An altered sputum macrophage transcriptome contributes to the neutrophilic asthma endotype

Michael Fricker; Ling Qin; Stephany Sánchez-Ovando; Jodie L Simpson; Katherine J Baines; Carlos Riveros; Hayley A Scott; Lisa G Wood; Peter Ab Wark; Nazanin Z Kermani; Kian Fan Chung; Peter G Gibson

doi:10.1111/all.15087

An altered sputum macrophage transcriptome contributes to the neutrophilic asthma endotype

Allergy. 2022 Apr;77(4):1204-1215. doi: 10.1111/all.15087. Epub 2021 Sep 28.

Authors

Michael Fricker^{1

2

3}, Ling Qin⁴, Stephany Sánchez-Ovando^{1

3}, Jodie L Simpson^{1

3

5}, Katherine J Baines^{1

3}, Carlos Riveros⁶, Hayley A Scott^{3

7}, Lisa G Wood^{3

7}, Peter Ab Wark^{1

3

5}, Nazanin Z Kermani^{8

9}, Kian Fan Chung^{8

9}, Peter G Gibson^{1

2

3

5}

Affiliations

¹ School of Medicine and Public Health, Faculty of Health and Medicine and Priority Research Centre for Healthy Lungs, The University of Newcastle, Callaghan, NSW, Australia.
² National Health and Medical Research Council Centre for Excellence in Severe Asthma, Newcastle, NSW, Australia.
³ Hunter Medical Research Institute, Newcastle, NSW, Australia.
⁴ Department of Respiratory Medicine, Department of Pulmonary and Critical Care Medicine, Xiangya Hospital, Central South University, Changsha, China.
⁵ Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, NSW, Australia.
⁶ Statistical services (CReDITSS), Hunter Medical Research Institute, Newcastle, NSW, Australia.
⁷ School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, Priority Research Centre for Healthy Lungs, The University of Newcastle, Newcastle, NSW, Australia.
⁸ Data Science Institute, Imperial College London, London, UK.
⁹ National Heart and Lung Institute, Imperial College London, London, UK.

Abstract

Background: Neutrophilic asthma (NA) is a clinically important asthma phenotype, the cellular and molecular basis of which is not completely understood. Airway macrophages are long-lived immune cells that exert important homeostatic and inflammatory functions which are dysregulated in asthma. Unique transcriptomic programmes reflect varied macrophage phenotypes in vitro. We aimed to determine whether airway macrophages are transcriptomically altered in NA.

Methods: We performed RNASeq analysis on flow cytometry-isolated sputum macrophages comparing NA (n = 7) and non-neutrophilic asthma (NNA, n = 13). qPCR validation of RNASeq results was performed (NA n = 13, NNA n = 23). Pathway analysis (PANTHER, STRING) of differentially expressed genes (DEGs) was performed. Gene set variation analysis (GSVA) was used to test for enrichment of NA macrophage transcriptomic signatures in whole sputum microarray (cohort 1 - controls n = 16, NA n = 29, NNA n = 37; cohort 2 U-BIOPRED - controls n = 16, NA n = 47, NNA n = 57).

Results: Flow cytometry-sorting significantly enriched sputum macrophages (99.4% post-sort, 44.9% pre-sort, p < .05). RNASeq analysis confirmed macrophage purity and identified DEGs in NA macrophages. Selected DEGs (SLAMF7, DYSF, GPR183, CSF3, PI3, CCR7, all p < .05 NA vs. NNA) were confirmed by qPCR. Pathway analysis of NA macrophage DEGs was consistent with responses to bacteria, contribution to neutrophil recruitment and increased expression of phagocytosis and efferocytosis factors. GSVA demonstrated neutrophilic macrophage gene signatures were significantly enriched in whole sputum microarray in NA vs. NNA and controls in both cohorts.

Conclusions: We demonstrate a pathophysiologically relevant sputum macrophage transcriptomic programme in NA. The finding that there is transcriptional activation of inflammatory programmes in cell types other than neutrophils supports the concept of NA as a specific endotype.

Keywords: asthma; endotype; macrophage; neutrophil; transcriptome.

Publication types

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

MeSH terms

Asthma* / diagnosis
Asthma* / genetics
Humans
Macrophages
Neutrophils
Sputum
Transcriptome*