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Perotin JM, Muggeo A, Lecomte-Thenot Q, Brisebarre A, Dury S, Launois C, Ancel J, Dormoy V, Guillard T, Deslee G. High Blood Eosinophil Count at Stable State is Not Associated with Airway Microbiota Distinct Profile in COPD. Int J Chron Obstruct Pulmon Dis 2024; 19:765-771. [PMID: 38524398 PMCID: PMC10959750 DOI: 10.2147/copd.s453526] [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: 01/08/2024] [Accepted: 02/21/2024] [Indexed: 03/26/2024] Open
Abstract
Purpose The heterogeneity of clinical features in COPD at stable state has been associated with airway microbiota. Blood eosinophil count (BEC) represents a biomarker for a pejorative evolution of COPD, including exacerbations and accelerated FEV1 decline. We aimed to analyse the associations between BEC and airway microbiota in COPD at stable state. Patients and Methods Adult COPD patients at stable state (RINNOPARI cohort) were included and characterised for clinical, functional, biological and morphological features. BEC at inclusion defined 2 groups of patients with low BEC <300/mm3 and high BEC ≥300/mm3. Sputa were collected and an extended microbiological culture was performed for the identification of viable airway microbiota. Results Fifty-nine subjects were included. When compared with the low BEC (n=40, 67.8%), the high BEC group (n=19, 32.2%) had more frequent exacerbations (p<0.001) and more pronounced cough and sputum (p<0.05). The global composition, the number of bacteria per sample and the α-diversity of the microbiota did not differ between groups, as well as the predominant phyla (Firmicutes), or the gender repartition. Conclusion In our study, high BEC in COPD at stable state was associated with a clinical phenotype including frequent exacerbation, but no distinct profile of viable airway microbiota compared with low BEC.
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Affiliation(s)
- Jeanne-Marie Perotin
- Université de Reims Champagne-Ardenne, INSERM UMR-S 1250, P3Cell, Reims, France
- CHU de Reims, Service des Maladies Respiratoires, Reims, France
| | - Anaëlle Muggeo
- Université de Reims Champagne-Ardenne, INSERM UMR-S 1250, P3Cell, CHU de Reims, Laboratoire de bactériologie-Virologie-Hygiène hospitalière-Parasitologie-Mycologie, Reims, France
| | - Quentin Lecomte-Thenot
- Université de Reims Champagne-Ardenne, INSERM UMR-S 1250, P3Cell, CHU de Reims, Laboratoire de bactériologie-Virologie-Hygiène hospitalière-Parasitologie-Mycologie, Reims, France
| | - Audrey Brisebarre
- Université de Reims Champagne-Ardenne, INSERM UMR-S 1250, P3Cell, Reims, France
| | - Sandra Dury
- CHU de Reims, Service des Maladies Respiratoires, Reims, France
| | - Claire Launois
- Université de Reims Champagne-Ardenne, INSERM UMR-S 1250, P3Cell, Reims, France
- CHU de Reims, Service des Maladies Respiratoires, Reims, France
| | - Julien Ancel
- Université de Reims Champagne-Ardenne, INSERM UMR-S 1250, P3Cell, Reims, France
- CHU de Reims, Service des Maladies Respiratoires, Reims, France
| | - Valérian Dormoy
- Université de Reims Champagne-Ardenne, INSERM UMR-S 1250, P3Cell, Reims, France
| | - Thomas Guillard
- Université de Reims Champagne-Ardenne, INSERM UMR-S 1250, P3Cell, CHU de Reims, Laboratoire de bactériologie-Virologie-Hygiène hospitalière-Parasitologie-Mycologie, Reims, France
| | - Gaëtan Deslee
- Université de Reims Champagne-Ardenne, INSERM UMR-S 1250, P3Cell, Reims, France
- CHU de Reims, Service des Maladies Respiratoires, Reims, France
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Gao J, Yi X, Wang Z. The application of multi-omics in the respiratory microbiome: Progresses, challenges and promises. Comput Struct Biotechnol J 2023; 21:4933-4943. [PMID: 37867968 PMCID: PMC10585227 DOI: 10.1016/j.csbj.2023.10.016] [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: 06/13/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 10/24/2023] Open
Abstract
The study of the respiratory microbiome has entered a multi-omic era. Through integrating different omic data types such as metagenome, metatranscriptome, metaproteome, metabolome, culturome and radiome surveyed from respiratory specimens, holistic insights can be gained on the lung microbiome and its interaction with host immunity and inflammation in respiratory diseases. The power of multi-omics have moved the field forward from associative assessment of microbiome alterations to causative understanding of the lung microbiome in the pathogenesis of chronic, acute and other types of respiratory diseases. However, the application of multi-omics in respiratory microbiome remains with unique challenges from sample processing, data integration, and downstream validation. In this review, we first introduce the respiratory sample types and omic data types applicable to studying the respiratory microbiome. We next describe approaches for multi-omic integration, focusing on dimensionality reduction, multi-omic association and prediction. We then summarize progresses in the application of multi-omics to studying the microbiome in respiratory diseases. We finally discuss current challenges and share our thoughts on future promises in the field.
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Affiliation(s)
- Jingyuan Gao
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China
| | - Xinzhu Yi
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China
| | - Zhang Wang
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China
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Saber Cherif L, Diabasana Z, Perotin JM, Ancel J, Petit LMG, Devilliers MA, Bonnomet A, Lalun N, Delepine G, Maskos U, Gosset P, Polette M, Muggeo A, Guillard T, Deslée G, Dormoy V. The Nicotinic Receptor Polymorphism rs16969968 Is Associated with Airway Remodeling and Inflammatory Dysregulation in COPD Patients. Cells 2022; 11:cells11192937. [PMID: 36230899 PMCID: PMC9563397 DOI: 10.3390/cells11192937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/08/2022] [Accepted: 09/15/2022] [Indexed: 11/17/2022] Open
Abstract
Genome-wide association studies unveiled the associations between the single nucleotide polymorphism rs16969968 of CHRNA5, encoding the nicotinic acetylcholine receptor alpha5 subunit (α5SNP), and nicotine addiction, cancer, and COPD independently. Here, we investigated α5SNP-induced epithelial remodeling and inflammatory response in human COPD airways. We included 26 α5SNP COPD patients and 18 wild-type α5 COPD patients in a multi-modal study. A comparative histologic analysis was performed on formalin-fixed paraffin-embedded lung tissues. Isolated airway epithelial cells from bronchial brushings were cultivated in the air-liquid interface. Broncho-alveolar fluids were collected to detect inflammatory mediators. Ciliogenesis was altered in α5SNP COPD bronchial and bronchiolar epithelia. Goblet cell hyperplasia was exacerbated in α5SNP small airways. The broncho-alveolar fluids of α5SNP COPD patients exhibited an increase in inflammatory mediators. The involvement of the rs16969968 polymorphism in airway epithelial remodeling and related inflammatory response in COPD prompts the development of innovative personalized diagnostic and therapeutic strategies.
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Affiliation(s)
- Lynda Saber Cherif
- Inserm P3Cell UMR-S 1250, Université de Reims Champagne-Ardenne, 51092 Reims, France
| | - Zania Diabasana
- Inserm P3Cell UMR-S 1250, Université de Reims Champagne-Ardenne, 51092 Reims, France
| | - Jeanne-Marie Perotin
- Inserm P3Cell UMR-S 1250, Université de Reims Champagne-Ardenne, 51092 Reims, France
- Département des Maladies Respiratoires, CHU de Reims, 51092 Reims, France
| | - Julien Ancel
- Inserm P3Cell UMR-S 1250, Université de Reims Champagne-Ardenne, 51092 Reims, France
- Département des Maladies Respiratoires, CHU de Reims, 51092 Reims, France
| | - Laure M. G. Petit
- Inserm P3Cell UMR-S 1250, Université de Reims Champagne-Ardenne, 51092 Reims, France
| | - Maëva A. Devilliers
- Inserm P3Cell UMR-S 1250, Université de Reims Champagne-Ardenne, 51092 Reims, France
| | - Arnaud Bonnomet
- Inserm P3Cell UMR-S 1250, Université de Reims Champagne-Ardenne, 51092 Reims, France
- Plateforme d’Imagerie Cellulaire et Tissulaire (PICT), Université de Reims Champagne-Ardenne, 51097 Reims, France
| | - Nathalie Lalun
- Inserm P3Cell UMR-S 1250, Université de Reims Champagne-Ardenne, 51092 Reims, France
| | - Gonzague Delepine
- Inserm P3Cell UMR-S 1250, Université de Reims Champagne-Ardenne, 51092 Reims, France
- Département de Chirurgie Thoracique, CHU de Reims, 51092 Reims, France
| | - Uwe Maskos
- CNRS UMR 3571, Unité de Neurobiologie Intégrative des Systèmes Cholinergiques, Institut Pasteur de Paris, Université de Paris Cité, 75006 Paris, France
| | - Philippe Gosset
- CNRS UMR 9017, Inserm U1019, Institut Pasteur de Lille, Université de Lille, CHU de Lille, 59000 Lille, France
| | - Myriam Polette
- Inserm P3Cell UMR-S 1250, Université de Reims Champagne-Ardenne, 51092 Reims, France
- Département de Biopathologie, CHU de Reims, 51092 Reims, France
| | - Anaëlle Muggeo
- Inserm P3Cell UMR-S 1250, Université de Reims Champagne-Ardenne, 51092 Reims, France
- Laboratoire de Bactériologie, Virologie, Hygiène Hospitalière, Parasitologie, Mycologie, CHU de Reims, 51092 Reims, France
| | - Thomas Guillard
- Inserm P3Cell UMR-S 1250, Université de Reims Champagne-Ardenne, 51092 Reims, France
- Laboratoire de Bactériologie, Virologie, Hygiène Hospitalière, Parasitologie, Mycologie, CHU de Reims, 51092 Reims, France
| | - Gaëtan Deslée
- Inserm P3Cell UMR-S 1250, Université de Reims Champagne-Ardenne, 51092 Reims, France
- Département des Maladies Respiratoires, CHU de Reims, 51092 Reims, France
| | - Valérian Dormoy
- Inserm P3Cell UMR-S 1250, Université de Reims Champagne-Ardenne, 51092 Reims, France
- Correspondence: ; Tel.: +33-(0)3-10-73-62-28
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Chen Z, Tian Y, Wang Y, Zhao H, Chen C, Zhang F. Profile of the Lower Respiratory Tract Microbiome in Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome and Lung Disease. Front Microbiol 2022; 13:888996. [PMID: 35814692 PMCID: PMC9260662 DOI: 10.3389/fmicb.2022.888996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/23/2022] [Indexed: 12/12/2022] Open
Abstract
Once an human immunodeficiency virus (HIV)-infected individual enters the onset period, a variety of opportunistic infections may occur, affecting various systems and organs throughout the body, due to the considerable reduction in the body’s immune function. The objectives of this study were to explore the relationship between immune status and microbial communities in the lungs of individuals with HIV infection. A total of 88 patients with lung disease [80 (91%) HIV-positive and 8 (9%) HIV-negative] were enrolled in our study between January and July 2018, and 88 bronchoalveolar lavage fluid (BALF) samples were obtained during bronchoscopy. In this cross-sectional study, we investigated differences in the pulmonary microbiome of patients with HIV who had different immune statuses. The diversity of bacteria in the lungs of HIV-positive individuals was lower than that in HIV-negative individuals (p < 0.05). There was a significant difference in the composition and distribution of bacteria and fungi between the HIV-positive and HIV-negative groups (p < 0.01). The number of fungal species in the BALF of HIV-positive patients was higher than in HIV-negative patients. The diversity of bacteria and fungi in the BALF of HIV-positive patients increased with decreasing CD4 T-cell counts. Linear regression analysis showed that Pneumocystis (R2 = 6.4e−03, p < 0.05), Cryptosphaeria (R2 = 7.2e−01, p < 0.05), Candida (R2 = 3.9e−02, p < 0.05), and Trichosporon (R2 = 7.7e−01, p < 0.05) were negatively correlated with CD4 counts (F-test, p < 0.05). The samples collected from HIV-positive patients exhibited a different pattern relative to those from the HIV-negative group. Differences in host immune status cause differences in the diversity and structure of lower respiratory tract microorganisms.
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Affiliation(s)
- Zhen Chen
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Ya Tian
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Yu Wang
- Affiliated Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Hongxin Zhao
- Affiliated Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Chen Chen
- Affiliated Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- *Correspondence: Chen Chen,
| | - Fujie Zhang
- Affiliated Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Fujie Zhang,
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