Emerging Roles of Airway Epithelial Cells in Idiopathic Pulmonary Fibrosis

Abstract

Idiopathic pulmonary fibrosis (IPF) is a fatal disease with incompletely understood aetiology and limited treatment options. Traditionally, IPF was believed to be mainly caused by repetitive injuries to the alveolar epithelium. Several recent lines of evidence, however, suggest that IPF equally involves an aberrant airway epithelial response, which contributes significantly to disease development and progression. In this review, based on recent clinical, high-resolution imaging, genetic, and single-cell RNA sequencing data, we summarize alterations in airway structure, function, and cell type composition in IPF. We furthermore give a comprehensive overview on the genetic and mechanistic evidence pointing towards an essential role of airway epithelial cells in IPF pathogenesis and describe potentially implicated aberrant epithelial signalling pathways and regulation mechanisms in this context. The collected evidence argues for the investigation of possible therapeutic avenues targeting these processes, which thus represent important future directions of research.

Keywords: IPF; MUC5B; airway epithelium; basal cells; bronchial epithelium; epithelial populations; lung fibrosis; single cell RNA sequencing.

Figure 1

Schematic overview of airways in healthy lung and idiopathic pulmonary fibrosis (IPF). (A) Airways in the healthy lung, depicting normal cell type distribution in the proximal and distal airways as well as in the bronchioalveolar duct junction. (B) Airways in the IPF lung, depicting dilated bronchioles, impaired mucociliary clearance and the thickened basement membrane in the distal airways, two types of honeycomb cysts (HC, mucociliary, basaloid), and accumulation of extracellular matrix (ECM) in the alveolar region. AT1, alveolar cell type 1; AT2, alveolar cell type II; ECM, extracellular matrix; SMC, smooth muscle cell. Figure was created with biorender.com.

Figure 2

Airway epithelial abnormalities in IPF. (A) Comparison of airway features in control and IPF lungs as monitored by computed tomography (CT, adapted from Ikezoe et al. [12] with permission of the American Thoracic Society). Computed tomography (CT) scans from lungs of a control subject (upper row) and a case of IPF (lower row). The panels show from left to right: (1) Axial midslice multidetector computed tomography (MDCT) scans indicating where a random tissue sample was obtained for microCT (red circles); (2) reconstructed airway tree for the same scan from the lateral perspective; (3) midslice microCT scans of the tissue sample circled in red; (4) small airway tree segmentations obtained from the microCT scans visualized in three dimensions, identifying terminal bronchioles (TB, white arrowheads) and transitional bronchioles (asterisks); (5) representative cross-sectional image of the terminal bronchiole (TB) highlighted by the yellow arrowhead. This figure panel is adapted from Ikezoe et al. [12] with permission of the American Thoracic Society. Copyright © 2022 American Thoracic Society. All rights reserved. The American Journal of Respiratory and Critical Care Medicine is an official journal of the American Thoracic Society. Readers are encouraged to read the entire article for the correct context at https://www.atsjournals.org/doi/10.1164/rccm.202103-0585OC (last accessed 8 March 2022). The authors, editors, and The American Thoracic Society are not responsible for errors or omissions in adaptations. (B) Immunofluorescent stainings of serial lung sections of a representative control subject (upper row) and a case of IPF (lower row) with mouse isotype control antibody (mIgG1) and antibodies directed towards keratin 5 (KRT5), keratin 14 (KRT14), club cell-specific protein 10 (CC10), α-smooth muscle actin (α-SMA) as a marker for smooth muscle cells and myofibroblasts, and type I collagen (Coll I). Scale bar 100 µm.

Figure 3

Single cell RNA-Sequencing has revealed drastic changes in epithelial cell populations in ILD. (A) Uniform Manifold Approximation and Projection (UMAP)-based dimension reduction of single cell transcriptomic data to delineate epithelial cell types, labelled by cell type. (B) Same UMAP visualization labelled by ILD cohort. Data used for visualization was derived from in total four datasets [42,43,44,45] of control and interstitial lung disease (ILD) samples: New Haven [45], Nashville [44], Chicago [42], and Munich [43]. (C) Same UMAP visualization labelled by disease. (D) Relative frequencies of epithelial cell populations demonstrate a consistent increase in conducting airway cell populations in ILD at the expense of alveolar type 1 (AT1) and 2 (AT2) cells. ab., aberrant.

Figure 4

Cell type-specific markers for epithelial cell populations in ILD derived from scRNA-Seq data. Using the data set described in Figure 3, the top 5 specific markers for the described epithelial populations are plotted, (A) ranked by adjusted p-value or (B) ranked by log fold changes of relevant cell type vs. all other epithelial cell types. pct., percentage; avg. expr., average expression; ab., aberrant.

Figure 5

Epithelial cell populations show distinct expression changes in ILD. Using the data set described in Figure 3, differential gene expression analysis was performed with diffxpy (https://github.com/theislab/diffxpy, last accessed 22 December 2021) while accounting for number of transcripts per cell and patient cohort. The top 50 deregulated genes in specific subpopulations of epithelial cells are given, ranked by log2 fold change. (A) Top 50 genes induced in aberrant basaloid cells relative to gene expression of all other healthy epithelial cell types. (B) Top 50 genes increased in ILD in other airway epithelial cell populations. pct., percentage; avg. expr., average expression; ab., aberrant.

Figure 6

Expression of selected risk factor genes in epithelial cell populations. Using the data set described in Figure 3, expression of selected genes harbouring IPF risk-associated SNPs is given. Selection was based on previous reports on their expression in airway epithelium (see text for more details). pct., percentage; avg. expr., average expression; ab., aberrant.

Figure 7

Hypothetical contributions of the airway epithelium to IPF pathogenesis. Summarizing scheme linking established environmental and genetic risk factors via the bronchial and bronchiolar epithelium to IPF-specific disease mechanisms and outcomes like bronchiolization and interstitial scarring. Figure was created with biorender.com.