164/rccm.201909-1867oc] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Rationale: Vitamin D deficiency is common in patients with asthma and chronic obstructive pulmonary disease (COPD). Low 25-hydroxyvitamin D (25[OH]D) levels may represent a cause or a consequence of these conditions.Objectives: To determine whether vitamin D metabolism is altered in asthma or COPD.Methods: We conducted a longitudinal study in 186 adults to determine whether the 25(OH)D response to six oral doses of 3 mg vitamin D3, administered over 1 year, differed between those with asthma or COPD versus control subjects. Serum concentrations of vitamin D3, 25(OH)D3, and 1α,25-dihydroxyvitamin D3 (1α,25[OH]2D3) were determined presupplementation and postsupplementation in 93 adults with asthma, COPD, or neither condition, and metabolite-to-parent compound molar ratios were compared between groups to estimate hydroxylase activity. Additionally, we analyzed 14 datasets to compare expression of 1α,25(OH)2D3-inducible gene expression signatures in clinical samples taken from adults with asthma or COPD versus control subjects.Measurements and Main Results: The mean postsupplementation 25(OH)D increase in participants with asthma (20.9 nmol/L) and COPD (21.5 nmol/L) was lower than in control subjects (39.8 nmol/L; P = 0.001). Compared with control subjects, patients with asthma and COPD had lower molar ratios of 25(OH)D3-to-vitamin D3 and higher molar ratios of 1α,25(OH)2D3-to-25(OH)D3 both presupplementation and postsupplementation (P ≤ 0.005). Intergroup differences in 1α,25(OH)2D3-inducible gene expression signatures were modest and variable if statistically significant.Conclusions: Attenuation of the 25(OH)D response to vitamin D supplementation in asthma and COPD associated with reduced molar ratios of 25(OH)D3-to-vitamin D3 and increased molar ratios of 1α,25(OH)2D3-to-25(OH)D3 in serum, suggesting that vitamin D metabolism is dysregulated in these conditions.
Collapse
Affiliation(s)
- David A Jolliffe
- Asthma UK Centre for Applied Research, Institute of Population Health Sciences, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Christos Stefanidis
- Asthma UK Centre for Applied Research, Institute of Population Health Sciences, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Zhican Wang
- Department of Pharmaceutics, University of Washington, Seattle, Washington
| | | | - Vassil Dimitrov
- Department of Physiology, McGill University, Montreal, Quebec, Canada
| | - John H White
- Department of Physiology, McGill University, Montreal, Quebec, Canada
| | | | - Wim Janssens
- Laboratory of Respiratory Diseases and Thoracic Surgery, Department of Chronic Diseases, Metabolism and Ageing, Katholieke Universiteit Leuven, Leuven, Belgium; and
| | - Paul Pfeffer
- Asthma UK Centre for Applied Research, Institute of Population Health Sciences, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Christopher J Griffiths
- Asthma UK Centre for Applied Research, Institute of Population Health Sciences, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Andrew Bush
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Yike Guo
- Data Science Institute, William Penney Laboratory and
| | - Stephanie Christenson
- Division of Pulmonary, Critical Care, Allergy, & Sleep Medicine, Department of Medicine, University of California, San Francisco, California
| | - Ian M Adcock
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Kian Fan Chung
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Kenneth E Thummel
- Department of Pharmaceutics, University of Washington, Seattle, Washington
| | - Adrian R Martineau
- Asthma UK Centre for Applied Research, Institute of Population Health Sciences, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| |
Collapse
|
22
|
Groth EE, Weber M, Bahmer T, Pedersen F, Kirsten A, Börnigen D, Rabe KF, Watz H, Ammerpohl O, Goldmann T. Exploration of the sputum methylome and omics deconvolution by quadratic programming in molecular profiling of asthma and COPD: the road to sputum omics 2.0. Respir Res 2020; 21:274. [PMID: 33076907 PMCID: PMC7574293 DOI: 10.1186/s12931-020-01544-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/11/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND To date, most studies involving high-throughput analyses of sputum in asthma and COPD have focused on identifying transcriptomic signatures of disease. No whole-genome methylation analysis of sputum cells has been performed yet. In this context, the highly variable cellular composition of sputum has potential to confound the molecular analyses. METHODS Whole-genome transcription (Agilent Human 4 × 44 k array) and methylation (Illumina 450 k BeadChip) analyses were performed on sputum samples of 9 asthmatics, 10 healthy and 10 COPD subjects. RNA integrity was checked by capillary electrophoresis and used to correct in silico for bias conferred by RNA degradation during biobank sample storage. Estimates of cell type-specific molecular profiles were derived via regression by quadratic programming based on sputum differential cell counts. All analyses were conducted using the open-source R/Bioconductor software framework. RESULTS A linear regression step was found to perform well in removing RNA degradation-related bias among the main principal components of the gene expression data, increasing the number of genes detectable as differentially expressed in asthma and COPD sputa (compared to controls). We observed a strong influence of the cellular composition on the results of mixed-cell sputum analyses. Exemplarily, upregulated genes derived from mixed-cell data in asthma were dominated by genes predominantly expressed in eosinophils after deconvolution. The deconvolution, however, allowed to perform differential expression and methylation analyses on the level of individual cell types and, though we only analyzed a limited number of biological replicates, was found to provide good estimates compared to previously published data about gene expression in lung eosinophils in asthma. Analysis of the sputum methylome indicated presence of differential methylation in genomic regions of interest, e.g. mapping to a number of human leukocyte antigen (HLA) genes related to both major histocompatibility complex (MHC) class I and II molecules in asthma and COPD macrophages. Furthermore, we found the SMAD3 (SMAD family member 3) gene, among others, to lie within differentially methylated regions which has been previously reported in the context of asthma. CONCLUSIONS In this methodology-oriented study, we show that methylation profiling can be easily integrated into sputum analysis workflows and exhibits a strong potential to contribute to the profiling and understanding of pulmonary inflammation. Wherever RNA degradation is of concern, in silico correction can be effective in improving both sensitivity and specificity of downstream analyses. We suggest that deconvolution methods should be integrated in sputum omics analysis workflows whenever possible in order to facilitate the unbiased discovery and interpretation of molecular patterns of inflammation.
Collapse
Affiliation(s)
- Espen E Groth
- LungenClinic Grosshansdorf, Großhansdorf, Germany. .,Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Großhansdorf, Germany. .,Department of Internal Medicine I, Pneumology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany. .,Department of Oncology, Hematology and BMT with Section Pneumology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Melanie Weber
- Program in Applied and Computational Mathematics, Princeton University, Princeton, NJ, USA
| | - Thomas Bahmer
- LungenClinic Grosshansdorf, Großhansdorf, Germany.,Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Großhansdorf, Germany.,Department of Internal Medicine I, Pneumology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Frauke Pedersen
- LungenClinic Grosshansdorf, Großhansdorf, Germany.,Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Großhansdorf, Germany.,Pulmonary Research Institute at LungenClinic Grosshansdorf, Großhansdorf, Germany
| | - Anne Kirsten
- Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Großhansdorf, Germany.,Pulmonary Research Institute at LungenClinic Grosshansdorf, Großhansdorf, Germany
| | - Daniela Börnigen
- Bioinformatics Core Unit, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Klaus F Rabe
- LungenClinic Grosshansdorf, Großhansdorf, Germany.,Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Großhansdorf, Germany
| | - Henrik Watz
- Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Großhansdorf, Germany.,Pulmonary Research Institute at LungenClinic Grosshansdorf, Großhansdorf, Germany
| | - Ole Ammerpohl
- Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Großhansdorf, Germany.,Institute of Human Genetics, University Medical Center Ulm, Ulm, Germany
| | - Torsten Goldmann
- Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Großhansdorf, Germany.,Research Center Borstel, Pathology, Borstel, Germany
| |
Collapse
|
23
|
Wilson AC, Kumar PL, Lee S, Parker MM, Arora I, Morrow JD, Wouters EFM, Casaburi R, Rennard SI, Lomas DA, Agusti A, Tal-Singer R, Dransfield MT, Wells JM, Bhatt SP, Washko G, Thannickal VJ, Tiwari HK, Hersh CP, Castaldi PJ, Silverman EK, McDonald MLN. Heme metabolism genes Downregulated in COPD Cachexia. Respir Res 2020; 21:100. [PMID: 32354332 PMCID: PMC7193359 DOI: 10.1186/s12931-020-01336-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/11/2020] [Indexed: 11/27/2022] Open
Abstract
INTRODUCTION Cachexia contributes to increased mortality and reduced quality of life in Chronic Obstructive Pulmonary Disease (COPD) and may be associated with underlying gene expression changes. Our goal was to identify differential gene expression signatures associated with COPD cachexia in current and former smokers. METHODS We analyzed whole-blood gene expression data from participants with COPD in a discovery cohort (COPDGene, N = 400) and assessed replication (ECLIPSE, N = 114). To approximate the consensus definition using available criteria, cachexia was defined as weight-loss > 5% in the past 12 months or low body mass index (BMI) (< 20 kg/m2) and 1/3 criteria: decreased muscle strength (six-minute walk distance < 350 m), anemia (hemoglobin < 12 g/dl), and low fat-free mass index (FFMI) (< 15 kg/m2 among women and < 17 kg/m2 among men) in COPDGene. In ECLIPSE, cachexia was defined as weight-loss > 5% in the past 12 months or low BMI and 3/5 criteria: decreased muscle strength, anorexia, abnormal biochemistry (anemia or high c-reactive protein (> 5 mg/l)), fatigue, and low FFMI. Differential gene expression was assessed between cachectic and non-cachectic subjects, adjusting for age, sex, white blood cell counts, and technical covariates. Gene set enrichment analysis was performed using MSigDB. RESULTS The prevalence of COPD cachexia was 13.7% in COPDGene and 7.9% in ECLIPSE. Fourteen genes were differentially downregulated in cachectic versus non-cachectic COPD patients in COPDGene (FDR < 0.05) and ECLIPSE (FDR < 0.05). DISCUSSION Several replicated genes regulating heme metabolism were downregulated among participants with COPD cachexia. Impaired heme biosynthesis may contribute to cachexia development through free-iron buildup and oxidative tissue damage.
Collapse
Affiliation(s)
- Ava C Wilson
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Preeti L Kumar
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sool Lee
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Margaret M Parker
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Itika Arora
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jarrett D Morrow
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Emiel F M Wouters
- Centre of expertise for chronic organ failure, Horn, the Netherlands
| | - Richard Casaburi
- Rehabilitation Clinical Trials Center, Los Angeles Biomedical Research Institute at Harbor Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Stephen I Rennard
- Department of Medicine, Nebraska Medical Center, Omaha, NE, USA
- BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - David A Lomas
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Alvar Agusti
- Fundació Investigació Sanitària Illes Balears (FISIB), Ciber Enfermedades Respiratorias (CIBERES), Barcelona, Catalunya, Spain
- Thorax Institute, Hospital Clinic, IDIBAPS, University of Barcelona, Barcelona, Spain
| | | | - Mark T Dransfield
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - J Michael Wells
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Surya P Bhatt
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - George Washko
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Victor J Thannickal
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hemant K Tiwari
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Peter J Castaldi
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Merry-Lynn N McDonald
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA.
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.
| |
Collapse
|
24
|
Regan EA, Hersh CP, Castaldi PJ, DeMeo DL, Silverman EK, Crapo JD, Bowler RP. Omics and the Search for Blood Biomarkers in Chronic Obstructive Pulmonary Disease. Insights from COPDGene. Am J Respir Cell Mol Biol 2020; 61:143-149. [PMID: 30874442 DOI: 10.1165/rcmb.2018-0245ps] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
There is an unmet need for blood biomarkers in diagnosis and prognosis of chronic obstructive pulmonary disease (COPD). The search for these biomarkers has been revolutionized by high-throughput sequencing techniques and multiplex platforms that can measure thousands of gene transcripts, proteins, or metabolites. We review COPDGene (Genetic Epidemiology of COPD) project publications that include DNA methylation, transcriptomic, proteomic, and metabolomic blood biomarkers and discuss their impact on COPD. Key contributions from COPDGene include identification of DNA methylation effects from smoking and genetic variation, new transcriptomic signatures in the blood, identification of protein biomarkers associated with severity and progression (e.g., sRAGE [soluble receptor for advanced glycosylation end products], inflammatory cytokines IL-6 and IL-8), and identification of small molecules (ceramides and sphingomyelin) that may be pathogenic. COPDGene studies have revealed that some of the COPD genome-wide association study polymorphisms are strongly associated with blood biomarkers (e.g., rs2070600 in AGER is a pQTL [protein quantitative trait locus] for sRAGE), underscoring the importance of combining omics results. Investigators have developed molecular networks identifying lower CD4+ resting memory cells associated with COPD. Genes, proteins, and metabolite networks are particularly important because the explanatory value of any single molecule is small (1-10%) compared with panels of multiple markers. COPDGene has been a useful resource in the identification and validation of multiple biomarkers for COPD. These biomarkers, either combined in multiple biomarker panels or integrated with other omics data types, may lead to novel diagnostic and prognostic tests for COPD phenotypes and may be relevant for assessing novel therapies.
Collapse
Affiliation(s)
- Elizabeth A Regan
- 1Department of Medicine, National Jewish Health, Denver, Colorado; and
| | - Craig P Hersh
- 2Channing Division of Network Medicine and.,3Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Peter J Castaldi
- 2Channing Division of Network Medicine and.,3Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Dawn L DeMeo
- 2Channing Division of Network Medicine and.,3Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Edwin K Silverman
- 2Channing Division of Network Medicine and.,3Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - James D Crapo
- 1Department of Medicine, National Jewish Health, Denver, Colorado; and
| | - Russell P Bowler
- 1Department of Medicine, National Jewish Health, Denver, Colorado; and
| |
Collapse
|
25
|
Maiorino E, Baek SH, Guo F, Zhou X, Kothari PH, Silverman EK, Barabási AL, Weiss ST, Raby BA, Sharma A. Discovering the genes mediating the interactions between chronic respiratory diseases in the human interactome. Nat Commun 2020; 11:811. [PMID: 32041952 PMCID: PMC7010776 DOI: 10.1038/s41467-020-14600-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 01/17/2020] [Indexed: 12/21/2022] Open
Abstract
The molecular and clinical features of a complex disease can be influenced by other diseases affecting the same individual. Understanding disease-disease interactions is therefore crucial for revealing shared molecular mechanisms among diseases and designing effective treatments. Here we introduce Flow Centrality (FC), a network-based approach to identify the genes mediating the interaction between two diseases in a protein-protein interaction network. We focus on asthma and COPD, two chronic respiratory diseases that have been long hypothesized to share common genetic determinants and mechanisms. We show that FC highlights potential mediator genes between the two diseases, and observe similar outcomes when applying FC to 66 additional pairs of related diseases. Further, we perform in vitro perturbation experiments on a widely replicated asthma gene, GSDMB, showing that FC identifies candidate mediators of the interactions between GSDMB and COPD-associated genes. Our results indicate that FC predicts promising gene candidates for further study of disease-disease interactions.
Collapse
Affiliation(s)
- Enrico Maiorino
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Network Science Institute, Center for Complex Network Research, Department of Physics, Northeastern University, Boston, MA, USA.
| | - Seung Han Baek
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Feng Guo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Xiaobo Zhou
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Parul H Kothari
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Albert-László Barabási
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Network Science Institute, Center for Complex Network Research, Department of Physics, Northeastern University, Boston, MA, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Benjamin A Raby
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Amitabh Sharma
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
26
|
Patel H, Iniesta R, Stahl D, Dobson RJ, Newhouse SJ. Working Towards a Blood-Derived Gene Expression Biomarker Specific for Alzheimer's Disease. J Alzheimers Dis 2020; 74:545-561. [PMID: 32065794 PMCID: PMC7175937 DOI: 10.3233/jad-191163] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2020] [Indexed: 11/15/2022]
Abstract
BACKGROUND The typical approach to identify blood-derived gene expression signatures as a biomarker for Alzheimer's disease (AD) have relied on training classification models using AD and healthy controls only. This may inadvertently result in the identification of markers for general illness rather than being disease-specific. OBJECTIVE Investigate whether incorporating additional related disorders in the classification model development process can lead to the discovery of an AD-specific gene expression signature. METHODS Two types of XGBoost classification models were developed. The first used 160 AD and 127 healthy controls and the second used the same 160 AD with 6,318 upsampled mixed controls consisting of Parkinson's disease, multiple sclerosis, amyotrophic lateral sclerosis, bipolar disorder, schizophrenia, coronary artery disease, rheumatoid arthritis, chronic obstructive pulmonary disease, and cognitively healthy subjects. Both classification models were evaluated in an independent cohort consisting of 127 AD and 687 mixed controls. RESULTS The AD versus healthy control models resulted in an average 48.7% sensitivity (95% CI = 34.7-64.6), 41.9% specificity (95% CI = 26.8-54.3), 13.6% PPV (95% CI = 9.9-18.5), and 81.1% NPV (95% CI = 73.3-87.7). In contrast, the mixed control models resulted in an average of 40.8% sensitivity (95% CI = 27.5-52.0), 95.3% specificity (95% CI = 93.3-97.1), 61.4% PPV (95% CI = 53.8-69.6), and 89.7% NPV (95% CI = 87.8-91.4). CONCLUSIONS This early work demonstrates the value of incorporating additional related disorders into the classification model developmental process, which can result in models with improved ability to distinguish AD from a heterogeneous aging population. However, further improvement to the sensitivity of the test is still required.
Collapse
Affiliation(s)
- Hamel Patel
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
- NIHR BioResource Centre Maudsley, NIHR Maudsley Biomedical Research Centre (BRC) at South London and Maudsley NHS Foundation Trust (SLaM) & Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King’s College London, London, UK
| | - Raquel Iniesta
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
| | - Daniel Stahl
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
| | - Richard J.B. Dobson
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
- NIHR BioResource Centre Maudsley, NIHR Maudsley Biomedical Research Centre (BRC) at South London and Maudsley NHS Foundation Trust (SLaM) & Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King’s College London, London, UK
- Health Data Research UK London, University College London, London, UK
- Institute of Health Informatics, University College London, London, UK
- The National Institute for Health Research University College London Hospitals Biomedical Research Centre, University College London, London, UK
| | - Stephen J. Newhouse
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
- NIHR BioResource Centre Maudsley, NIHR Maudsley Biomedical Research Centre (BRC) at South London and Maudsley NHS Foundation Trust (SLaM) & Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King’s College London, London, UK
- Health Data Research UK London, University College London, London, UK
- Institute of Health Informatics, University College London, London, UK
- The National Institute for Health Research University College London Hospitals Biomedical Research Centre, University College London, London, UK
| |
Collapse
|
27
|
Gene expression microarray public dataset reanalysis in chronic obstructive pulmonary disease. PLoS One 2019; 14:e0224750. [PMID: 31730674 PMCID: PMC6857915 DOI: 10.1371/journal.pone.0224750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 10/21/2019] [Indexed: 12/20/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) was classified by the Centers for Disease Control and Prevention in 2014 as the 3rd leading cause of death in the United States (US). The main cause of COPD is exposure to tobacco smoke and air pollutants. Problems associated with COPD include under-diagnosis of the disease and an increase in the number of smokers worldwide. The goal of our study is to identify disease variability in the gene expression profiles of COPD subjects compared to controls, by reanalyzing pre-existing, publicly available microarray expression datasets. Our inclusion criteria for microarray datasets selected for smoking status, age and sex of blood donors reported. Our datasets used Affymetrix, Agilent microarray platforms (7 datasets, 1,262 samples). We re-analyzed the curated raw microarray expression data using R packages, and used Box-Cox power transformations to normalize datasets. To identify significant differentially expressed genes we used generalized least squares models with disease state, age, sex, smoking status and study as effects that also included binary interactions, followed by likelihood ratio tests (LRT). We found 3,315 statistically significant (Storey-adjusted q-value <0.05) differentially expressed genes with respect to disease state (COPD or control). We further filtered these genes for biological effect using results from LRT q-value <0.05 and model estimates’ 10% two-tailed quantiles of mean differences between COPD and control), to identify 679 genes. Through analysis of disease, sex, age, and also smoking status and disease interactions we identified differentially expressed genes involved in a variety of immune responses and cell processes in COPD. We also trained a logistic regression model using the common array genes as features, which enabled prediction of disease status with 81.7% accuracy. Our results give potential for improving the diagnosis of COPD through blood and highlight novel gene expression disease signatures.
Collapse
|
28
|
Halper-Stromberg E, Yun JH, Parker MM, Singer RT, Gaggar A, Silverman EK, Leach S, Bowler RP, Castaldi PJ. Systemic Markers of Adaptive and Innate Immunity Are Associated with Chronic Obstructive Pulmonary Disease Severity and Spirometric Disease Progression. Am J Respir Cell Mol Biol 2019; 58:500-509. [PMID: 29206476 DOI: 10.1165/rcmb.2017-0373oc] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The progression of chronic obstructive pulmonary disease (COPD) is associated with marked alterations in circulating immune cell populations, but no studies have characterized alterations in these cell types across the full spectrum of lung function impairment in current and former smokers. In 6,299 subjects from the COPDGene and ECLIPSE (Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints) studies, we related Coulter blood counts and proportions to cross-sectional forced expiratory volume in 1 second (FEV1), adjusting for current smoking status. We also related cell count measures to 3-year change in FEV1 in ECLIPSE subjects. In a subset of subjects with blood gene expression data, we used cell type deconvolution methods to infer the proportions of immune cell subpopulations, and we related these to COPD clinical status. We observed that FEV1 levels are positively correlated with lymphocytes and negatively correlated with myeloid populations, such as neutrophils and monocytes. In multivariate models, absolute cell counts and proportions were associated with cross-sectional FEV1, and lymphocytes, monocytes, and eosinophil counts were predictive of 3-year change in lung function. Using cell type deconvolution to study immune cell subpopulations, we observed that subjects with COPD had a lower proportion of CD4+ resting memory cells and naive B cells compared with smokers without COPD. Alterations in circulating immune cells in COPD support a mixed pattern of lymphocyte suppression and an enhanced myeloid cell immune response. Cell counts and proportions contribute independent information to models predicting lung function, suggesting a critical role for immune response in long-term COPD outcomes. Cell type deconvolution is a promising method for immunophenotyping in large cohorts.
Collapse
Affiliation(s)
- Eitan Halper-Stromberg
- 1 University of Colorado School of Medicine, Aurora, Colorado.,2 National Jewish Health, Denver, Colorado
| | - Jeong H Yun
- 3 Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,4 Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Margaret M Parker
- 3 Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | | | - Amit Gaggar
- 6 Division of Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama; and
| | - Edwin K Silverman
- 3 Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,4 Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | | | - Russell P Bowler
- 1 University of Colorado School of Medicine, Aurora, Colorado.,2 National Jewish Health, Denver, Colorado
| | - Peter J Castaldi
- 3 Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,7 Division of General Internal Medicine and Primary Care, Brigham and Women's Hospital, Boston, Massachusetts
| |
Collapse
|
29
|
Paska C, Barta I, Drozdovszky O, Antus B. Elimination of bacterial DNA during RNA isolation from sputum: Bashing bead vortexing is preferable over prolonged DNase treatment. PLoS One 2019; 14:e0214609. [PMID: 30921416 PMCID: PMC6438495 DOI: 10.1371/journal.pone.0214609] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/17/2019] [Indexed: 11/18/2022] Open
Abstract
Sputum often contains large amounts of contaminating bacterial DNA that, if not eliminated during RNA isolation, may interfere with gene expression studies. During RNA isolation only repeated DNase treatment can effectively remove contaminating bacterial DNA from samples, but this compromises RNA quality. In this study we tested alternative methods to facilitate the removal of DNA and improve the quality of RNA obtained. Sputum samples obtained from patients with chronic obstructive pulmonary disease were processed with dithiothreitol and subjected to various RNA isolation methods, yet with modified protocols. Modifications included prolonged DNase treatment or vortexing of sputum cells in the presence of beads prior to RNA isolation. Bacterial DNA contamination was tested by PCR using universal bacterial primers, while RNA quality was assessed by real-time PCR using GAPDH primers for amplicons of different length. We found that the RNeasy Plus Mini kit equipped with the gDNA eliminator spin column was able to completely eliminate bacterial DNA, if sputum cells were lysed in the presence of bashing beads. Notably, compared with the standard protocol, the modified procedure yielded better quality RNA as well, as indicated by improved threshold profiles of qPCR. Bead vortexing of cells was less effective when combined with other RNA isolation methods, and the repeated DNase treatment needed to completely remove contaminating DNA from the samples reduced the quality of RNA markedly. Bead vortexing in combination with certain RNA extraction methods greatly facilitates the isolation of sputum RNA that is free of contaminating bacterial DNA, and is suitable for downstream applications.
Collapse
Affiliation(s)
- Csilla Paska
- Department of Pathophysiology, National Koranyi Institute of Pulmonology, Budapest, Hungary
| | - Imre Barta
- Department of Pathophysiology, National Koranyi Institute of Pulmonology, Budapest, Hungary
| | - Orsolya Drozdovszky
- Department of Pathophysiology, National Koranyi Institute of Pulmonology, Budapest, Hungary
| | - Balazs Antus
- Department of Pathophysiology, National Koranyi Institute of Pulmonology, Budapest, Hungary
- Department of Pulmonology, National Koranyi Institute of Pulmonology, Budapest, Hungary
- * E-mail:
| |
Collapse
|
30
|
Gradin R, Lindstedt M, Johansson H. Batch adjustment by reference alignment (BARA): Improved prediction performance in biological test sets with batch effects. PLoS One 2019; 14:e0212669. [PMID: 30794641 PMCID: PMC6386283 DOI: 10.1371/journal.pone.0212669] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 02/07/2019] [Indexed: 12/15/2022] Open
Abstract
Many biological data acquisition platforms suffer from inadvertent inclusion of biologically irrelevant variance in analyzed data, collectively termed batch effects. Batch effects can lead to difficulties in downstream analysis by lowering the power to detect biologically interesting differences and can in certain instances lead to false discoveries. They are especially troublesome in predictive modelling where samples in training sets and test sets are often completely correlated with batches. In this article, we present BARA, a normalization method for adjusting batch effects in predictive modelling. BARA utilizes a few reference samples to adjust for batch effects in a compressed data space spanned by the training set. We evaluate BARA using a collection of publicly available datasets and three different prediction models, and compare its performance to already existing methods developed for similar purposes. The results show that data normalized with BARA generates high and consistent prediction performances. Further, they suggest that BARA produces reliable performances independent of the examined classifiers. We therefore conclude that BARA has great potential to facilitate the development of predictive assays where test sets and training sets are correlated with batch.
Collapse
Affiliation(s)
| | - Malin Lindstedt
- Department of Immunotechnology, Lund University, Lund, Sweden
| | | |
Collapse
|
31
|
Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations. Nat Commun 2019; 10:880. [PMID: 30787307 PMCID: PMC6382865 DOI: 10.1038/s41467-019-08469-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 01/08/2019] [Indexed: 12/15/2022] Open
Abstract
Asthma is a complex disease with striking disparities across racial and ethnic groups. Despite its relatively high burden, representation of individuals of African ancestry in asthma genome-wide association studies (GWAS) has been inadequate, and true associations in these underrepresented minority groups have been inconclusive. We report the results of a genome-wide meta-analysis from the Consortium on Asthma among African Ancestry Populations (CAAPA; 7009 asthma cases, 7645 controls). We find strong evidence for association at four previously reported asthma loci whose discovery was driven largely by non-African populations, including the chromosome 17q12-q21 locus and the chr12q13 region, a novel (and not previously replicated) asthma locus recently identified by the Trans-National Asthma Genetic Consortium (TAGC). An additional seven loci reported by TAGC show marginal evidence for association in CAAPA. We also identify two novel loci (8p23 and 8q24) that may be specific to asthma risk in African ancestry populations.
Collapse
|
32
|
Faner R, Morrow JD, Casas-Recasens S, Cloonan SM, Noell G, López-Giraldo A, Tal-Singer R, Miller BE, Silverman EK, Agustí A, Hersh CP. Do sputum or circulating blood samples reflect the pulmonary transcriptomic differences of COPD patients? A multi-tissue transcriptomic network META-analysis. Respir Res 2019; 20:5. [PMID: 30621695 PMCID: PMC6325784 DOI: 10.1186/s12931-018-0965-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 12/16/2018] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Previous studies have identified lung, sputum or blood transcriptomic biomarkers associated with the severity of airflow limitation in COPD. Yet, it is not clear whether the lung pathobiology is mirrored by these surrogate tissues. The aim of this study was to explore this question. METHODS We used Weighted Gene Co-expression Network Analysis (WGCNA) to identify shared pathological mechanisms across four COPD gene-expression datasets: two sets of lung tissues (L1 n = 70; L2 n = 124), and one each of induced sputum (S; n = 121) and peripheral blood (B; n = 121). RESULTS WGCNA analysis identified twenty-one gene co-expression modules in L1. A robust module preservation between the two L datasets was observed (86%), with less preservation in S (33%) and even less in B (23%). Three modules preserved across lung tissues and sputum (not blood) were associated with the severity of airflow limitation. Ontology enrichment analysis showed that these modules included genes related to mitochondrial function, ion-homeostasis, T cells and RNA processing. These findings were largely reproduced using the consensus WGCNA network approach. CONCLUSIONS These observations indicate that major differences in lung tissue transcriptomics in patients with COPD are poorly mirrored in sputum and are unrelated to those determined in blood, suggesting that the systemic component in COPD is independently regulated. Finally, the fact that one of the preserved modules associated with FEV1 was enriched in mitochondria-related genes supports a role for mitochondrial dysfunction in the pathobiology of COPD.
Collapse
Affiliation(s)
- Rosa Faner
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), C/Casanova 143, Cellex, P2A, 08036, Barcelona, Spain.
| | - Jarrett D Morrow
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Sandra Casas-Recasens
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), C/Casanova 143, Cellex, P2A, 08036, Barcelona, Spain
| | - Suzanne M Cloonan
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Guillaume Noell
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), C/Casanova 143, Cellex, P2A, 08036, Barcelona, Spain
| | - Alejandra López-Giraldo
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), C/Casanova 143, Cellex, P2A, 08036, Barcelona, Spain
- Respiratory Institute, Hospital Clinic, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Ruth Tal-Singer
- Respiratory Therapy Area Unit GSK R and D, Collegeville, PA, USA
| | - Bruce E Miller
- Respiratory Therapy Area Unit GSK R and D, Collegeville, PA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Alvar Agustí
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), C/Casanova 143, Cellex, P2A, 08036, Barcelona, Spain
- Respiratory Institute, Hospital Clinic, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| |
Collapse
|
33
|
Sharma A, Kitsak M, Cho MH, Ameli A, Zhou X, Jiang Z, Crapo JD, Beaty TH, Menche J, Bakke PS, Santolini M, Silverman EK. Integration of Molecular Interactome and Targeted Interaction Analysis to Identify a COPD Disease Network Module. Sci Rep 2018; 8:14439. [PMID: 30262855 PMCID: PMC6160419 DOI: 10.1038/s41598-018-32173-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 08/20/2018] [Indexed: 12/21/2022] Open
Abstract
The polygenic nature of complex diseases offers potential opportunities to utilize network-based approaches that leverage the comprehensive set of protein-protein interactions (the human interactome) to identify new genes of interest and relevant biological pathways. However, the incompleteness of the current human interactome prevents it from reaching its full potential to extract network-based knowledge from gene discovery efforts, such as genome-wide association studies, for complex diseases like chronic obstructive pulmonary disease (COPD). Here, we provide a framework that integrates the existing human interactome information with experimental protein-protein interaction data for FAM13A, one of the most highly associated genetic loci to COPD, to find a more comprehensive disease network module. We identified an initial disease network neighborhood by applying a random-walk method. Next, we developed a network-based closeness approach (CAB) that revealed 9 out of 96 FAM13A interacting partners identified by affinity purification assays were significantly close to the initial network neighborhood. Moreover, compared to a similar method (local radiality), the CAB approach predicts low-degree genes as potential candidates. The candidates identified by the network-based closeness approach were combined with the initial network neighborhood to build a comprehensive disease network module (163 genes) that was enriched with genes differentially expressed between controls and COPD subjects in alveolar macrophages, lung tissue, sputum, blood, and bronchial brushing datasets. Overall, we demonstrate an approach to find disease-related network components using new laboratory data to overcome incompleteness of the current interactome.
Collapse
Affiliation(s)
- Amitabh Sharma
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, USA. .,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA. .,Center for Complex Networks Research and Department of Physics, Northeastern University, Boston, MA, 02115, USA. .,Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.
| | - Maksim Kitsak
- Center for Complex Networks Research and Department of Physics, Northeastern University, Boston, MA, 02115, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, USA.,Pulmonary and Critical Care Division, Brigham and Women's Hospital and Harvard Medical School, Boston, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Asher Ameli
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, USA.,Department of Physics, Northeastern University, Boston, MA, 02115, United States
| | - Xiaobo Zhou
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Zhiqiang Jiang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, USA
| | - James D Crapo
- Department of Medicine, National Jewish Health, Denver, Colorado, USA
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jörg Menche
- Department of Bioinformatics, CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, A-1090, Vienna, Austria
| | - Per S Bakke
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Marc Santolini
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, USA.,Center for Complex Networks Research and Department of Physics, Northeastern University, Boston, MA, 02115, USA.,Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, USA. .,Pulmonary and Critical Care Division, Brigham and Women's Hospital and Harvard Medical School, Boston, USA. .,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
| |
Collapse
|
34
|
Vishweswaraiah S, George L, Purushothaman N, Ganguly K. A candidate gene identification strategy utilizing mouse to human big-data mining: "3R-tenet" in COPD genetic research. Respir Res 2018; 19:92. [PMID: 29871630 PMCID: PMC5989378 DOI: 10.1186/s12931-018-0795-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 04/27/2018] [Indexed: 12/13/2022] Open
Abstract
Background Early life impairments leading to lower lung function by adulthood are considered as risk factors for chronic obstructive pulmonary disease (COPD). Recently, we compared the lung transcriptomic profile between two mouse strains with extreme total lung capacities to identify plausible pulmonary function determining genes using microarray analysis (GSE80078). Advancement of high-throughput techniques like deep sequencing (eg. RNA-seq) and microarray have resulted in an explosion of genomic data in the online public repositories which however remains under-exploited. Strategic curation of publicly available genomic data with a mouse-human translational approach can effectively implement “3R- Tenet” by reducing screening experiments with animals and performing mechanistic studies using physiologically relevant in vitro model systems. Therefore, we sought to analyze the association of functional variations within human orthologs of mouse lung function candidate genes in a publicly available COPD lung RNA-seq data-set. Methods Association of missense single nucleotide polymorphisms, insertions, deletions, and splice junction variants were analyzed for susceptibility to COPD using RNA-seq data of a Korean population (GSE57148). Expression of the associated genes were studied using the Gene Paint (mouse embryo) and Human Protein Atlas (normal adult human lung) databases. The genes were also assessed for replication of the associations and expression in COPD−/mouse cigarette smoke exposed lung tissues using other datasets. Results Significant association (p < 0.05) of variations in 20 genes to higher COPD susceptibility have been detected within the investigated cohort. Association of HJURP, MCRS1 and TLR8 are novel in relation to COPD. The associated ADAM19 and KIT loci have been reported earlier. The remaining 15 genes have also been previously associated to COPD. Differential transcript expression levels of the associated genes in COPD- and/ or mouse emphysematous lung tissues have been detected. Conclusion Our findings suggest strategic mouse-human datamining approaches can identify novel COPD candidate genes using existing datasets in the online repositories. The candidates can be further evaluated for mechanistic role through in vitro studies using appropriate primary cells/cell lines. Functional studies can be limited to transgenic animal models of only well supported candidate genes. This approach will lead to a significant reduction of animal experimentation in respiratory research. Electronic supplementary material The online version of this article (10.1186/s12931-018-0795-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | - Leema George
- SRM Research Institute, SRM University, Chennai, 603203, India
| | - Natarajan Purushothaman
- Department of Genetic Engineering, School of Bioengineering, Faculty of Engineering and Technology, SRM University, Chennai, 603203, India
| | - Koustav Ganguly
- SRM Research Institute, SRM University, Chennai, 603203, India. .,Work Environment Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Box 287, SE-171 77, Stockholm, Sweden.
| |
Collapse
|
35
|
Whole Blood Gene Expression Profiling Predicts Severe Morbidity and Mortality in Cystic Fibrosis: A 5-Year Follow-Up Study. Ann Am Thorac Soc 2018; 15:589-598. [DOI: 10.1513/annalsats.201707-527oc] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
|
36
|
Shaddox E, Stingo FC, Peterson CB, Jacobson S, Cruickshank-Quinn C, Kechris K, Bowler R, Vannucci M. A Bayesian Approach for Learning Gene Networks Underlying Disease Severity in COPD. STATISTICS IN BIOSCIENCES 2018; 10:59-85. [PMID: 33912251 DOI: 10.1007/s12561-016-9176-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
In this paper, we propose a Bayesian hierarchical approach to infer network structures across multiple sample groups where both shared and differential edges may exist across the groups. In our approach, we link graphs through a Markov random field prior. This prior on network similarity provides a measure of pairwise relatedness that borrows strength only between related groups. We incorporate the computational efficiency of continuous shrinkage priors, improving scalability for network estimation in cases of larger dimensionality. Our model is applied to patient groups with increasing levels of chronic obstructive pulmonary disease severity, with the goal of better understanding the break down of gene pathways as the disease progresses. Our approach is able to identify critical hub genes for four targeted pathways. Furthermore, it identifies gene connections that are disrupted with increased disease severity and that characterize the disease evolution. We also demonstrate the superior performance of our approach with respect to competing methods, using simulated data.
Collapse
Affiliation(s)
- Elin Shaddox
- Department of Statistics, Rice University, Houston, USA
| | - Francesco C Stingo
- Dipartimento di Statistica, Informatica, Applicazioni "G.Parenti", University of Florence, Florence, Italy
| | | | - Sean Jacobson
- Department of Medicine, National Jewish Health, Denver, CO, USA
| | - Charmion Cruickshank-Quinn
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Colorado Denver, Denver, CO, USA
| | - Katerina Kechris
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Denver, Denver, CO, USA
| | - Russell Bowler
- Department of Medicine, National Jewish Health, Denver, CO, USA
| | | |
Collapse
|
37
|
Schlauch D, Glass K, Hersh CP, Silverman EK, Quackenbush J. Estimating drivers of cell state transitions using gene regulatory network models. BMC SYSTEMS BIOLOGY 2017; 11:139. [PMID: 29237467 PMCID: PMC5729420 DOI: 10.1186/s12918-017-0517-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 11/21/2017] [Indexed: 12/12/2022]
Abstract
Background Specific cellular states are often associated with distinct gene expression patterns. These states are plastic, changing during development, or in the transition from health to disease. One relatively simple extension of this concept is to recognize that we can classify different cell-types by their active gene regulatory networks and that, consequently, transitions between cellular states can be modeled by changes in these underlying regulatory networks. Results Here we describe MONSTER, MOdeling Network State Transitions from Expression and Regulatory data, a regression-based method for inferring transcription factor drivers of cell state conditions at the gene regulatory network level. As a demonstration, we apply MONSTER to four different studies of chronic obstructive pulmonary disease to identify transcription factors that alter the network structure as the cell state progresses toward the disease-state. Conclusions We demonstrate that MONSTER can find strong regulatory signals that persist across studies and tissues of the same disease and that are not detectable using conventional analysis methods based on differential expression. An R package implementing MONSTER is available at github.com/QuackenbushLab/MONSTER. Electronic supplementary material The online version of this article (doi:10.1186/s12918-017-0517-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Daniel Schlauch
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, 02115, MA, USA.,Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, 02115, MA, USA
| | - Kimberly Glass
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, 02115, MA, USA.,Department of Medicine, Harvard Medical School, Boston, 02115, MA, USA
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, 02115, MA, USA.,Department of Medicine, Harvard Medical School, Boston, 02115, MA, USA.,Pulmonary and Critical Care Division, Brigham and Women's Hospital, Boston, 02115, MA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, 02115, MA, USA.,Department of Medicine, Harvard Medical School, Boston, 02115, MA, USA.,Pulmonary and Critical Care Division, Brigham and Women's Hospital, Boston, 02115, MA, USA
| | - John Quackenbush
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, 02115, MA, USA. .,Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, 02115, MA, USA.
| |
Collapse
|
38
|
Thamrin C, Frey U, Kaminsky DA, Reddel HK, Seely AJE, Suki B, Sterk PJ. Systems Biology and Clinical Practice in Respiratory Medicine. The Twain Shall Meet. Am J Respir Crit Care Med 2017; 194:1053-1061. [PMID: 27556336 DOI: 10.1164/rccm.201511-2288pp] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Respiratory diseases are highly complex, being driven by host-environment interactions and manifested by inflammatory, structural, and functional abnormalities that vary over time. Traditional reductionist approaches have contributed vastly to our knowledge of biological systems in health and disease to date; however, they are insufficient to provide an understanding of the behavior of the system as a whole. In this Pulmonary Perspective, we discuss systems biology approaches, especially but not limited to the study of the lung as a complex system. Such integrative approaches take into account the large number of dynamic subunits and their interactions found in biological systems. Borrowing methods from physics and mathematics, it is possible to study the collective behavior of these systems over time and in a multidimensional manner. We first examine the physiological basis for complexity in the respiratory system and its implications for disease. We then expand on the potential applications of systems biology methods to study complex systems, within the context of diagnosis and monitoring of respiratory diseases including asthma, chronic obstructive pulmonary disease (COPD), and critical illness. We summarize the significant advances made in recent years using systems approaches for disease phenotyping, applied to data ranging from the molecular to clinical level, obtained from large-scale asthma and COPD networks. We describe new studies using temporal complexity patterns to characterize asthma and COPD and predict exacerbations as well as predict adverse outcomes in critical care. We highlight new methods that are emerging with this approach and discuss remaining questions that merit greater attention in the field.
Collapse
Affiliation(s)
- Cindy Thamrin
- 1 Woolcock Institute of Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - Urs Frey
- 2 University Children's Hospital Basel, Basel, Switzerland
| | - David A Kaminsky
- 3 University of Vermont College of Medicine, Burlington, Vermont
| | - Helen K Reddel
- 1 Woolcock Institute of Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - Andrew J E Seely
- 4 Ottawa Hospital Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Béla Suki
- 5 Department of Biomedical Engineering, Boston University, Boston, Massachusetts; and
| | - Peter J Sterk
- 6 Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| |
Collapse
|
39
|
Mohan S, Ho T, Kjarsgaard M, Radford K, Borhan ASM, Thabane L, Nair P. Hemosiderin in sputum macrophages may predict infective exacerbations of chronic obstructive pulmonary disease: a retrospective observational study. BMC Pulm Med 2017; 17:60. [PMID: 28403845 PMCID: PMC5389091 DOI: 10.1186/s12890-017-0408-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 04/07/2017] [Indexed: 11/18/2022] Open
Abstract
Background Infective exacerbations of COPD are common and are accompanied by neutrophilic bronchitis in sputum. Increased respiratory iron content has been associated with respiratory tract infection, though it is unclear if this represents a predisposing factor for infection or the sequelae of inflammation. Iron overload, as assessed in the airways, may be an important biomarker for recurrent infective exacerbations of COPD. The purpose of our study was to determine if hemosiderin in sputum macrophages is related to infective exacerbations of COPD. Methods We undertook a retrospective observational study of 54 consecutive patients who presented with an exacerbation of COPD and had sputum examined including assessment for hemosiderin in alveolar macrophages. The relation between infective exacerbations in the previous two years and the percent of hemosiderin-positive macrophages was analyzed with linear regression. To account for the non-parametric distribution of infective exacerbations, negative binomial regression modelling was used to account for other covariates. Results The percent of hemosiderin positive alveolar macrophages (hemosiderin index), analyzed parametrically and non-parametrically, demonstrated a significant correlation with increasing numbers of infective exacerbations in the previous two years. In a multivariate regression analysis, hemosiderin index was an independent predictor of infective exacerbations. COPD patients with raised hemosiderin index (≥20%) had higher levels of sputum IL-6 compared to patients with lower levels (<20%). Conclusions High hemosiderin index in sputum alveolar macrophages measured at the time of AECOPD may be related to the frequency of infective exacerbations of COPD.
Collapse
Affiliation(s)
- Sindu Mohan
- Division of Respirology, St Joseph's Healthcare and Department of Medicine, McMaster University, Hamilton, ON, Canada.,Firestone Institute for Respiratory Health, St Joseph's Healthcare, 50 Charlton Avenue East, Hamilton, ON, L8N 4A6, Canada
| | - Terence Ho
- Division of Respirology, St Joseph's Healthcare and Department of Medicine, McMaster University, Hamilton, ON, Canada.,Firestone Institute for Respiratory Health, St Joseph's Healthcare, 50 Charlton Avenue East, Hamilton, ON, L8N 4A6, Canada
| | - Melanie Kjarsgaard
- Firestone Institute for Respiratory Health, St Joseph's Healthcare, 50 Charlton Avenue East, Hamilton, ON, L8N 4A6, Canada
| | - Katherine Radford
- Firestone Institute for Respiratory Health, St Joseph's Healthcare, 50 Charlton Avenue East, Hamilton, ON, L8N 4A6, Canada
| | - A S M Borhan
- Department of Health Research Methods, McMaster University, Hamilton, ON, Canada
| | - Lehana Thabane
- Department of Health Research Methods, McMaster University, Hamilton, ON, Canada
| | - Parameswaran Nair
- Division of Respirology, St Joseph's Healthcare and Department of Medicine, McMaster University, Hamilton, ON, Canada. .,Firestone Institute for Respiratory Health, St Joseph's Healthcare, 50 Charlton Avenue East, Hamilton, ON, L8N 4A6, Canada.
| |
Collapse
|
40
|
Zhou A, Zhou Z, Zhao Y, Chen P. The recent advances of phenotypes in acute exacerbations of COPD. Int J Chron Obstruct Pulmon Dis 2017; 12:1009-1018. [PMID: 28392685 PMCID: PMC5375638 DOI: 10.2147/copd.s128604] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Exacerbations of COPD are clinically relevant events with therapeutic and prognostic implications. Yet, significant heterogeneity of clinical presentation and disease progression exists within acute exacerbations of COPD (AECOPD). Currently, different phenotypes have been widely used to describe the characteristics among patients with AECOPD. This has proved to be significant in the treatment and prediction of the outcomes of the disease. In this review of published literature, the phenotypes of AECOPD were classified according to etiology, inflammatory biomarkers, clinical manifestation, comorbidity, the frequency of exacerbations, and so on. This review concentrates on advancements in the use of phenotypes of AECOPD.
Collapse
Affiliation(s)
- Aiyuan Zhou
- Department of Respiratory Medicine, The Second Xiangya Hospital; Research Unit of Respiratory Disease; Diagnosis and Treatment Center of Respiratory Disease, Central South University, Changsha, Hunan, People's Republic of China
| | - Zijing Zhou
- Department of Respiratory Medicine, The Second Xiangya Hospital; Research Unit of Respiratory Disease; Diagnosis and Treatment Center of Respiratory Disease, Central South University, Changsha, Hunan, People's Republic of China
| | - Yiyang Zhao
- Department of Respiratory Medicine, The Second Xiangya Hospital; Research Unit of Respiratory Disease; Diagnosis and Treatment Center of Respiratory Disease, Central South University, Changsha, Hunan, People's Republic of China
| | - Ping Chen
- Department of Respiratory Medicine, The Second Xiangya Hospital; Research Unit of Respiratory Disease; Diagnosis and Treatment Center of Respiratory Disease, Central South University, Changsha, Hunan, People's Republic of China
| |
Collapse
|
41
|
Ho T, Dasgupta A, Hargreave FE, Nair P. The use of cellular and molecular biomarkers to manage COPD exacerbations. Expert Rev Respir Med 2017; 11:403-411. [PMID: 28347199 DOI: 10.1080/17476348.2017.1307738] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
INTRODUCTION Chronic obstructive pulmonary disease (COPD) exacerbations are a common cause of respiratory morbidity and mortality, and have various etiologies. Multiple cellular and molecular biomarkers have been associated with exacerbations. Quantitative sputum cell counts are able to identify the presence and type of bronchitis, which is an important contributor to exacerbations. Their utility to monitor bronchitis and to help treat exacerbations has been evaluated, yet they are not used in routine clinical practice. Areas covered: This review will provide a brief summary of biomarkers utilized in COPD, with a focus on the application of cellular markers for the management of exacerbations. A case study will demonstrate the application of these methods. With quantitative sputum cell counts, the presence of eosinophilic bronchitis predicts corticosteroid-responsiveness, while neutrophilic bronchitis identifies infection and suggests the need for antibiotics. Gastroesophageal reflux-related aspiration and heart failure can also be identified by examining sputum. Expert commentary: Quantitative sputum cytometry is an essential tool in the management of exacerbations of COPD, particularly those prone to frequent exacerbations. Treatment based on sputum cell counts is superior to current guideline-based recommendations to prevent future exacerbations and hospitalizations in observational and single-centre controlled trials. Large multicentre clinical trials are necessary to confirm this.
Collapse
Affiliation(s)
- Terence Ho
- a Firestone Institute for Respiratory Health, St Joseph's Healthcare Hamilton, and Department of Medicine , McMaster University , Hamilton , ON , Canada
| | - Angira Dasgupta
- a Firestone Institute for Respiratory Health, St Joseph's Healthcare Hamilton, and Department of Medicine , McMaster University , Hamilton , ON , Canada
| | - Frederick E Hargreave
- a Firestone Institute for Respiratory Health, St Joseph's Healthcare Hamilton, and Department of Medicine , McMaster University , Hamilton , ON , Canada
| | - Parameswaran Nair
- a Firestone Institute for Respiratory Health, St Joseph's Healthcare Hamilton, and Department of Medicine , McMaster University , Hamilton , ON , Canada
| |
Collapse
|
42
|
Nguyen HQ, Herting JR, Pike KC, Gharib SA, Matute-Bello G, Borson S, Kohen R, Adams SG, Fan VS. Symptom profiles and inflammatory markers in moderate to severe COPD. BMC Pulm Med 2016; 16:173. [PMID: 27914470 PMCID: PMC5135800 DOI: 10.1186/s12890-016-0330-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 11/22/2016] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Physical and psychological symptoms are the hallmark of patients' subjective perception of their illness. The purpose of this analysis was to determine if patients with COPD have distinctive symptom profiles and to examine the association of symptom profiles with systemic biomarkers of inflammation. METHODS We conducted latent class analyses of three physical (dyspnea, fatigue, and pain) and two psychological symptoms (depression and anxiety) in 302 patients with moderate to severe COPD using baseline data from a longitudinal observational study of depression in COPD. Systemic inflammatory markers included IL1, IL8, IL10, IL12, IL13, INF, GM-CSF, TNF-α (levels >75thcentile was considered high); and CRP (levels >3 mg/L was considered high). Multinominal logistic regression models were used to examine the association between symptom classes and inflammation while adjusting for key socio-demographic and disease characteristics. RESULTS We found that a 4-class model best fit the data: 1) low physical and psychological symptoms (26%, Low-Phys/Low-Psych), 2) low physical but moderate psychological symptoms (18%, Low-Phys/Mod Psych), 3) high physical but moderate psychological symptoms (25%, High-Phys/Mod Psych), and 4) high physical and psychological symptoms (30%, High-Phys/High Psych). Unadjusted analyses showed associations between symptom class with high levels of IL7, IL-8 (p ≤ .10) and CRP (p < .01). In the adjusted model, those with a high CRP level were less likely to be in the High-Phys/Mod-Psych class compared to the Low-Phys/Low-Psych (OR: 0.41, 95%CI 0.19, 0.90) and Low-Phys/Mod-Psych classes (OR: 0.35, 95%CI 0.16, 0.78); elevated CRP was associated with in increased odds of being in the High-Phys/High-Psych compared to the High-Phys/Mod-Psych class (OR: 2.22, 95%CI 1.08, 4.58). Younger age, having at least a college education, oxygen use and depression history were more prominent predictors of membership in the higher symptom classes. CONCLUSIONS Patients with COPD can be classified into four distinct symptom classes based on five commonly co-occurring physical and psychological symptoms. Systemic biomarkers of inflammation were not associated with symptom class. Additional work to test the reliability of these symptom classes, their biological drivers and their validity for prognostication and tailoring therapy in larger and more diverse samples is needed. TRIAL REGISTRATION Clinicaltrials.gov, NCT01074515 .
Collapse
Affiliation(s)
- Huong Q Nguyen
- Kaiser Permanente Southern California, 100 S. Los Robles, Pasadena, CA, 91101, USA.
| | | | | | | | | | | | | | - Sandra G Adams
- University of Texas Health Science Center at San Antonio and The South Texas Veterans Health Care System, San Antonio, Texas, USA
| | - Vincent S Fan
- University of Washington & Puget Sound Veterans Administration, Seattle, USA
| |
Collapse
|
43
|
Criner GJ. Giants in Chest Medicine: Bartolome Celli, MD, FCCP. Chest 2016; 150:995-997. [PMID: 27832893 DOI: 10.1016/j.chest.2016.08.1464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 08/16/2016] [Indexed: 10/20/2022] Open
Affiliation(s)
- Gerard J Criner
- Professor and Chair, Department of Thoracic Medicine and Surgery, Lewis Katz School of Medicine at Temple University, Philadelphia, PA.
| |
Collapse
|
44
|
Geerdink JX, Simons SO, Pike R, Stauss HJ, Heijdra YF, Hurst JR. Differences in systemic adaptive immunity contribute to the 'frequent exacerbator' COPD phenotype. Respir Res 2016; 17:140. [PMID: 27793198 PMCID: PMC5084432 DOI: 10.1186/s12931-016-0456-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 10/24/2016] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Some COPD patients are more susceptible to exacerbations than others. Mechanisms underlying these differences in susceptibility are not well understood. We hypothesized that altered cell mediated immune responses may underlie a propensity to suffer from frequent exacerbations in COPD. METHODS Peripheral blood mononuclear cells (PBMCs) were obtained from 24 stable COPD patients, eight frequent exacerbators (≥3 diary-card exacerbations/year) and 16 infrequent exacerbators (< 3 diary-card exacerbations/year). Detailed multi-parameter flow cytometry was used to study differences in innate and adaptive systemic immune function between frequent and infrequently exacerbating COPD patients. RESULTS The 24 COPD patients had a mean (SD) age of 76.3 (9.4) years and FEV1 1.43 (0.60)L, 53.3 (18.3)% predicted. PBMCs of frequent exacerbators (FE) contained lower frequencies of CD4+ T central memory cells (CD4+ Tcm) compared to infrequent exacerbators (IE) (FE = 18.7 %; IE = 23.9 %; p = 0.035). This observation was also apparent in absolute numbers of CD4+ Tcm cells (FE = 0.17 × 10^6/mL; IE = 0.25 × 10^6/mL; p = 0.035). PBMCs of FE contained a lower frequency of CD8+ T effector memory cells expressing HLA-DR (Human Leukocyte Antigen - D Related) compared to IE COPD patients (FE = 22.7 %; IE = 31.5 %; p = 0.007). CONCLUSION Differences in the adaptive systemic immune system might associate with exacerbation susceptibility in the 'frequent exacerbator' COPD phenotype. These differences include fewer CD4+ T central memory cells and CD8+ T effector memory cells. TRIAL REGISTRATION Not applicable.
Collapse
Affiliation(s)
- Jasper X Geerdink
- Department of Respiratory Medicine, Radboud University Medical Centre, Nijmegen, The Netherlands.,UCL Respiratory, University College London, London, UK
| | - Sami O Simons
- Department of Respiratory Medicine, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Rebecca Pike
- Institute of Immunity and Transplantation, University College London, London, UK
| | - Hans J Stauss
- Institute of Immunity and Transplantation, University College London, London, UK
| | - Yvonne F Heijdra
- Department of Respiratory Medicine, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - John R Hurst
- UCL Respiratory, University College London, London, UK.
| |
Collapse
|
45
|
Polverino F, Seys LJM, Bracke KR, Owen CA. B cells in chronic obstructive pulmonary disease: moving to center stage. Am J Physiol Lung Cell Mol Physiol 2016; 311:L687-L695. [PMID: 27542809 DOI: 10.1152/ajplung.00304.2016] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 08/15/2016] [Indexed: 12/22/2022] Open
Abstract
Chronic inflammatory responses in the lungs contribute to the development and progression of chronic obstructive pulmonary disease (COPD). Although research studies focused initially on the contributions of the innate immune system to the pathogenesis of COPD, more recent studies have implicated adaptive immune responses in COPD. In particular, studies have demonstrated increases in B cell counts and increases in the number and size of B cell-rich lymphoid follicles in COPD lungs that correlate directly with COPD severity. There are also increases in lung levels of mediators that promote B cell maturation, activation, and survival in COPD patients. B cell products such as autoantibodies directed against lung cells, components of cells, and extracellular matrix proteins are also present in COPD lungs. These autoantibodies may contribute to lung inflammation and injury in COPD patients, in part, by forming immune complexes that activate complement components. Studies of B cell-deficient mice and human COPD patients have linked B cells most strongly to the emphysema phenotype. However, B cells have protective activities during acute exacerbations of COPD by promoting adaptive immune responses that contribute to host defense against pathogens. This review outlines the evidence that links B cells and B cell-rich lymphoid follicles to the pathogenesis of COPD and the mechanisms involved. It also reviews the potential and limitations of B cells as therapeutic targets to slow the progression of human COPD.
Collapse
Affiliation(s)
- Francesca Polverino
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts; COPD Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico; University of Parma, Parma, Italy; and
| | - Leen J M Seys
- Laboratory for Translational Research in Obstructive Pulmonary Diseases, Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Ken R Bracke
- Laboratory for Translational Research in Obstructive Pulmonary Diseases, Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Caroline A Owen
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts; COPD Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico;
| |
Collapse
|
46
|
Jones AW, Robinson R, Mohamed P, Davison G, Izzat HJ, Lewis KE. Impaired Blood Neutrophil Function in the Frequent Exacerbator of Chronic Obstructive Pulmonary Disease: A Proof-of-Concept Study. Lung 2016; 194:881-887. [PMID: 27530251 PMCID: PMC5093205 DOI: 10.1007/s00408-016-9930-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 08/07/2016] [Indexed: 11/30/2022]
Abstract
PURPOSE The underlying biological mechanisms of the frequent exacerbator phenotype of COPD remain unclear. We compared systemic neutrophil function in COPD patients with or without frequent exacerbations. METHODS Whole blood from COPD frequent exacerbators (defined as ≥2 moderate-severe exacerbations in the previous 2 years) and non-exacerbators (no exacerbations in the preceding 2 years) was assayed for neutrophil function. Neutrophil function in healthy ex-smoking volunteers was also measured as a control (reference) group. RESULTS A total of 52 subjects were included in this study: 26 frequent exacerbators, 18 non-exacerbators and 8 healthy controls. COPD frequent exacerbators had blunted blood neutrophil fMLP-stimulated oxidative burst compared to both non-exacerbators (p < 0.01) and healthy controls (p < 0.001). There were no differences between COPD frequent exacerbators and non-exacerbators in blood neutrophil PMA-stimulated oxidative burst, but both COPD groups had reduced responses compared to healthy controls (p < 0.001). Bacterial-stimulated neutrophil degranulation was greater in frequent exacerbators than non-exacerbators (p < 0.05). CONCLUSION This study is the first to report aberrant receptor-mediated blood neutrophil function in the frequent exacerbator of COPD.
Collapse
Affiliation(s)
- Arwel Wyn Jones
- Lincoln Institute for Health, University of Lincoln, Brayford Pool, Lincoln, LN6 7TS, UK.
| | - Richard Robinson
- Department of Respiratory Medicine, Prince Philip Hospital, Hywel Dda University Health Board, Llanelli, SA14 8QF, UK
| | - Peer Mohamed
- Department of Respiratory Medicine, Prince Philip Hospital, Hywel Dda University Health Board, Llanelli, SA14 8QF, UK
| | - Glen Davison
- School of Sport and Exercise Sciences, University of Kent, Medway Campus, Chatham Maritime, ME4 4AG, UK
| | - Hassan Jaysen Izzat
- Department of Respiratory Medicine, Prince Philip Hospital, Hywel Dda University Health Board, Llanelli, SA14 8QF, UK
| | - Keir Edward Lewis
- Department of Respiratory Medicine, Prince Philip Hospital, Hywel Dda University Health Board, Llanelli, SA14 8QF, UK.,College of Medicine, Swansea University, Swansea, SA2 8PP, UK
| |
Collapse
|
47
|
Hilzendeger C, da Silva J, Henket M, Schleich F, Corhay JL, Kebadze T, Edwards MR, Mallia P, Johnston SL, Louis R. Reduced sputum expression of interferon-stimulated genes in severe COPD. Int J Chron Obstruct Pulmon Dis 2016; 11:1485-94. [PMID: 27418822 PMCID: PMC4934534 DOI: 10.2147/copd.s105948] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Exacerbations of COPD are frequent and commonly triggered by respiratory tract infections. The purpose of our study was to investigate innate immunity in stable COPD patients. METHODS Induced sputum was collected from 51 stable consecutive COPD patients recruited from the COPD Clinic of CHU Liege and 35 healthy subjects. Expression of interferons beta (IFN-β) and lambda1 (IL-29), IFN-stimulated genes (ISGs) MxA, OAS, and viperin were measured in total sputum cells by reverse transcription quantitative polymerase chain reaction (RT-qPCR). The presence of Picornaviruses was assessed by RT-PCR, while potential pathogenic microorganisms (PPM) were identified by sputum bacteriology. RESULTS Expression of IL-29 was found in 16 of 51 COPD patients (31%) and in nine of 35 healthy subjects (26%), while IFN-β was detected in six of 51 COPD patients (12%) and in two of 35 healthy subjects (6%). ISGs were easily detectable in both groups. In the whole group of COPD patients, OAS expression was decreased (P<0.05), while that of viperin was increased (P<0.01) compared to healthy subjects. No difference was found with respect to MxA. COPD patients from group D of Global Initiative for Chronic Obstructive Lung Disease (GOLD) had reduced expression of all three ISGs (P<0.01 for MxA, P<0.05 for OAS, and P<0.01 for viperin) as compared to those of group B patients. Picornaviruses were detected in eight of 51 (16%) COPD patients vs four of 33 (12%) healthy subjects, while PPM were detected in seven of 39 (18%) COPD patients and associated with raised sputum neutrophil counts. IFN-β expression was raised when either picornavirus or PPM were detected (P=0.06), but no difference was seen regarding IL-29 or ISGs. CONCLUSION ISGs expression was reduced in severe COPD that may favor exacerbation and contribute to disease progress by altering response to infection.
Collapse
Affiliation(s)
- Clarissa Hilzendeger
- Department of Respiratory Medicine, Centre Hospitalier Universitaire (CHU) Liege, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA) I University of Liege, Belgium
| | - Jane da Silva
- Department of Medicine, Post-graduate Program in Health Sciences, University of Southern Santa Catarina, Palhoça-SC, Brazil
| | - Monique Henket
- Department of Respiratory Medicine, Centre Hospitalier Universitaire (CHU) Liege, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA) I University of Liege, Belgium
| | - Florence Schleich
- Department of Respiratory Medicine, Centre Hospitalier Universitaire (CHU) Liege, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA) I University of Liege, Belgium
| | - Jean Louis Corhay
- Department of Respiratory Medicine, Centre Hospitalier Universitaire (CHU) Liege, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA) I University of Liege, Belgium
| | - Tatiana Kebadze
- Airway Disease Division, Airway Disease Infection Section, National Heart and Lung Institute, Imperial College, London, UK
| | - Michael R Edwards
- Airway Disease Division, Airway Disease Infection Section, National Heart and Lung Institute, Imperial College, London, UK
| | - Patrick Mallia
- Airway Disease Division, Airway Disease Infection Section, National Heart and Lung Institute, Imperial College, London, UK
| | - Sebastian L Johnston
- Airway Disease Division, Airway Disease Infection Section, National Heart and Lung Institute, Imperial College, London, UK
| | - Renaud Louis
- Department of Respiratory Medicine, Centre Hospitalier Universitaire (CHU) Liege, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA) I University of Liege, Belgium
| |
Collapse
|
48
|
Chang Y, Glass K, Liu YY, Silverman EK, Crapo JD, Tal-Singer R, Bowler R, Dy J, Cho M, Castaldi P. COPD subtypes identified by network-based clustering of blood gene expression. Genomics 2016; 107:51-58. [PMID: 26773458 DOI: 10.1016/j.ygeno.2016.01.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 12/04/2015] [Accepted: 01/06/2016] [Indexed: 01/22/2023]
Abstract
One of the most common smoking-related diseases, chronic obstructive pulmonary disease (COPD), results from a dysregulated, multi-tissue inflammatory response to cigarette smoke. We hypothesized that systemic inflammatory signals in genome-wide blood gene expression can identify clinically important COPD-related disease subtypes, and we leveraged pre-existing gene interaction networks to guide unsupervised clustering of blood microarray expression data. Using network-informed non-negative matrix factorization, we analyzed genome-wide blood gene expression from 229 former smokers in the ECLIPSE Study, and we identified novel, clinically relevant molecular subtypes of COPD. These network-informed clusters were more stable and more strongly associated with measures of lung structure and function than clusters derived from a network-naïve approach, and they were associated with subtype-specific enrichment for inflammatory and protein catabolic pathways. These clusters were successfully reproduced in an independent sample of 135 smokers from the COPDGene Study.
Collapse
Affiliation(s)
- Yale Chang
- Department of Computer Science, Northeastern University, Boston, USA
| | - Kimberly Glass
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, USA
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, USA; Pulmonary and Critical Care Division, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - James D Crapo
- Department of Medicine, National Jewish Health, Denver, USA
| | | | - Russ Bowler
- Department of Medicine, National Jewish Health, Denver, USA
| | - Jennifer Dy
- Department of Computer Science, Northeastern University, Boston, USA
| | - Michael Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, USA; Pulmonary and Critical Care Division, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - Peter Castaldi
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, USA; Division of General Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA.
| |
Collapse
|
49
|
Ambrosino N, Casaburi R, Chetta A, Clini E, Donner CF, Dreher M, Goldstein R, Jubran A, Nici L, Owen CA, Rochester C, Tobin MJ, Vagheggini G, Vitacca M, ZuWallack R. 8th international conference on management and rehabilitation of chronic respiratory failure: the long summaries – part 1. Multidiscip Respir Med 2015. [PMCID: PMC4595244 DOI: 10.1186/s40248-015-0026-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
This paper summarizes the Part 1 of the proceedings of the 8th International Conference on Management and Rehabilitation of Chronic Respiratory Failure, held in Pescara, Italy, on 7 and 8 May, 2015. It summarizes the contributions from numerous experts in the field of chronic respiratory disease and chronic respiratory failure. The outline follows the temporal sequence of presentations. This paper (Part 1) includes sections regarding: Advances in Asthma and COPD Therapy (Novel Therapeutic Targets for Asthma: Proteinases, Blood Biomarker Changes in COPD Patients); The problem of Hospital Re-Admission following Discharge after the COPD Exacerbation (Characteristics of the Hospitalized COPD Patient, Reducing Hospital Readmissions Following COPD Exacerbation).
Collapse
|