Pathways linked to unresolved inflammation and airway remodelling characterize the transcriptome in two independent severe asthma cohorts.

BACKGROUND AND OBJECTIVE: Severe asthma (SA) is a heterogeneous disease. Transcriptomic analysis contributes to the understanding of pathogenesis necessary for developing new therapies. We sought to identify and validate mechanistic pathways of SA across two independent cohorts. METHODS: Transcriptomic profiles from U-BIOPRED and Australian NOVocastrian Asthma cohorts were examined and grouped into SA, mild/moderate asthma (MMA) and healthy controls (HCs). Differentially expressed genes (DEGs), canonical pathways and gene sets were identified as central to SA mechanisms if they were significant across both cohorts in either endobronchial biopsies or induced sputum. RESULTS: Thirty-six DEGs and four pathways were shared across cohorts linking to tissue remodelling/repair in biopsies of SA patients, including SUMOylation, NRF2 pathway and oxidative stress pathways. MMA presented a similar profile to HCs. Induced sputum demonstrated IL18R1 as a shared DEG in SA compared with healthy subjects. We identified enrichment of gene sets related to corticosteroid treatment; immune-related mechanisms; activation of CD4+ T cells, mast cells and IL18R1; and airway remodelling in SA. CONCLUSION: Our results identified differentially expressed pathways that highlight the role of CD4+ T cells, mast cells and pathways linked to ongoing airway remodelling, such as IL18R1, SUMOylation and NRF2 pathways, as likely active mechanisms in the pathogenesis of SA.

The six-gene expression signature in whole sampled sputum provides clinically feasible inflammatory phenotyping of asthma.

Processing of induced sputum is time consuming and requires trained personnel, and consequently the use of induced sputum is limited to few sites globally. The six-gene signature (6GS) is an mRNA-based gene signature that was developed to provide a clinically feasible method for inflammatory phenotyping. In this study, we assessed whether the 6GS would perform similarly in induced sputum sampled using a simplified method, by which induced sputum can be sampled and stored directly for later qPCR analyses, to the conventional method of manual plug selection. Two separate sputum samples were collected from 27 patients with asthma; one processed as a whole sample in an Oragene-RNA RE 100 vial and one processed using manual plug selection. Expression of 6GS was measured in both samples, of which 20 pairs (74%) had enough samples and results of sufficient quality of gene expression for further analyses. We found a significantly higher median RNA concentration in whole sampled sputum and consistently stronger gene expression compared to the plug method. Further, we found the two methods to agree, as 97% of observations were within the limits of agreement, as well as having a good-to-excellent reliability using intraclass correlation. Finally, we found 6GS in the whole sampled sputum to perform equal to or better than the manually selected plugs for discriminating inflammatory phenotypes defined by sputum differential count. In conclusion, whole sampling of induced sputum provides a clinically feasible method for inflammatory phenotyping.

Innate immune responses are increased in chronic obstructive pulmonary disease.

BACKGROUND: Chronic obstructive pulmonary disease (COPD) is characterised by irreversible airflow obstruction, neutrophilic airway inflammation and chronic bacterial colonisation, however the role of the innate immune response in the pathogenesis of COPD remains unclear. METHODS: Induced sputum was obtained from adults with COPD (n=22), and healthy controls (n=29) and was processed for differential cell counts. The sputum supernatant was assayed for innate immune mediators using ELISA, whilst sputum gene expression was measured using real-time PCR. Peripheral blood neutrophils were isolated and their response to lipopolysaccaride (LPS) stimulation was assessed in a subgroup of participants with COPD (n=13) and healthy controls (n=21). RESULTS: Participants with COPD had significantly higher protein levels of interleukin (IL)-8, and neutrophil elastase (NE) and detection of oncostatin M (OSM) compared to healthy controls. Gene expression for toll-like receptor (TLR) 2, IL-8 and OSM were also significantly higher in COPD participants. The level of IL-1ß, surfactant protein (SP)-A, matrix metalloproteinase (MMP)-9 and TLR4 mRNA was not significantly different between groups. The level of innate immune response markers were highly associated with the presence of sputum neutrophils, each other and the degree of airflow limitation (FEV1/FVC). Peripheral blood neutrophils from participants with COPD had an increased response to stimulation by LPS; with a greater fold increase in the production of IL-8 and MMP-9 protein, and gene expression of IL-8, TLR2 and TLR4. CONCLUSIONS: The innate immune response is increased in the airways and circulating neutrophils in COPD, and may be an important mechanism involved in disease pathogenesis.