Smoking induces shifts in cellular composition and transcriptome within the bronchial mucus barrier

Senani N H Rathnayake; Benedikt Ditz; Jos van Nijnatten; Tayyaba Sadaf; Philip M Hansbro; Corry A Brandsma; Wim Timens; Annemarie van Schadewijk; Peter S Hiemstra; Nick H T Ten Hacken; Brian Oliver; Huib A M Kerstjens; Maarten van den Berge; Alen Faiz

doi:10.1111/resp.14401

Smoking induces shifts in cellular composition and transcriptome within the bronchial mucus barrier

Respirology. 2023 Feb;28(2):132-142. doi: 10.1111/resp.14401. Epub 2022 Nov 22.

Authors

Senani N H Rathnayake^{1

2}, Benedikt Ditz^{3

4}, Jos van Nijnatten^{1

4

5}, Tayyaba Sadaf^{1

6}, Philip M Hansbro⁶, Corry A Brandsma^{4

5}, Wim Timens^{4

5}, Annemarie van Schadewijk⁷, Peter S Hiemstra⁷, Nick H T Ten Hacken^{3

4}, Brian Oliver², Huib A M Kerstjens^{3

4}, Maarten van den Berge^{3

4}, Alen Faiz^{1

2

3}

Affiliations

¹ University of Technology Sydney, Respiratory Bioinformatics and Molecular Biology (RBMB), School of Life Sciences, Sydney, New South Wales, Australia.
² The University of Sydney, Respiratory Cellular and Molecular Biology (RCMB), Woolcock Institute of Medical Research, Sydney, New South Wales, Australia.
³ Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
⁴ University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands.
⁵ Department of Pathology & Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
⁶ Centre for Inflammation, Centenary Institute, and the University of Technology Sydney, Faculty of Science, Sydney, New South Wales, Australia.
⁷ Department of Pulmonology, Leiden University Medical Center, Leiden, the Netherlands.

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.

Keywords: bronchial mucus barrier; cellular deconvolution; gene expression; goblet cell; smoking.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Biopsy
Humans
Mucus / metabolism
Pulmonary Disease, Chronic Obstructive* / metabolism
Smoking / adverse effects
Smoking / genetics
Transcriptome* / genetics