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Khalenkow D, Brandsma CA, Timens W, Choy DF, Grimbaldeston MA, Rosenberger CM, Slebos DJ, Kerstjens HAM, Faiz A, Koppelman GH, Nawijn MC, van den Berge M, Guryev V. Alternative Splicing Is a Major Factor Shaping Transcriptome Diversity in Mild and Severe Chronic Obstructive Pulmonary Disease. Am J Respir Cell Mol Biol 2024; 70:414-423. [PMID: 38315810 DOI: 10.1165/rcmb.2023-0296oc] [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: 08/10/2023] [Accepted: 02/05/2024] [Indexed: 02/07/2024] Open
Abstract
The role of alternative splicing in chronic obstructive pulmonary disease (COPD) is still largely unknown. We aimed to investigate the differences in alternatively splicing events between patients with mild-to-moderate and severe COPD compared with non-COPD control subjects and to identify splicing factors associated with aberrant alternative splicing in COPD. For this purpose, we performed genome-wide RNA-sequencing analysis of bronchial brushings from 23 patients with mild-to-moderate COPD, 121 with severe COPD, and 23 non-COPD control subjects. We found a significant difference in the frequency of alternative splicing events in patients with mild-to-moderate and severe COPD compared with non-COPD control subjects. There were from two to eight times (depending on event type) more differential alternative splicing events in the severe than in the mild-to-moderate stage. The severe COPD samples showed less intron retention and more exon skipping. It is interesting that the transcript levels of the top 10 differentially expressed splicing factors were significantly correlated with the percentage of many alternatively spliced transcripts in severe COPD. The aberrant alternative splicing in severe COPD was predicted to increase the overall protein-coding capacity of gene products. In conclusion, we observed large and significant differences in alternative splicing between bronchial samples of patients with COPD and control subjects, with more events observed in severe than in mild-to-moderate COPD. The changes in the expression of several splicing factors correlated with prevalence of alternative splicing in severe COPD. Alternative splicing can indirectly impact gene expression by changing the relative abundance of protein-coding isoforms potentially influencing pathophysiological changes. The results provide a better understanding of COPD-related alternative splicing changes.
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Affiliation(s)
- Dmitry Khalenkow
- European Research Institute for the Biology of Ageing
- Groningen Research Institute for Asthma and COPD
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital
| | - Corry-Anke Brandsma
- Groningen Research Institute for Asthma and COPD
- Department of Pathology and Medical Biology
| | - Wim Timens
- Groningen Research Institute for Asthma and COPD
- Department of Pathology and Medical Biology
| | - David F Choy
- Genentech, Inc., South San Francisco, California; and
| | | | | | | | - Huib A M Kerstjens
- Department of Pulmonology and Tuberculosis, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Alen Faiz
- Faculty of Science, Centre for Inflammation, Centenary Institute and University of Technology Sydney, Sydney, Australia
| | - Gerard H Koppelman
- Groningen Research Institute for Asthma and COPD
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital
| | - Martijn C Nawijn
- Groningen Research Institute for Asthma and COPD
- Department of Pathology and Medical Biology
| | - Maarten van den Berge
- Groningen Research Institute for Asthma and COPD
- Department of Pulmonary Diseases, and
| | - Victor Guryev
- European Research Institute for the Biology of Ageing
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Bondeelle L, Salmona M, Houdouin V, Diaz E, Dutrieux J, Mercier-Delarue S, Constant S, Huang S, Bergeron A, LeGoff J. Inefficient antiviral response in reconstituted small-airway epithelium from chronic obstructive pulmonary disease patients following human parainfluenza virus type 3 infection. Virol J 2024; 21:78. [PMID: 38566231 PMCID: PMC10988791 DOI: 10.1186/s12985-024-02353-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 03/27/2024] [Indexed: 04/04/2024] Open
Abstract
Chronic obstructive pulmonary disease (COPD) affects over 250 million individuals globally and stands as the third leading cause of mortality. Respiratory viral infections serve as the primary drivers of acute exacerbations, hastening the decline in lung function and worsening the prognosis. Notably, Human Parainfluenza Virus type 3 (HPIV-3) is responsible for COPD exacerbations with a frequency comparable to that of Respiratory Syncytial Virus and Influenza viruses. However, the impact of HPIV-3 on respiratory epithelium within the context of COPD remains uncharacterized.In this study, we employed in vitro reconstitution of lower airway epithelia from lung tissues sourced from healthy donors (n = 4) and COPD patients (n = 5), maintained under air-liquid interface conditions. Through a next-generation sequencing-based transcriptome analysis, we compared the cellular response to HPIV-3 infection.Prior to infection, COPD respiratory epithelia exhibited a pro-inflammatory profile, notably enriched in canonical pathways linked to antiviral response, B cell signaling, IL-17 signaling, and epithelial-mesenchymal transition, in contrast to non-COPD epithelia. Intriguingly, post HPIV-3 infection, only non-COPD epithelia exhibited significant enrichment in interferon signaling, pattern recognition receptors of viruses and bacteria, and other pathways involved in antiviral responses. This deficiency could potentially hinder immune cell recruitment essential for controlling viral infections, thus fostering prolonged viral presence and persistent inflammation.
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Affiliation(s)
- Louise Bondeelle
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Maud Salmona
- Virology Department, AP-HP, Hôpital Saint-Louis, 1 Avenue Claude Vellefaux, Paris, F-75010, France
| | - Véronique Houdouin
- Service de Pneumologie, APHP, Hôpital Robert-Debré, Paris, F-75010, France
| | - Elise Diaz
- Université Paris Cité, Inserm U976, INSIGHT Team, Paris, F-75010, France
| | - Jacques Dutrieux
- Université Paris Cité, Institut Cochin, INSERM, U1016, CNRS, UMR8104, Paris, F-75014, France
| | - Séverine Mercier-Delarue
- Virology Department, AP-HP, Hôpital Saint-Louis, 1 Avenue Claude Vellefaux, Paris, F-75010, France
| | | | - Song Huang
- Epithelix Sarl, Geneva, 1228, Switzerland
| | - Anne Bergeron
- Pneumology Department, Geneva University Hospitals, Geneva, Switzerland
| | - Jérôme LeGoff
- Virology Department, AP-HP, Hôpital Saint-Louis, 1 Avenue Claude Vellefaux, Paris, F-75010, France.
- Université Paris Cité, Inserm U976, INSIGHT Team, Paris, F-75010, France.
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Blackburn JB, Schaff JA, Gutor S, Du RH, Nichols D, Sherrill T, Gutierrez AJ, Xin MK, Wickersham N, Zhang Y, Holtzman MJ, Ware LB, Banovich NE, Kropski JA, Blackwell TS, Richmond BW. Secretory Cells Are the Primary Source of pIgR in Small Airways. Am J Respir Cell Mol Biol 2022; 67:334-345. [PMID: 35687143 PMCID: PMC9447142 DOI: 10.1165/rcmb.2021-0548oc] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 06/13/2022] [Indexed: 11/24/2022] Open
Abstract
Loss of secretory IgA (SIgA) is common in chronic obstructive pulmonary disease (COPD) small airways and likely contributes to disease progression. We hypothesized that loss of SIgA results from reduced expression of pIgR (polymeric immunoglobulin receptor), a chaperone protein needed for SIgA transcytosis, in the COPD small airway epithelium. pIgR-expressing cells were defined and quantified at single-cell resolution in human airways using RNA in situ hybridization, immunostaining, and single-cell RNA sequencing. Complementary studies in mice used immunostaining, primary murine tracheal epithelial cell culture, and transgenic mice with secretory or ciliated cell-specific knockout of pIgR. SIgA degradation by human neutrophil elastase or secreted bacterial proteases from nontypeable Haemophilus influenzae was evaluated in vitro. We found that secretory cells are the predominant cell type responsible for pIgR expression in human and murine airways. Loss of SIgA in small airways was not associated with a reduction in secretory cells but rather a reduction in pIgR protein expression despite intact PIGR mRNA expression. Neutrophil elastase and nontypeable H. influenzae-secreted proteases are both capable of degrading SIgA in vitro and may also contribute to a deficient SIgA immunobarrier in COPD. Loss of the SIgA immunobarrier in small airways of patients with severe COPD is complex and likely results from both pIgR-dependent defects in IgA transcytosis and SIgA degradation.
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Affiliation(s)
- Jessica B. Blackburn
- Department of Veterans Affairs Medical Center, Nashville, Tennessee
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
| | - Jacob A. Schaff
- Department of Veterans Affairs Medical Center, Nashville, Tennessee
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
| | - Sergey Gutor
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
| | - Rui-Hong Du
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
| | - David Nichols
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
| | - Taylor Sherrill
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
| | | | - Matthew K. Xin
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
| | - Nancy Wickersham
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
| | - Yong Zhang
- Division of Pulmonary and Critical Care Medicine, Washington University–St. Louis, St. Louis, Missouri
| | - Michael J. Holtzman
- Division of Pulmonary and Critical Care Medicine, Washington University–St. Louis, St. Louis, Missouri
| | - Lorraine B. Ware
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
| | | | - Jonathan A. Kropski
- Department of Veterans Affairs Medical Center, Nashville, Tennessee
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee
| | - Timothy S. Blackwell
- Department of Veterans Affairs Medical Center, Nashville, Tennessee
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee
| | - Bradley W. Richmond
- Department of Veterans Affairs Medical Center, Nashville, Tennessee
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee
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