Ex vivo lung-organoid model for aberrant basaloid cell induction and activation

TL;DR

Researchers created a lab-grown lung model to study abnormal cells linked to lung scarring, which could help develop new treatments.

Contribution

A novel ex vivo lung-organoid model that induces and activates aberrant basaloid cells (ABCs) relevant to pulmonary fibrosis.

Findings

The organoid model showed dose-dependent structural and transcriptomic changes similar to in vivo fibrosis models.

Two distinct ABC subsets were identified, one of which (ABCs_2) was previously unobserved in traditional murine models.

BLM stimulation induced TGF-β2 in ABCs and Ephrin A signaling influenced ABC differentiation and epithelial proliferation.

Abstract

Pulmonary fibrosis (PF) is a severe lung disease characterized by the destruction of lung architecture resulting from chronic epithelial injury. The PF microenvironment induces PF-specific epithelial cells, such as aberrant basaloid cells (ABCs). However, limited experimental models capable of inducing and activating PF-specific epithelial cells hinder the understanding of their roles.

To address the lack of experimental models, in this study, we developed an ex vivo murine lung-organoid model designed to induce and activate ABCs. The organoids were subjected to bleomycin (BLM) stimulation. Dose-dependent reductions in number and size, structural disorganization, and transcriptomic changes were assessed following stimulation. Single-cell RNA-sequencing (scRNA-seq) analysis was performed to identify ABC subsets. Cell–cell interaction analysis was also conducted.

Following BLM stimulation, the organoids displayed dose-dependent reductions in number and size, along with structural disorganization and transcriptomic changes that were similar to those observed in the in vivo murine fibrosis model. scRNA-seq analysis identified two ABC subsets: Krt5low Tp63low Krt17+ ABCs_1, found in patients with idiopathic pulmonary fibrosis (IPF), and Krt5hi Tp63hi Krt17+ ABCs_2, which have been observed in cultured tissues from patients with IPF but not in traditional murine models. BLM stimulation led to the induction of transforming growth factor beta (TGF-β2) expression in ABCs. Cell–cell interaction analysis suggested that BLM-damaged type 2 alveolar epithelial cells (AT2s) enhanced their direct and indirect interactions with ABCs_2 via ephrin-A signaling. In line with this observation, stimulation experiments of BLM-damaged organoids revealed that Ephrin A4 induced ABC cell differentiation-related gene expression changes, whereas Ephrin A3 enhanced epithelial proliferation-related gene expression changes and suppressed fibroblast activation-related gene expression changes.

The developed organoid model serves as a novel platform for studying the roles and responses of PF-specific ABCs. This model may contribute to advancing the understanding of PF pathogenesis and facilitate the development of ABC-targeted therapies.

The online version contains supplementary material available at 10.1186/s41232-025-00396-z.

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