Single cell sequencing reveals cellular landscape alterations in the airway mucosa of patients with pulmonary long COVID

Firoozeh V Gerayeli; Hye Yun Park; Stephen Milne; Xuan Li; Chen Xi Yang; Josie Tuong; Rachel L Eddy; Seyed Milad Vahedi; Elizabeth Guinto; Chung Y Cheung; Julia Sw Yang; Cassie Gilchrist; Dina Yehia; Tara Stach; Hong Dang; Clarus Leung; Tawimas Shaipanich; Jonathon Leipsic; Graeme J Koelwyn; Janice M Leung; Don D Sin

doi:10.1183/13993003.01947-2023

Single cell sequencing reveals cellular landscape alterations in the airway mucosa of patients with pulmonary long COVID

Eur Respir J. 2024 Sep 26:2301947. doi: 10.1183/13993003.01947-2023. Online ahead of print.

Authors

Firoozeh V Gerayeli^{1

2}, Hye Yun Park^{1

3

2}, Stephen Milne^{1

4}, Xuan Li¹, Chen Xi Yang¹, Josie Tuong^{1

5}, Rachel L Eddy^{1

6}, Seyed Milad Vahedi^{1

5}, Elizabeth Guinto¹, Chung Y Cheung¹, Julia Sw Yang¹, Cassie Gilchrist¹, Dina Yehia¹, Tara Stach⁷, Hong Dang⁸, Clarus Leung^{1

6}, Tawimas Shaipanich⁶, Jonathon Leipsic⁹, Graeme J Koelwyn^{1

5}, Janice M Leung^{1

6}, Don D Sin^{1

6}

Affiliations

¹ Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC, Canada.
² Firoozeh V. Gerayeli and Hye Yun Park contributed equally as co-first authors.
³ Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
⁴ Faculty of Medicine & Health, University of Sydney, Sydney, NSW, Australia.
⁵ Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada.
⁶ Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.
⁷ Biomedical Research Centre, School of Biomedical Engineering, UBC, Vancouver, BC, Canada.
⁸ University of North Carolina Chapel Hill, Cystic Fibrosis and Pulmonary Disease Research and Treatment Center, Chapel Hill, USA.
⁹ Department of Radiology, University of British Columbia, Vancouver, Canada.

PMID: 39326914
DOI: 10.1183/13993003.01947-2023

Abstract

To elucidate the important cellular and molecular drivers of pulmonary long COVID, we generated a single-cell transcriptomic map of the airway mucosa using bronchial brushings from patients with long COVID who reported persistent pulmonary symptoms.Adults with and without long COVID were recruited from the general community in Greater Vancouver, Canada. The cohort was divided into those with pulmonary long COVID (PLC), which was defined as persons with new or worsening respiratory symptoms following at least one year from their initial acute SARS-CoV-2 infection (N=9); and control subjects defined as SARS-CoV-2 infected persons whose acute respiratory symptoms had fully resolved or individuals who had no history of acute COVID-19 (N=9). These participants underwent bronchoscopy from which a single cell suspension was created from bronchial brush samples and then sequenced.A total of 56 906 cells were recovered for the downstream analysis, with 34 840 cells belonging to the PLC group, which strikingly showed a unique cluster of neutrophils in the PLC group (p<0.05). Ingenuity Pathway Analysis revealed that the neutrophil degranulation pathway was enriched across epithelial cell clusters. Differential gene expression analysis between the PLC and control groups demonstrated upregulation of inflammatory chemokines and epithelial barrier dysfunction across epithelial cell clusters, as well as over-expression of mucin genes across secretory cell clusters.In conclusion, a single-cell transcriptomic landscape of the small airways suggest that neutrophils may play a significant role in mediating the chronic small airway inflammation driving pulmonary symptoms of long COVID.