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Rathnayake SNH, Ditz B, van Nijnatten J, Sadaf T, Hansbro PM, Brandsma CA, Timens W, van Schadewijk A, Hiemstra PS, ten Hacken NHT, Oliver B, Kerstjens HAM, van den Berge M, Faiz A. Smoking induces shifts in cellular composition and transcriptome within the bronchial mucus barrier. Respirology 2023; 28:132-142. [PMID: 36414410 PMCID: PMC10947540 DOI: 10.1111/resp.14401] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 10/07/2022] [Indexed: 11/24/2022]
Abstract
BACKGROUND AND OBJECTIVE Smoking disturbs the bronchial-mucus-barrier. This study assesses the cellular composition and gene expression shifts of the bronchial-mucus-barrier with smoking to understand the mechanism of mucosal damage by cigarette smoke exposure. We explore whether single-cell-RNA-sequencing (scRNA-seq) based cellular deconvolution (CD) can predict cell-type composition in RNA-seq data. METHODS RNA-seq data of bronchial biopsies from three cohorts were analysed using CD. The cohorts included 56 participants with chronic obstructive pulmonary disease [COPD] (38 smokers; 18 ex-smokers), 77 participants without COPD (40 never-smokers; 37 smokers) and 16 participants who stopped smoking for 1 year (11 COPD and 5 non-COPD-smokers). Differential gene expression was used to investigate gene expression shifts. The CD-derived goblet cell ratios were validated by correlating with staining-derived goblet cell ratios from the COPD cohort. Statistics were done in the R software (false discovery rate p-value < 0.05). RESULTS Both CD methods indicate a shift in bronchial-mucus-barrier cell composition towards goblet cells in COPD and non-COPD-smokers compared to ex- and never-smokers. It shows that the effect was reversible within a year of smoking cessation. A reduction of ciliated and basal cells was observed with current smoking, which resolved following smoking cessation. The expression of mucin and sodium channel (ENaC) genes, but not chloride channel genes, were altered in COPD and current smokers compared to never smokers or ex-smokers. The goblet cell-derived staining scores correlate with CD-derived goblet cell ratios. CONCLUSION Smoking alters bronchial-mucus-barrier cell composition, transcriptome and increases mucus production. This effect is partly reversible within a year of smoking cessation. CD methodology can predict goblet-cell percentages from RNA-seq.
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Affiliation(s)
- Senani N. H. Rathnayake
- University of Technology Sydney, Respiratory Bioinformatics and Molecular Biology (RBMB), School of Life SciencesSydneyNew South WalesAustralia
- The University of Sydney, Respiratory Cellular and Molecular Biology (RCMB), Woolcock Institute of Medical ResearchSydneyNew South WalesAustralia
| | - Benedikt Ditz
- Department of Pulmonary DiseasesUniversity of Groningen, University Medical Center GroningenGroningenthe Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPDGroningenthe Netherlands
| | - Jos van Nijnatten
- University of Technology Sydney, Respiratory Bioinformatics and Molecular Biology (RBMB), School of Life SciencesSydneyNew South WalesAustralia
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPDGroningenthe Netherlands
- Department of Pathology & Medical BiologyUniversity of Groningen, University Medical Center GroningenGroningenthe Netherlands
| | - Tayyaba Sadaf
- University of Technology Sydney, Respiratory Bioinformatics and Molecular Biology (RBMB), School of Life SciencesSydneyNew South WalesAustralia
- Centre for InflammationCentenary Institute, and the University of Technology Sydney, Faculty of ScienceSydneyNew South WalesAustralia
| | - Philip M. Hansbro
- Centre for InflammationCentenary Institute, and the University of Technology Sydney, Faculty of ScienceSydneyNew South WalesAustralia
| | - Corry A. Brandsma
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPDGroningenthe Netherlands
- Department of Pathology & Medical BiologyUniversity of Groningen, University Medical Center GroningenGroningenthe Netherlands
| | - Wim Timens
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPDGroningenthe Netherlands
- Department of Pathology & Medical BiologyUniversity of Groningen, University Medical Center GroningenGroningenthe Netherlands
| | | | - Peter S. Hiemstra
- Department of PulmonologyLeiden University Medical CenterLeidenthe Netherlands
| | - Nick H. T. ten Hacken
- Department of Pulmonary DiseasesUniversity of Groningen, University Medical Center GroningenGroningenthe Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPDGroningenthe Netherlands
| | - Brian Oliver
- The University of Sydney, Respiratory Cellular and Molecular Biology (RCMB), Woolcock Institute of Medical ResearchSydneyNew South WalesAustralia
| | - Huib A. M. Kerstjens
- Department of Pulmonary DiseasesUniversity of Groningen, University Medical Center GroningenGroningenthe Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPDGroningenthe Netherlands
| | - Maarten van den Berge
- Department of Pulmonary DiseasesUniversity of Groningen, University Medical Center GroningenGroningenthe Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPDGroningenthe Netherlands
| | - Alen Faiz
- University of Technology Sydney, Respiratory Bioinformatics and Molecular Biology (RBMB), School of Life SciencesSydneyNew South WalesAustralia
- The University of Sydney, Respiratory Cellular and Molecular Biology (RCMB), Woolcock Institute of Medical ResearchSydneyNew South WalesAustralia
- Department of Pulmonary DiseasesUniversity of Groningen, University Medical Center GroningenGroningenthe Netherlands
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Mumby S, Adcock IM. Recent evidence from omic analysis for redox signalling and mitochondrial oxidative stress in COPD. J Inflamm (Lond) 2022; 19:10. [PMID: 35820851 PMCID: PMC9277949 DOI: 10.1186/s12950-022-00308-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/27/2022] [Indexed: 11/30/2022] Open
Abstract
COPD is driven by exogenous and endogenous oxidative stress derived from inhaled cigarette smoke, air pollution and reactive oxygen species from dysregulated mitochondria in activated inflammatory cells within the airway and lung. This is compounded by the loss in antioxidant defences including FOXO and NRF2 and other antioxidant transcription factors together with various key enzymes that attenuate oxidant effects. Oxidative stress enhances inflammation; airway remodelling including fibrosis and emphysema; post-translational protein modifications leading to autoantibody generation; DNA damage and cellular senescence. Recent studies using various omics technologies in the airways, lungs and blood of COPD patients has emphasised the importance of oxidative stress, particularly that derived from dysfunctional mitochondria in COPD and its role in immunity, inflammation, mucosal barrier function and infection. Therapeutic interventions targeting oxidative stress should overcome the deleterious pathologic effects of COPD if targeted to the lung. We require novel, more efficacious antioxidant COPD treatments among which mitochondria-targeted antioxidants and Nrf2 activators are promising.
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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.
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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
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Trivedi A, Bade G, Madan K, Ahmed Bhat M, Guleria R, Talwar A. Effect of Smoking and Its Cessation on the Transcript Profile of Peripheral Monocytes in COPD Patients. Int J Chron Obstruct Pulmon Dis 2022; 17:65-77. [PMID: 35027824 PMCID: PMC8749770 DOI: 10.2147/copd.s337635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/13/2021] [Indexed: 11/23/2022] Open
Abstract
Rationale Smoking is the primary cause of chronic obstructive pulmonary disease (COPD); however, only 10–20% of smokers develop the disease suggesting possible genomic association in the causation of the disease. In the present study, we aimed to explore the whole genome transcriptomics of blood monocytes from COPD smokers (COPD-S), COPD Ex-smokers (COPD-ExS), Control smokers (CS), and Control Never-smokers (CNS) to understand the differential effects of smoking, COPD and that of smoking cessation. Methods Exploratory analyses in form of principal component analysis (PCA) and hierarchical component analysis (uHCA) were performed to evaluate the similarity in gene expression patterns, while differential expression analyses of different supervised groups of smokers and never smokers were performed to study the differential effect of smoking, COPD and smoking cessation. Differentially expressed genes among groups were subjected to post-hoc enrichment analysis. Candidate genes were subjected to external validation by quantitative RT-PCR experiments. Results CNS made a cluster completely segregated from the other three subgroups (CS, COPDS and COPD-ExS). About 550, 8 and 5 genes showed differential expression, respectively, between CNS and CS, between CS and COPD-S, and between COPD-S and COPD-ExS. Apoptosis, immune response, cell adhesion, and inflammation were the top process networks identified in enrichment analysis. Two candidate genes (CASP9 and TNFRSF1A) found to be integral to several pathways in enrichment analysis were validated in an external validation experiment. Conclusion Control never smokers had formed a cluster distinctively separated from all smokers (COPDS, COPD-ExS, and CS), while amongst all smokers, control smokers had aggregated in a separate cluster. Smoking cessation appeared beneficial if started at an early stage as many genes altered due to smoking started reverting towards the baseline, whereas only a few COPD-related genes showed reversal after smoking cessation.
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Affiliation(s)
- Anjali Trivedi
- Department of Physiology, All India Institute of Medical Sciences, New Delhi, India
| | - Geetanjali Bade
- Department of Physiology, All India Institute of Medical Sciences, New Delhi, India
| | - Karan Madan
- Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Muzaffer Ahmed Bhat
- Department of Physiology, All India Institute of Medical Sciences, New Delhi, India
| | - Randeep Guleria
- Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Anjana Talwar
- Department of Physiology, All India Institute of Medical Sciences, New Delhi, India
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Karim L, Kosmider B, Bahmed K. Mitochondrial ribosomal stress in lung diseases. Am J Physiol Lung Cell Mol Physiol 2021; 322:L507-L517. [PMID: 34873929 DOI: 10.1152/ajplung.00078.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Mitochondria are involved in a variety of critical cellular functions, and their impairment drives cell injury. The mitochondrial ribosome (mitoribosome) is responsible for the protein synthesis of mitochondrial DNA encoded genes. These proteins are involved in oxidative phosphorylation, respiration, and ATP production required in the cell. Mitoribosome components originate from both mitochondrial and nuclear genomes. Their dysfunction can be caused by impaired mitochondrial protein synthesis or mitoribosome misassembly, leading to a decline in mitochondrial translation. This decrease can trigger mitochondrial ribosomal stress and contribute to pulmonary cell injury, death, and diseases. This review focuses on the contribution of the impaired mitoribosome structural components and function to respiratory disease pathophysiology. We present recent findings in the fields of lung cancer, chronic obstructive pulmonary disease, interstitial lung disease, and asthma. We also include reports on the mitoribosome dysfunction in pulmonary hypertension, high altitude pulmonary edema, bacterial and viral infections. Studies of the mitoribosome alterations in respiratory diseases can lead to novel therapeutic targets.
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Affiliation(s)
- Loukmane Karim
- Department of Microbiology, Immunology, and Inflammation, Temple University, Philadelphia, PA, United States.,Center for Inflammation and Lung Research, Temple University, Philadelphia, PA, United States
| | - Beata Kosmider
- Department of Microbiology, Immunology, and Inflammation, Temple University, Philadelphia, PA, United States.,Center for Inflammation and Lung Research, Temple University, Philadelphia, PA, United States.,Department of Biomedical Education and Data Science, Temple University, Philadelphia, PA, United States
| | - Karim Bahmed
- Center for Inflammation and Lung Research, Temple University, Philadelphia, PA, United States.,Department of Thoracic Medicine and Surgery, Temple University, Philadelphia, PA, United States
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