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Willis-Owen SAG, Thompson A, Kemp PR, Polkey MI, Cookson WOCM, Moffatt MF, Natanek SA. COPD is accompanied by co-ordinated transcriptional perturbation in the quadriceps affecting the mitochondria and extracellular matrix. Sci Rep 2018; 8:12165. [PMID: 30111857 PMCID: PMC6093887 DOI: 10.1038/s41598-018-29789-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 07/16/2018] [Indexed: 12/04/2022] Open
Abstract
Skeletal muscle dysfunction is a frequent extra-pulmonary manifestation of Chronic Obstructive Pulmonary Disease (COPD) with implications for both quality of life and survival. The underlying biology nevertheless remains poorly understood. We measured global gene transcription in the quadriceps using Affymetrix HuGene1.1ST arrays in an unselected cohort of 79 stable COPD patients in secondary care and 16 healthy age- and gender-matched controls. We detected 1,826 transcripts showing COPD-related variation. Eighteen exhibited ≥2fold changes (SLC22A3, FAM184B, CDKN1A, FST, LINC01405, MUSK, PANX1, ANKRD1, C12orf75, MYH1, POSTN, FRZB, TNC, ACTC1, LINC00310, MYH3, MYBPH and AREG). Thirty-one transcripts possessed previous reported evidence of involvement in COPD through genome-wide association, including FAM13A. Network analysis revealed a substructure comprising 6 modules of co-expressed genes. We identified modules with mitochondrial and extracellular matrix features, of which IDH2, a central component of the mitochondrial antioxidant pathway, and ABI3BP, a proposed switch between proliferation and differentiation, represent hubs respectively. COPD is accompanied by coordinated patterns of transcription in the quadriceps involving the mitochondria and extracellular matrix and including genes previously implicated in primary disease processes.
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Affiliation(s)
- Saffron A G Willis-Owen
- Centre for Genomic Medicine, National Heart and Lung Institute, Imperial College London, SW3 6LY, London, United Kingdom.
| | - Anna Thompson
- Centre for Genomic Medicine, National Heart and Lung Institute, Imperial College London, SW3 6LY, London, United Kingdom
| | - Paul R Kemp
- Respiratory Sciences, National Heart and Lung Institute, Imperial College London, SW3 6NP, London, United Kingdom
| | - Michael I Polkey
- Respiratory Sciences, National Heart and Lung Institute, Imperial College London, SW3 6NP, London, United Kingdom
| | - William O C M Cookson
- Centre for Genomic Medicine, National Heart and Lung Institute, Imperial College London, SW3 6LY, London, United Kingdom
| | - Miriam F Moffatt
- Centre for Genomic Medicine, National Heart and Lung Institute, Imperial College London, SW3 6LY, London, United Kingdom
| | - Samantha A Natanek
- Respiratory Sciences, National Heart and Lung Institute, Imperial College London, SW3 6NP, London, United Kingdom.
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Yeo J, Morales DA, Chen T, Crawford EL, Zhang X, Blomquist TM, Levin AM, Massion PP, Arenberg DA, Midthun DE, Mazzone PJ, Nathan SD, Wainz RJ, Nana-Sinkam P, Willey PFS, Arend TJ, Padda K, Qiu S, Federov A, Hernandez DAR, Hammersley JR, Yoon Y, Safi F, Khuder SA, Willey JC. RNAseq analysis of bronchial epithelial cells to identify COPD-associated genes and SNPs. BMC Pulm Med 2018; 18:42. [PMID: 29506519 PMCID: PMC5838965 DOI: 10.1186/s12890-018-0603-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 02/23/2018] [Indexed: 01/09/2023] Open
Abstract
Background There is a need for more powerful methods to identify low-effect SNPs that contribute to hereditary COPD pathogenesis. We hypothesized that SNPs contributing to COPD risk through cis-regulatory effects are enriched in genes comprised by bronchial epithelial cell (BEC) expression patterns associated with COPD. Methods To test this hypothesis, normal BEC specimens were obtained by bronchoscopy from 60 subjects: 30 subjects with COPD defined by spirometry (FEV1/FVC < 0.7, FEV1% < 80%), and 30 non-COPD controls. Targeted next generation sequencing was used to measure total and allele-specific expression of 35 genes in genome maintenance (GM) genes pathways linked to COPD pathogenesis, including seven TP53 and CEBP transcription factor family members. Shrinkage linear discriminant analysis (SLDA) was used to identify COPD-classification models. COPD GWAS were queried for putative cis-regulatory SNPs in the targeted genes. Results On a network basis, TP53 and CEBP transcription factor pathway gene pair network connections, including key DNA repair gene ERCC5, were significantly different in COPD subjects (e.g., Wilcoxon rank sum test for closeness, p-value = 5.0E-11). ERCC5 SNP rs4150275 association with chronic bronchitis was identified in a set of Lung Health Study (LHS) COPD GWAS SNPs restricted to those in putative regulatory regions within the targeted genes, and this association was validated in the COPDgene non-hispanic white (NHW) GWAS. ERCC5 SNP rs4150275 is linked (D’ = 1) to ERCC5 SNP rs17655 which displayed differential allelic expression (DAE) in BEC and is an expression quantitative trait locus (eQTL) in lung tissue (p = 3.2E-7). SNPs in linkage (D’ = 1) with rs17655 were predicted to alter miRNA binding (rs873601). A classifier model that comprised gene features CAT, CEBPG, GPX1, KEAP1, TP73, and XPA had pooled 10-fold cross-validation receiver operator characteristic area under the curve of 75.4% (95% CI: 66.3%–89.3%). The prevalence of DAE was higher than expected (p = 0.0023) in the classifier genes. Conclusions GM genes comprised by COPD-associated BEC expression patterns were enriched for SNPs with cis-regulatory function, including a putative cis-rSNP in ERCC5 that was associated with COPD risk. These findings support additional total and allele-specific expression analysis of gene pathways with high prior likelihood for involvement in COPD pathogenesis. Electronic supplementary material The online version of this article (10.1186/s12890-018-0603-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jiyoun Yeo
- Department of Pathology, The University of Toledo College of Medicine, 3000 Arlington Avenue, HEB 219, Toledo, OH, 43614, USA
| | - Diego A Morales
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, HEB 219, Toledo, OH, 43614, USA
| | - Tian Chen
- Department of Mathematics and Statistics, The University of Toledo, 2801 W. Bancroft Street, Toledo, OH, 43606, USA
| | - Erin L Crawford
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, HEB 219, Toledo, OH, 43614, USA
| | - Xiaolu Zhang
- Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, Toledo, OH, 43614, USA
| | - Thomas M Blomquist
- Department of Pathology, The University of Toledo College of Medicine, 3000 Arlington Avenue, HEB 219, Toledo, OH, 43614, USA
| | - Albert M Levin
- Department of Biostatistics, Henry Ford Health System, 1 Ford Place Detroit, MI, Detroit, MI, 48202, USA
| | - Pierre P Massion
- Thoracic Program, Vanderbilt Ingram Cancer Center, Nashville, TN, 37232, USA
| | | | - David E Midthun
- Department of Pulmonary and Critical Care Medicine, Mayo Clinic, 200 1st St SW, Rochester, MN, 55905, USA
| | - Peter J Mazzone
- Department of Pulmonary Medicine, Cleveland Clinic, 9500 Euclid Ave, Cleveland, OH, 44195, USA
| | - Steven D Nathan
- Department of Pulmonary Medicine, Inova Fairfax Hospital, 3300 Gallows Road, Falls Church, VA, 22042-3300, USA
| | - Ronald J Wainz
- The Toledo Hospital, 2142 N Cove Blvd, Toledo, OH, 43606, USA
| | - Patrick Nana-Sinkam
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, USA, Richmond, VA, 23284-2512, USA.,Ohio State University James Comprehensive Cancer Center and Solove Research Institute, Columbus, OH, USA
| | - Paige F S Willey
- American Enterprise Institute, 1789 Massachusetts Ave NW, Washington, DC, 20036, USA
| | - Taylor J Arend
- The University of Toledo College of Medicine, 3000 Arlington Avenue, Toledo, OH, 43614, USA
| | - Karanbir Padda
- Emory University School of Medicine, 1648 Pierce Dr NE, Atlanta, GA, 30307, USA
| | - Shuhao Qiu
- Department of Medicine, The University of Toledo Medical Center, 3000 Arlington Avenue, Toledo, OH, 43614, USA
| | - Alexei Federov
- Department of Mathematics and Statistics, The University of Toledo, 2801 W. Bancroft Street, Toledo, OH, 43606, USA.,Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, Toledo, OH, 43614, USA
| | - Dawn-Alita R Hernandez
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, RHC 0012, Toledo, OH, 43614, USA
| | - Jeffrey R Hammersley
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, RHC 0012, Toledo, OH, 43614, USA
| | - Youngsook Yoon
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, RHC 0012, Toledo, OH, 43614, USA
| | - Fadi Safi
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, RHC 0012, Toledo, OH, 43614, USA
| | - Sadik A Khuder
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, RHC 0012, Toledo, OH, 43614, USA
| | - James C Willey
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, Toledo, OH, 43614, USA.
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Hecker L. Mechanisms and consequences of oxidative stress in lung disease: therapeutic implications for an aging populace. Am J Physiol Lung Cell Mol Physiol 2017; 314:L642-L653. [PMID: 29351446 DOI: 10.1152/ajplung.00275.2017] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The rapid expansion of the elderly population has led to the recent epidemic of age-related diseases, including increased incidence and mortality of chronic and acute lung diseases. Numerous studies have implicated aging and oxidative stress in the pathogenesis of various pulmonary diseases; however, despite recent advances in these fields, the specific contributions of aging and oxidative stress remain elusive. This review will discuss the consequences of aging on lung morphology and physiology, and how redox imbalance with aging contributes to lung disease susceptibility. Here, we focus on three lung diseases for which aging is a significant risk factor: acute respiratory distress syndrome (ARDS), chronic obstructive pulmonary disease (COPD), and idiopathic pulmonary fibrosis (IPF). Preclinical and clinical development for redox- and senescence-altering therapeutic strategies are discussed, as well as scientific advancements that may direct current and future therapeutic development. A deeper understanding of how aging impacts normal lung function, redox balance, and injury-repair processes will inspire the development of new therapies to prevent and/or reverse age-associated pulmonary diseases, and ultimately increase health span and longevity. This review is intended to encourage basic, clinical, and translational research that will bridge knowledge gaps at the intersection of aging, oxidative stress, and lung disease to fuel the development of more effective therapeutic strategies for lung diseases that disproportionately afflict the elderly.
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Affiliation(s)
- Louise Hecker
- Division of Pulmonary, Allergy and Critical Care and Sleep Medicine, University of Arizona , Tucson, Arizona and Southern Arizona Veterans Affairs Health Care System, Tucson, Arizona
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Horsfall LJ, Hardy R, Wong A, Kuh D, Swallow DM. Genetic variation underlying common hereditary hyperbilirubinaemia (Gilbert's syndrome) and respiratory health in the 1946 British birth cohort. J Hepatol 2014; 61:1344-51. [PMID: 25086287 DOI: 10.1016/j.jhep.2014.07.028] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 07/17/2014] [Accepted: 07/21/2014] [Indexed: 01/01/2023]
Abstract
BACKGROUND & AIMS Bilirubin has potent antioxidant properties in vitro and raised serum levels have been associated with lower rates of respiratory disease. The enzyme uridine diphosphate glucuronosyltransferase polypeptide 1A1 (UGT1A1) is solely responsible for clearing bilirubin from the blood and homozygosity for seven thymine-adenine (TA) repeats in the TATA box regulatory element of the UGT1A1 gene underlies a mild hereditary unconjugated hyperbilirubinaemia (Gilbert's syndrome). Our aim was to investigate whether this genetic variation is associated with differences in respiratory health. METHODS The relationship between the promoter genotype underlying Gilbert's syndrome (UGT1A1 rs8175347 [TA]7/7) and respiratory outcomes assessed at ages 43, 53, and 60-64 were examined in 2190 members of the 1946 British birth cohort. RESULTS The (TA)7/7 genotype, present in 9% of the cohort, was associated with higher forced expiratory volume (FEV1) and forced vital capacity (FVC). The relationship was strongest for heavy smokers (⩾20 cigarettes per day) at age 53 with mean FEV1 409 ml higher (191 to 627; p<0.001) and mean FVC 530 ml higher (95% CI 262-798; p<0.001) for UGT1A1 (TA)7/7 Gilbert's syndrome participants than for all others, indicating a protection from the pulmonary consequences of heavy smoking. The odds of respiratory disease (chronic obstructive pulmonary disease, self-reported asthma, or prescription of respiratory drugs) were half in those with Gilbert's syndrome genotype (odds ratio 0.49 [95% CI 0.39-0.74]; p<0.001) compared to those without this genotype. CONCLUSIONS Genetically raised unconjugated serum bilirubin is associated with higher adult respiratory function and protection from respiratory disease.
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Affiliation(s)
- Laura J Horsfall
- Research Department of Primary Care and Population Health, Institute of Epidemiology & Health, University College London, UK; Research Department of Genetic, Environment and Evolution, University College London, UK.
| | - Rebecca Hardy
- MRC University Unit for Lifelong Health and Ageing at University College London, UK
| | - Andrew Wong
- MRC University Unit for Lifelong Health and Ageing at University College London, UK
| | - Diana Kuh
- MRC University Unit for Lifelong Health and Ageing at University College London, UK
| | - Dallas M Swallow
- Research Department of Genetic, Environment and Evolution, University College London, UK
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