Identification and validation of cilia-associated molecular candidates deregulated in severe asthma

TL;DR

This study identifies three cilia-related genes linked to severe asthma, showing their potential as biomarkers or treatment targets.

Contribution

The study identifies and validates three cilia-associated genes (PHLDB2, NEK6, SCNN1G) as novel molecular drivers in severe asthma.

Findings

Seventeen cilia-associated genes were significantly dysregulated in severe asthma patients across three cohorts.

PHLDB2, NEK6, and SCNN1G showed upregulated protein levels in ex vivo and in vitro models of severe asthma.

SCNN1G expression increased under IL-13 stimulation, suggesting a role in inflammation-driven epithelial changes.

Abstract

Asthma is characterised by a chronic inflammation and airway remodelling. The functionality of the asthma airway epithelium is altered, suggesting a central role in the pathophysiology. Cilia-associated abnormalities have been reported in the airway epithelium of asthmatic patients, but the mechanisms remain elusive. This study investigated cilia-associated dysregulations in cohorts of patients with severe asthma to identify and characterize key molecular drivers of epithelial airway remodelling.

Transcriptomic data from epithelial bronchial brushing samples of three large cohorts of severe asthma patients and non-asthmatic were analysed: U-BIOPRED (GSE76226, n = 105), SARP (GSE63142, n = 81) and IMSA (GSE158752, n = 42). We focused on cilia-associated genes to highlight common differentially expressed genes in all three cohorts, comparing the non-asthmatic and severe asthma groups. Localisation and expression of the three most dysregulated genes were then validated on ex vivo and in vitro samples and correlated to epithelial airway remodelling features and clinical data.

Seventeen genes were significantly dysregulated between the non-asthma and severe asthma groups in all three datasets. We identified the three most dysregulated: PHLDB2 (12.7% [4.6–22.4], p < 0.05), NEK6 (8.4% [5.5–12.8], p < 0.05) and SCNN1G (6.8% [4.3–9.9], p < 0.05) as molecular candidates. In ex vivo severe asthma bronchial biopsies, the protein levels were upregulated 1.2-fold for PHLDB2 (p = 0.2844), 2.4-fold (p < 0.01) for NEK6, and 2.0-fold for SCNN1G (p < 0.05). The expressions of these candidates were correlated with epithelial remodelling features in both groups. In vitro, the expression of SCNN1G was upregulated in airway epithelial cells upon IL-13 stimulation, suggesting that SCNN1G may be dynamically regulated during epithelial differentiation under pro-inflammatory conditions. Finally, protein expression of PHLDB2, NEK6 and SCNN1G in fully differentiated air-liquid interface culture was associated with epithelial remodelling features with or without inflammatory stimulation.

This study highlights the dysregulation of three cilia-associated genes, PHLDB2, NEK6, and SCNN1G, in the bronchial epithelium of patients with SA. Their association with epithelial remodelling features and altered differentiation under inflammatory conditions highlights their potential involvement in asthma pathogenesis and their potential as predictive biomarkers or therapeutic targets in severe asthma.

The online version contains supplementary material available at 10.1186/s12931-026-03548-y.

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